Tesis-Bases Moleculares de La Especificidad Peptídica de HLA-B27

Universidad Autónoma de Madrid
Facultad de ciencias
Departamento de Biología Molecular
BASE MOLECULAR DE LA
ESPECIFICIDAD PEPTÍDICA DE
HLA-B27
JOSÉ RAMÓN LAMAS LÓPEZ

Madrid, 1999
Universidad Autónoma de Madrid
Facultad de ciencias
Departamento de Biología Molecular
Base molecular de la especificidad

peptídica de HLA-B27
Memoria para optar al grado de Doctor en Ciencias
presentada por: José Ramón Lamas López
Director: Dr. José Antonio López de Castro Álvarez

Profesor de investigación del C.S.I.C
Centro de Biología Molecular "Severo Ochoa"
Madrid, Junio de 1999.

ABREVIATURAS
APC Células presentadoras de antígeno.

AR Artritis reactiva
Aua Ácido 11-amino undecanoico.
EA Espondilitis anquilosante.
EBNA Antígeno nuclear del EBV.
EBV Virus de Epstein-Barr.
β 2m β2-microglobulina.
BCR Receptor de células B.
CD Cluster of Differentiation.
C-terminal Extremo Carboxilo.
CTL Linfocito T citotóxico.
HB (R)-3-Hidroxibutirato.
HLA Antígenos Leucocitarios Humanos.
Kb Kilobase.
kDa Kilodalton.
LMP Proteína latente de membrana del EBV
MHC Complejo principal de histocompatibilidad.
N-terminal Extremo amino.
PX Posición X del péptido.
PΩ Posición C-terminal.
RE Retículo Endoplásmico.
TAP Transportador asociado con la presentación de antígeno.
TCR Receptor de célula T.
GLICINA ASPARAGINA GLUTAMINA METIONINA CISTEÍNA
(Gly) (Asn) (Gln) (Met) (Cys)
G N Q M C
COO- COO- COO- COO- COO-
+H N C H +H N C H +H N C H +H N C H +H N C H
3 3 3 3 3
H CH2 CH2 CH2 CH2
C CH2 CH2 SH
O NH2 C S
O NH2 CH3
TREONINA SERINA TIROSINA FENILALANINA TRIPTÓFANO

(Thr) (Ser) (Tyr) (Phe) (Trp)
T S Y F W
3 3 3 3 3
H C OH H C OH CH2 CH2 CH2
CH3 H
NH
OH
Aminoácidos polares (sin carga) Aminoácidos apolares aromáticos
ALANINA VALINA LEUCINA ISOLEUCINA PROLINA

(Ala) (Val) (Leu) (Ile) (Pro)
A V L I P
3 3 3 3 2
CH3 CH CH2 H C CH3
H2C CH2
H3C CH3 CH CH2 CH2
H3C CH3 CH3
Aminoácidos apolares alifáticos
Ác. ASPÁRTICO Ác. GLUTÁMICO LISINA HISTIDINA ARGININA

(Asp) (Glu) (Lys) (His) (Arg)
D E K H R
3 3 3 3 3
CH2 CH2 CH2 CH2 CH2
C CH2 CH2 +HN
CH2
NH
O - C CH2 CH2
O
O - NH
O CH2
NH 3+ C=NH 2+
NH2
Aminoácidos polares (con carga)
ÍNDICE -i-
I. INTRODUCCIÓN. ...................................................................................................................................................................................... 1
I.1. Características generales del sistema inmunitario. .................................................................................................... 3
I.2. Organización genómica y estructural del MHC humano. ...................................................................................... 4
I.2.1. Organización de los genes del MHC de clase I y clase II. ...................................................................... 4
I.3. Estructura de las proteínas de clase I. ............................................................................................................................. 6
I.3.1. La cadena pesada y la Beta-2 microglobulina (β2m). . .............................................................................. 6

I.3.2. Los péptidos. ................................................................................................................................................................ 8
I.4. Procesamiento de antígeno. Formación, transporte y presentación de los complejos
péptido-MHC de clase I. .......................................................................................................................................................... 9
I.4.1. Origen y procesamiento de los péptidos antigénicos. ................................................................................ 9
I.4.2. Translocación al Reticulo Endoplásmico. ...................................................................................................... 10
I.4.3. Biosíntesis, Ensamblaje y expresión en membrana de las moléculas de clase I. ........................... 11
I.5. TCR y reconocimiento de los complejos MHC-péptido. ........................................................................................... 11

I.5.1. Características estructurales del TCR y reconocimiento de los complejos MHC-péptido. ....... 11
I.6. HLA-B27. ...................................................................................................................................................................................... 13
I.6.1. Subcavidad A. ............................................................................................................................................................. 13

I.6.2. Subcavidad B. ............................................................................................................................................................. 13
I.6.3. Subcavidades C y F. ................................................................................................................................................ 14
I.6.4. Subcavidades D y E. ................................................................................................................................................ 15
I.7. HLA-B27 y espondiloartropatías. ....................................................................................................................................... 15
I.7.1. Posible papel patogénico de la presentación de péptidos por HLA-B27. ......................................... 16
I.7.2. Distribución étnica y asociación a enfermedad de los subtipos de HLA-B27. ................................ 17
II. OBJETIVOS. ............................................................................................................................................................................................... 21
III. MATERIALES Y MÉTODOS. .......................................................................................................................................................... 25
III.1. Líneas celulares. ..................................................................................................................................................................................27

III.2. Anticuerpos monoclonales (mAb). ............................................................................................................................................27
III.3. Síntesis, purificación y cuantificación de péptidos. ..........................................................................................................27

II.3.1. Síntesis y purificación de péptidos y análogos no peptídicos ........................................................................27
III.3.2. Cuantificación. ...................................................................................................................................................................28
III.4. Ensayo de unión de péptidos. .......................................................................................................................................................28
III.4.1. Análisis por citometría de flujo. ................................................................................................................................29
III.4.2. Cálculo de la unión de péptidos. ...............................................................................................................................29

IV. RESULTADOS. ........................................................................................................................................................................................ 31
IV.1 Efecto del polimorfismo de HLA-B27 sobre la especificidad de unión de péptidos. . .......................................33
IV.1.1. Unión de péptidos a HLA-B*2705, B*2704 y B*2706. Modulación de la especificidad
por el residuo peptídico C-terminal. ........................................................................................................................33
IV.1.1.1. Efectos de la pérdidas y ganancias de residuos cargados en las

subcavidades E/C/F. ..................................................................................................................................34
ÍNDICE -ii-
IV.1.2. Unión de péptidos a B*2701 y B*2702. Efecto del polimorfismo sobre la

especicificidad de los residuos en P2. ........................................................................................................ 37
IV.1.3. Unión de péptidos a B*2703:Papel del polimorfismo de la subcavidad A. ........................................ 40
IV.1.3.1. Propiedades dinámicas vs afinidad de unión de péptidos. ................................................. 40
IV.1.3.2. Fluctuaciones atómicas, áreas accesibles y no accesibles. ............................................... 41
IV.1.3.3. Analisis cualitativo y cuantitativo de los puentes de hidrógeno. ..................................... 42
IV.2. Relación entre la unión de péptidos y la selección de epítopos virales por células T. ............................. 43
IV.2.1. Unión de péptidos virales a diferentes subtipos deHLA-B27, y su relación

con la inmunogenicidad. ....................................................................................................................... 43
IV.2.2. Reconocimiento de péptidos de EBV por CTLs restringidos por HLA-B27. .................. 44
IV.2.3. El motivo Arg2, anclaje principal de los péptidos unidos a HLA-B27, no es

esencial para mantener la capacidad antigénica del péptido. .............................................. 44
IV.3. Modulación de la especificidad en las posiciones de anclaje P1, P3 y PΩ, por el
polimorfismo de HLA-B27. ............................................................................................................................................. 47
IV.3.1. Especificidad de B*2705, B*2704 y B*2706 por los residuos en P1, P3 y P9. .............. 47
IV.3.2. La unión de un péptido es el resultado de la contribución aditiva de varios
residuos de anclaje. .................................................................................................................................. 48
IV.3.3. Distribución de los residuos P1, P3 y PΩ. entre los ligandos naturales de B*2705. . 52
IV.4. Unión de análogos no peptídicos a HLA-B27. .......................................................................................................... 55
IV.4.1. Reemplazamiento de la parte central de epítopos naturales con un

espaciador monofuncional. .............................................................................................................. 55
IV.4.2. Reemplazamiento de la parte central de epítopos naturales con
espaciadores bifuncionales. ............................................................................................................. 56
IV.4.3. Modelado molecular de la unión de análogos con espaciadores no
peptídicos a B*2705. ........................................................................................................................... 56
V. DISCUSIÓN. ................................................................................................................................................................................................. 59
V.1. Polimorfismo de HLA-B27 y solapamiento de repertorios peptídicos entre subtipos. .............................. 61
V.1.1. Influencia del polimorfismo de la cavidad C/F sobre la especificidad por el

extremo C-terminal del péptido. Diferencias entre B*2704 y B*2706. ............................. 61
V.1.2. El polimorfismo de la cavidad C/F determina parcialmente la especificidad
de la subcavidad B. . ................................................................................................................................ 63
V.1.3. Análisis del efecto del polimorfismo de la subcavidad A sobre la unión de
péptidos. ........................................................................................................................................................ 65
V.2. Relación entre la unión de péptidos y la selección de epítopos por células T. .............................................. 67
V.3. La especificidad de péptidos por los subtipos de HLA-B27 es modulada en múltiples
posiciones de anclaje. ............................................................................................................................................................ 70
V.4. Unión de análogos no peptídicos a HLA-B27. ............................................................................................................ 72
Resumen y discusión general. ...................................................................................................................................................... 73
VI. CONCLUSIONES. .................................................................................................................................................................................. 75
VII. REFERENCIAS. .................................................................................................................................................................................... 79
VIII. ANEXOS. ................................................................................................................................................................................................. 91

-1-
I. INTRODUCCIÓN
INTRODUCCIÓN -3-
I. INTRODUCCIÓN
I.1. CARACTERÍSTICAS GENERALES DEL SISTEMA INMUNITARIO.
l sistema inmunitario es el encargado de proteger a un organismo discriminando entre
E lo que le pertenece y lo extraño a él. Cuando esta función falla y lo propio no es

reconocido como tal, se desencadena una respuesta autoinmune.
Funcionalmente, se distinguen dos mecanismos inmunitarios perfectamente coordinados.
El sistema inmune innato o no adaptativo, genera respuestas rápidas e inespecíficas dirigidas
hacia características generales del agente patógeno, creando una primera barrera defensiva tanto
a nivel físico y bioquímico, a cargo de la piel, mucosas, secreciones y diferentes factores
solubles, como celular por células fagocíticas (polimorfonucleares neutrófilos, monocitos y
macrófagos), células citotóxicas NK (Natural Killer) o células secretoras (eosinófilos, basófilos
y mastocitos).
El sistema inmune específico o adaptativo a diferencia del anterior, está adaptado a la
naturaleza del patógeno, a su estrategia invasora y posee memoria, lo que le permite generar una
respuesta más potente y rápida ante una reexposición al antígeno que provocó la respuesta
inicial.
Los mecanismos efectores de la respuesta adaptativa dependen de receptores expresados en
los linfocitos B y T que reconocen antígenos de diferentes características. Los receptores de los
linfocitos B o BCR (B Cell Receptor) reconocen el antígeno en su estado nativo, activando la
diferenciación y maduración de los linfocitos B para secretar las inmunoglobulinas (Ig) o
anticuerpos, una versión soluble del receptor que mantiene su especificidad original.
Los receptores de los linfocitos T o TCR (T Cell Receptor), reconocen fragmentos
peptídicos derivados del procesamiento del antígeno, unidos a moléculas del MHC (Major
Histocompatibility Complex). Para ello requieren la presencia de células presentadoras
encargadas de procesar el antígeno y de presentarlo en la superficie celular para su
reconocimiento por los receptores antigénicos de los linfocitos T. Basándose en su estructura y
función se distinguen dos tipos de moléculas del MHC: de clase I y de clase II.
INTRODUCCIÓN -4-
Los linfocitos T se distribuyen en dos subpoblaciones dependiendo del tipo de proteína

correceptora, CD4 o CD8, que expresan en su membrana. Estos correceptores en general no se
expresan juntos en un mismo linfocito T diferenciado, y la presencia de uno u otro determina
diferentes patrones de restricción por MHC (Zinkernagel y Doherty, 1974). Los linfocitos T
citotóxicos (CD8+) o CTLs (Citotoxic T Lymphocytes), son células efectoras líticas, que
reconocen el péptido presentado por moléculas del MHC de clase I, se dice que están
restringidas por el MHC de clase I. Las células Th (helper) o reguladoras (CD4+), están
restringidas por el MHC de clase II. El reconocimiento de péptidos unidos a estas moléculas
inicia una serie de procesos esenciales para desencadenar una respuesta inmune, puesto que de
ello depende tanto la diferenciación de los linfocitos B en células plasmáticas secretoras de
anticuerpos, como la activación y diferenciación de los linfocitos T CD8+ en células efectoras.
I.2. ORGANIZACIÓN GENÓMICA Y ESTRUCTURAL DEL MHC HUMANO.
Las moléculas del MHC, denominadas en humanos HLA (Human Leukocyte Antigens),
son codificadas por un conjunto de genes agrupados en una zona de aproximadamente 3.500 Kb,
en el brazo corto del cromosoma 6 (Francke y Pellegrino, 1977; Dunham et al., 1987) donde se
diferencian tres regiones: de clase I, II y III.
I.2.1. Organización de los genes del MHC de clase I y clase II.
La región de clase I abarca una extensión de 1600 Kb orientada hacia el extremo

telomérico, donde se emplazan los loci codificantes de las cadenas α o cadenas pesadas de los
antígenos de clase Ia o clásicos (HLA-A, -B y -C) y los de clase Ib o no clásicos (HLA-E, F, G)
(Figura 1).
Los genes que codifican las cadenas pesadas de los antígenos de clase Ia, son muy
polimórficos (Parham et al., 1995) y se expresan en la mayoría de las células somáticas de forma
codominante y a niveles de expresión variables, aunque típicamente elevados en las células de
linaje hematopoyético. Por el contrario, los genes codificantes de las moléculas de clase Ib, son
poco polimórficos y su expresión tisular está más limitada (Wei y Orr, 1990). Estructuralmente
son semejantes a los antígenos de clase I clásicos pero reconocen antígenos de diferente
naturaleza. Entre estos antígenos de clase Ib, se incluyen además, las moléculas CD1 (Melián et
al., 1996) aunque son codificadas por el cromosoma 1, fuera del MHC. Recientemente se ha
identificado una familia de cinco genes ubicados en las regiones de clase I y III denominada
-5- INTRODUCCIÓN
MIC (MHC class I Chain related) (Bahram et al., 1994), que codifican cadenas pesadas con
secuencias muy divergentes de las otras cadenas de clase I codificadas en el MHC.
Orientada hacia el extremo centromérico, la región de clase II tiene una amplitud de 900
Kb, donde se ubican los loci HLA-DP, -DQ y -DR que codifican a las cadenas α y β de las
moléculas de clase II. Estas moléculas se expresan exclusivamente en macrófagos, células
dendríticas y células B activadas, conocidas como células presentadoras de antígeno
“profesionales” o APCs (Antigen-Presenting Cells). En esta región se localizan además otros
genes que codifican a varias proteínas implicadas en el procesamiento, transporte y presentación
de antígeno como TAP1 y TAP2 (Spies et al., 1990; Trowsdale et al., 1990) la Tapasina
(Herberg et al., 1998) y las subunidades del proteosoma LMP2 y LMP7 (Large Multifunctional
Proteasome). (Kelly et al., 1991; Glynne et al., 1991).
Entre las regiones de clase I y clase II, se sitúa la región de clase III. Esta región de unas
1000 Kb, comprende a un grupo de genes denominados en conjunto genes de clase III, que
codifican entre otras, a las proteínas de los factores del complemento C2, C4, B y F y los factores
de necrosis tumoral TNFα y TNFβ (Tumor Necrosis Factor α y β).
Clase II Clase III Clase I

DP DM DQ DR Factores del BC E A GF
complemento
TNFα TNFβ
Tapasina
LMP
TAP
β α β α β α β β α MIC B MIC A MIC C MIC D MIC E
Figura 1: Mapa genético del complejo principal de histocompatibilidad humano, ubicado en el

brazo corto del cromosoma 6.
INTRODUCCIÓN -6-
I.3. ESTRUCTURA DE LAS PROTEÍNAS DE CLASE I.
Las moléculas HLA de clase I, son glicoproteínas de membrana formadas por la

asociación no covalente de tres componentes: una cadena pesada, HC (Heavy Chain) o
cadena α, de 45 kDa, codificada en el MHC, una cadena ligera de 12 kDa denominada Beta-2
microglobulina (β2m) (Ploegh et al., 1981), codificada en el cromosoma 15 (Goodfellow et al.,
1975) y un péptido antigénico de entre ocho y once aminoácidos. Sus funciónes inmunológicas
son la de actuar como receptoras y presentadoras de péptidos al TCR y la de ser reconocidas por
receptores de células NK (Ljunggren y Kärre, 1990a; Moretta et al., 1994; Phillips et al., 1996)
I.3.1. La cadena pesada y la Beta-2 microglobulina (β2m).
Los genes que codifican la cadena pesada de las moléculas de clase I se distribuyen en
ocho exones de diferente longitud separados por siete intrones (Jordan et al., 1985). Cada exón
codifica fundamentalmente un dominio de la proteína. El exón 1, situado en el extremo 5’ del
gen, codifica una porción no traducida de 18 pares de nucleótidos y un péptido señal de 24
aminoácidos. Los exones 2 y 3 (270 pares de nucleótidos) y 4 (276 pares de nucleótidos)
codifican los dominios extracelulares de la cadena pesada, α1, α2, y α3 respectivamente. El
exón 5 (117 pares de nucleótidos) codifica la región transmembrana y los residuos que la
flanquean. Los exones 6, 7 y 8 (33, 48 y 400 pares de nucleótidos respectivamente) codifican la
región intracitoplásmica y la región 3’ no traducida.
La cadena pesada resultante, consta de aproximadamente 340 aminoácidos estructurados
en tres regiones bien definidas: una región amino terminal extracelular de 274 aminoácidos,
formada por los dominios α1, α2 y α3 de aproximadamente 90 aminoácidos cada uno, una
región transmembrana hidrofóbica de 25 aminoácidos y una intracitoplásmica hidrofílica de unos
30 aminoácidos (Ploegh et al., 1981).
Mediante técnicas de difracción de rayos X, ha podido determinarse la similar
organización tridimensional de estos dominios en distintas moléculas de clase I, humanas y
murinas (Bjorkman et al., 1987; Garrett et al., 1989; Saper et al., 1991; Madden et al., 1991;
Madden et al., 1992; Fremont et al., 1992; Zhang et al., 1992; Young et al., 1994; Smith et al.,
1996b; Smith et al., 1996c). Los dominios α1 y α2, que son estructuralmente idénticos, constan
cada uno de una lámina β antiparalela formada por cuatro cadenas polipeptídicas y de una larga
región en α-hélice (Figura 2). Tras el plegamiento de ambos dominios las dos estructuras en α-
-7- INTRODUCCIÓN
hélice coronan una base constituida por ocho

láminas β-plegadas, delimitando una hendidura,
denominada surco de unión del péptido, de
aproximadamente 25Å de largo por 10Å de ancho.
El polimorfismo de los antígenos de clase I,
se concentra principalmente en los residuos
situados en el interior y las zonas próximas a este
surco, donde se distinguen seis subcavidades
(Saper et al., 1991) denominadas A-F. Su forma,
tamaño y polaridad, está determinada por los
residuos polimórficos que las constituyen, y que
generan diferentes especificidades por los péptidos
unidos (Figura 2). B C
A
F
En el residuo Asn86 del dominio α1 se situa
D E
un carbohidrato de 3,3 kDa y un puente disulfuro
intradominio en α2 conecta las Cisteínas 101 y
164.
El dominio α3, que está muy conservado Figura 2: (Arriba, vista de perfil), diagrama
(Parham et al., 1988), es estructuralmente esquemático que representa la estructura
tridimensional adoptada por los diferentes dominios
homólogo a la β2m, y a los dominios constantes de de una molécula de clase I. No aparecen
representadas ni la región transmembrana ni el
las inmunoglobulinas (Orr et al., 1979). Un puente fragmento que une los dominios extracelulares a la
superficie celular. En la figura inferior (vista
disulfuro conecta los residuos Cys203 y Cys259 y apicalmente) se detalla la localización de las
diferentes subcavidades distribuidas a ambos lados
una corta α-hélice adicional entre los residuos del surco de unión del péptido.
177-181, conecta este dominio con el α2.
Contigua al dominio α3 se encuentra la región transmembrana encargada del anclaje de la
molécula a la membrana celular.
La β2-microglobulina, de la que sólo se conoce un alelo en humanos, consta de 99
aminoácidos muy conservados entre diferentes especies. Carece de dominio intracitoplásmico y
se mantiene asociada a la región extracitoplásmica de la cadena pesada interaccionando con sus
tres dominios, lo que determina en gran medida la conformación y estabilidad de ésta (Krangel et
al., 1979; Seong et al., 1988).
INTRODUCCIÓN -8-
La β2m y el dominio α3 se sitúan por debajo de la lámina β de α1/α2 dejando una cavidad
entre ellos donde el correceptor CD8 de la célula T interacciona con la molécula de clase I
(Salter et al., 1990, Gao et al., 1997).
I.3.2. Los péptidos.
Los péptidos unidos a las moléculas de clase I, funcionan como una parte integral de las
mismas permitiendo su plegamiento y expresión estable en la membrana celular, y participando
en la selección de repertorios de células T CD8+ (Abe et al., 1992). La cinética de unión entre un
péptido y la molécula de clase I, está gobernada por las constantes de asociación y disociación, a
su vez determinantes de su afinidad y estabilidad. Esta última parece ser el factor determinante
de la inmunogenicidad de los péptidos (Brooks et al.1998).
Desde un punto de vista estructural, la unión de un péptido está determinada por dos
características básicas: una es su tamaño, generalmente comprendido entre 8 y 11 aminoácidos
(Jardetzky et al., 1991; Falk et al., 1991) y la otra, es la conservación en determinadas posiciones
de residuos de anclaje cuya localización y contribución varían en función del polimorfismo de la
molécula de clase I a la que se unen. La presencia de un único aminoácido o aminoácidos con
cadenas laterales similares en una posición de la secuencia del péptido, define los motivos de
anclaje primarios, frecuentemente P2 y el residuo C-terminal (PΩ). Otras posiciones de la
secuencia del péptido como P1, P3, y P7, son menos restrictivas respecto al aminoácido que las
ocupa, y definen los motivos de anclaje secundarios que contribuyen adicionalmente a la unión
del péptido.
La unión tiene lugar principalmente entre los extremos N-terminal y C-terminal con los
residuos que conforman las subcavidades A y F respectivamente, adoptando una conformación
extendida (Madden et al., 1991), y arqueandose en su parte central (Guo et al., 1992), aunque en
péptidos más largos puede sobresalir un extremo (Collins et al., 1994). Otras posiciones de la
cadena principal del péptido (P2, P3, P7), interaccionan con el resto de las subcavidades (Garrett
et al., 1989). En la parte central, que es la más accesible al contacto con el TCR, las cadenas
laterales de los residuos P4, P5, P6 y P8 del péptido, pueden adoptar distintas orientaciones en
función de su secuencia (Madden et al., 1993).
-9- INTRODUCCIÓN
I.4. PROCESAMIENTO DE ANTÍGENO. FORMACIÓN, TRANSPORTE Y PRESENTACIÓN DE

LOS COMPLEJOS PÉPTIDO-MHC DE CLASE I.
I.4.1. Origen y procesamiento de los péptidos antigénicos.
Los linfocitos T, reconocen los antígenos en forma de péptidos unidos a las moléculas del
MHC. El origen de la proteína antigénica determina tanto la vía de procesamiento, como el
ulterior mecanismo de respuesta inmunitaria. Así, las moléculas del MHC de clase II presentan
principalmente péptidos derivados de proteínas de origen exógeno, que son endocitadas por
APCs y degradadas en el endosoma, en condiciones de pH ácido. Las moléculas de clase I
presentan principalmente péptidos procedentes de la degradación en el citosol de proteínas
propias o de secuencias señal (Wei y Cresswell, 1992) por un mecanismo independiente de la vía
endocítica o lisosómica (Morrison et al., 1986).
La degradación de proteínas citosólicas es un proceso estrechamente regulado para evitar
la degradación indiscriminada de proteínas propias. Las formas de “etiquetar” la futura
degradación proteica son variadas; unas se basan en características de la propia proteína, como la
identidad del aminoácido N-terminal (Townsend et al., 1988; Varshavsky, 1992) o la presencia
de secuencias de aminoácidos, como las secuencias "PEST" ricas en Pro, Gln, Ser y Thr (Rogers
et al., 1986) o las denominadas “destruction boxes” (Glotzer et al., 1991) que determinan la
degradación específica en un determinado momento del ciclo celular. En otras ocasiones, las
proteínas que deben ser degradadas, son ubiquitinadas enzimáticamente como paso previo a su
degradación específica. La mayor parte de la actividad proteolítica del citosol es realizada por el
proteosoma, un complejo proteico multicatalítico con actividad proteasa y dependiente de ATP,
encargado del reciclaje de proteínas propias dentro de la célula (Rock et al., 1994, Fentenay et
al., 1995).
Existen dos variantes funcionales del proteosoma: El proteosoma 20S de 700 kDa, está
formado por cuatro anillos superpuestos, de siete subunidades cada uno (Löwe et al., 1995; Groll
et al., 1997). Los anillos exteriores poseen subunidades α cuya función es esencialmente
estructural y reguladora. Los dos anillos internos poseen subunidades β de función catalítica.
Entre los componentes del proteosoma se encuentran las subunidades constitutivas X, Y(δ)
y Z. Tras la inducción por interferón-γ (IFN-γ), éstas son sustituidas por las subunidades
funcionales LMP7, LMP2 y MECL-1 respectivamente (Kelly et al., 1991; Glynne et al., 1991;
Groettrup et al., 1996). Los estudios realizados sobre la función de las subunidades inducibles
son poco concluyentes; así, mientras unos sugieren que en la presentación de antígeno no son
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necesarias (Arnold et al., 1992; Momburg et al., 1992; Yewdell et al., 1994), otros indican que
en su ausencia la presentación es menor (Cerundolo et al., 1995). En otros estudios estas
subunidades parecen alterar el patrón de corte del proteosoma (Gaczynska et al., 1993;
Gaczynska et al., 1994; Driscoll et al., 1993), y mientras que LMP7 incrementa la ruptura
catalítica tras residuos hidrofóbicos y básicos, LMP2 reduce la capacidad de corte tras residuos
ácidos. Por último, en un estudio reciente (Eleuteri et al., 1997) LMP7 favorece alguna de las
diferentes actividades catalíticas del proteosoma. En concreto, disminuye la actividad de tipo
quimotripsina, de corte tras residuos hidrofobicos, y aumenta la preferencia de corte tras
aminoácidos aromáticos o con cadenas laterales ramificadas.
La otra variante del proteosoma, encargada de la ruptura de proteínas ubiquitinadas, es la
26S de 1500 kDa. Su núcleo catalítico está formado por el proteosoma 20S asociado a proteínas
adicionales que regulan su actividad (Pamer y Cresswell, 1998).
Aunque hay evidencias tanto de la existencia de un recorte o “trimming” por
endopeptidasas dentro del RE (Retículo Endoplásmico) (Snyder et al., 1994; Hughes et al.,
1996), como de la retrotranslocación al citoplasma previamente a su recorte (Roelse et al., 1994),
se desconoce la importancia que tiene esta variante generadora de péptidos.
I.4.2. Translocación al Retículo Endoplásmico.
Una vez generados en el citosol, los péptidos pasan al RE donde se unen a las moléculas de
clase I nacientes, para formar complejos péptido/MHC de clase I estables que son translocados
hasta la superficie celular.
La demostración de que la expresión de las moléculas de clase I era recuperada en células
mutantes tras añadir péptido exógeno (Townsend et al., 1989), y de que la expresión era
recuperable transfectando dos genes localizados en la subregión de clase II (Spies et al., 1991),
sugerían el importante papel del péptido en la estabilización de la molécula de clase I, y la
implicación de un transportador responsable de la trasnslocación de péptidos al RE. El
responsable resultó ser una proteína heterodimérica, expresada en la membrana del RE,
dependiente de ATP y perteneciente a la familia de los ABC (ATP Binding Cassette)
(Androlewicz et al., 1994) denominada TAP (Transporter associated with Antigen Processing).
El TAP está constituido por la asociación de los monómeros TAP1 y TAP2. Ambos poseen una
región N-terminal con múltiples dominios transmembrana, y un dominio C-terminal de unión a
ATP.
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TAP muestra preferencia por péptidos de 9-10 aminoácidos, el tamaño canónico de los
péptidos unidos a las moléculas de clase I. La identidad del aminoácido C-terminal parece
importante en la selectividad del TAP que en humanos une preferentemente péptidos con
residuos C-terminales hidrofóbicos y básicos y no acepta Prolina ni Glicina (Momburg et al.,
1994). El tamaño de los péptidos translocados por TAP, oscila entre 8 y 13 aminoácidos aunque
pueden ser mayores (Androlewicz et al., 1994; Schumacher et al., 1994). La translocación de los
péptidos al RE, a diferencia de la unión de péptidos a TAP, es un proceso dependiente de ATP.
I.4.3. Biosíntesis, Ensamblaje y expresión en membrana de las moléculas de clase I.
Tras la biosíntesis de las proteínas de clase I, en el correcto plegamiento y ensamblaje de

HLA intervienen secuencialmente diferentes chaperonas del RE rugoso; éstas actúan como un
control de calidad, que impide la asociación de las subunidades plegadas incorrectamente. Las
cadenas pesadas de las moléculas de clase I formadas de novo, son retenidas en primera instancia
por la Calnexina, una chaperona de membrana de 88 kDa (Jackson et al., 1994; Rajagopalan et
al., 1994) que las mantiene parcialmente plegadas hasta que se une la β2m. Una vez formado el
heterodímero Cadena α/β2m, se disocia de la Calnexina y se une a otra chaperona similar,
aunque no insertada en la membrana, la Calreticulina (Sadasivan et al., 1996) y a la Tapasina
(Sadasivan et al., 1996; Ortmann et al., 1997), una glicoproteína transmembranal de 48 kDa. La
Tapasina mantiene asociado al heterodímero parcialmente plegado con la subunidad TAP1 en
espera de que un péptido translocado se una. La unión del péptido induce un cambio de
conformación que estabiliza el complejo trimérico Péptido/Cadena pesada/β2m y desestabiliza la
union con TAP, lo que provoca la disociación del complejo. El complejo péptido/MHC de clase I
es posteriormente transportado, pasando por el TGN (Trans Golgi Network) y por un sistema de
vesículas, hacia la superficie celular.
I.5. TCR Y RECONOCIMIENTO DE LOS COMPLEJOS MHC-PÉPTIDO.
I.5.1. Características estructurales del TCR y reconocimiento de los complejos MHC-péptido.
El receptor de antígeno de los linfocitos T maduros, está compuesto por heterodímeros

clonotípicos α:β, el más común en los linfocitos humanos de sangre periférica, o γ:δ. Las
subunidades están unidas por puentes disulfuro, formando una estructura muy similar a la del
fragmento Fab de una inmunoglobulina. Cada uno de los monómeros se estructura en dos
dominios: uno distal muy variable, responsable de la unión a los complejos MHC/Péptido, y otro
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proximal constante. Ambos dominios tienen unido un carbohidrato. Éstos heterodímeros se

asocian no-covalentemente al complejo CD3, que está formado por tres polipéptidos: γ, δ y ε;
asociados a dos subunidades independientes, las cadenas ζ y η que forman homodímeros ζζ o
heterodímeros ζη unidos por puentes disulfuro.
CD3 participa en el proceso de transducción de señales al interior celular tras el
reconocimiento por el TCR de un complejo MHC/Péptido (Weiss y Littman, 1994) y en el
mantenimiento de la expresión del TCR en la superficie celular.
Los genes codificantes del TCR se asemejan a los de las inmunoglobulinas, tanto en su
secuencia, como en la forma de ensamblarse, mediante reordenamientos de los segmentos
génicos que codifican las regiones variables (V), de diversidad (D), de unión (J) (Joining) y
constantes (C). La cadena α se origina a partir de reordenamientos de segmentos génicos V-J
mientras que la cadena β surge de dos reordenamientos sucesivos V-D-J para generar exones
funcionales. Ambos segmentos reordenados se unen durante la maduración del linfocito en el
timo, a sus correspondientes regiones C. Tanto en las cadenas TCRα como TCRβ existen cuatro
regiones hipervariables, tres de las cuales forman bucles denominados CDRs (Complementarity-
Determining Regions) CDR1, CDR2 y CDR3 que participan directamente en el reconocimiento
del complejo MHC/Péptido.
Recientemente se ha podido resolver, mediante cristalografía de rayos X, la topología del
reconocimiento por el TCR del complejo MHC-péptido (Garboczi et al., 1996; García et al.,
1996). Los resultados obtenidos se ajustan en gran medida a predicciones indirectas previas,
basadas en el reconocimiento de análogos peptídicos (Jorgensen et al., 1992) y mutantes de
moléculas del MHC (Sun et al., 1995).
En el modelo cristalográfíco, El TCR cubre la superficie del péptido y parte de la molécula
del MHC transversalmente, de manera que el reconocimiento del complejo MHC-péptido es
realizado por los CDRs. Cada uno de los CDRs reconoce una parte diferente del complejo. Las
regiones CDR3α y CDR3β se sitúan sobre la parte central del péptido y las regiones CDR1α y
CDR1β sobre los extremos del péptido N- y C-terminales respectivamente. Las regiones CDR2α
y CDR2β interaccionan directamente con los dominios α2 y α1 respectivamente de la molécula
del MHC. Este modo de interaccion entre el TCR y los complejos MHC-péptido parece ser
general.
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I.6. HLA-B27.
El antígeno HLA-B27 es una de las moléculas de clase I humanas mejor estudiadas debido
a su fuerte asociación con las espondiloartropatías. El 95% de los pacientes que sufren
espondilitis anquilosante (EA), y entre el 60-80% de los que sufren artritis reactiva (AR), son
HLA-B27,
Hasta el momento se han identificado quince subtipos (Tabla 1) cuyo polimorfismo se
localiza fundamentalmente en el sitio de unión del péptido. La estructura cristalográfica del
subtipo principal, HLA-B*2705, ha permitido el análisis detallado de las interacciones de esta
molécula con péptidos. A continuación se detalla la estructura de las subcavidades del sitio de
unión de péptido y la naturaleza de las interacciones entre éstas y las cadenas laterales de los
péptidos unidos.
I.6.1. Subcavidad A.
Esta subcavidad es idéntica en todos los

Subcavidad A
subtipos de HLA-B27 a excepción de B*2703 α1 Lámina- β
que presenta el cambio Y59H. Tyr7
El extremo N-terminal del péptido se aloja Tyr59 P2

P1 P3
en esta subcavidad formando una red pentagonal
de puentes de hidrógeno con los residuos Tyr171
Tyr159
conservados Tyr7, Tyr59 y Tyr 171, y a través de
α2
una molécula de agua intermedia, con los
residuos Glu63 y Glu45 (Figura 3). El oxígeno
Figura 3: Red de puentes de hidrógeno que se
del grupo carbonilo de P1 establece un puente de establecen en la subcavidad A con el extremo N-
hidrógeno adicional con el residuo Tyr 159. La terminal del péptido. (Madden et al., 1992).
presencia de His59 en B*2703 provoca una

disrupción de esta red induciendo un reforzamiento de las interacciones en la subcavidad B
(Villadangos et al., 1995)
I.6.2. Subcavidad B.
Esta subcavidad está conservada entre los subtipos de HLA-B27 y es diferente en otras
moléculas de clase I a excepción de B73 (Parham et al., 1994; Vilches et al., 1994b). Está
constituida, entre otros residuos, por His9, Thr24, Glu45, Cys67 y Tyr99 y acomoda la cadena
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lateral del residuo P2 del péptido (Figura 4), que

Subcavidad B
en HLA-B27 es Arg y constituye el anclaje Cys67
peptídico principal (Jardetzky et al., 1991; Thr24

Glu45
Rammensee et al., 1995). His9
En el modelo cristalográfico, el grupo

guanidinio de la Arg2, establece cinco puentes P2
Arg
de hidrógeno, tres de ellos directamente con Tyr99
PEPTIDO
Glu45 y Thr24 y dos indirectos con His9 y Tyr99
por mediación de una molécula de agua. El
grupo sulfhidrilo de la Cys67 se sitúa Figura 4: Interacciones que tienen lugar entre la
cadena lateral de la Arginina y residuos de la
exactamente sobre el plano del grupo guanidinio. subcavidad B. (Madden et al., 1992)
El Glu45 es un residuo crítico en la especificidad
de la subcavidad B por Arg2 (Villadangos et. al., 1995).
La Lys70, un residuo exclusivo de HLA-B27 presente en casi todos los subtipos, se
localiza en las proximidades de esta subcavidad. Sin embargo su cadena lateral se orienta hacia
fuera de la subcavidad B porque establece un puente salino con el Asp74. La mutación Tyr74
presente en B*2701 impide la formación de dicho puente salino relajando la conformación de la
Lys70, lo que afecta a la especificidad de la subcavidad B y favorece la presencia de Gln en P2
(García et al., 1997c / Anexo 2).
I.6.3. Subcavidades C y F.
Las subcavidades C y F forman en HLA-B27 una única cavidad denominada C/F, donde el
extremo C-terminal del péptido establece una amplia red de puentes de hidrógeno (Figura 5). La
mayor parte de las diferencias entre los subtipos de HLA-B27 se concentra en esta cavidad, lo
que sugiere una tendencia evolutiva del polimorfismo de HLA-B27 centrado en modular las
especificidades por el extremo extremo C-terminal del péptido. En HLA-B27 esta posición
constituye junto con la posición 2 otro anclaje primario.
En el modelo cristalográfico, el residuo P9, enlaza directamente con Tyr84 y Thr143 e
indirectamente, a través de dos moléculas de agua, con Thr80 y Lys 146.
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Las cadenas laterales de los residuos

Subcavidad C/F
Asp77 y Asp116, favorecen la unión de residuos α1
C-terminales básicos (Guo et al., 1992; Silver et Asp77
Thr80
al., 1992). Sin embargo, en HLA-B27, esta PÉPTIDO Tyr84
P7 P8
situación no impide acomodar residuos P9 Lys146
hidrofóbicos debido, en parte a la influencia de Thr143
las cadenas laterales apolares de la Leu81, Trp147
Tyr123 y Thr143, y al hecho de que los residuos α2

C-terminales pueden adoptar distintas
orientaciones y contactar en la subcavidad C/F Figura 5: Interacciones entre el extremo C-terminal
del péptido y los residuos de la cavidad C/F de
según su naturaleza química. B*2705. Los residuos polimorficos aparecen
subrayados. (Madden et al., 1992).
I.6.4. Subcavidades D y E.
Las posiciones P3 y P7 constituyen anclajes secundarios de los péptidos que une HLA-
B27. La cadena lateral del residuo P3 interacciona en la subcavidad D. Ésta contiene las cadenas
laterales aromáticas Tyr99 y Tyr159 y la alifática Leu156 que determinan su naturaleza
predominantemente apolar. En B*2705 la subcavidad D, muestra preferencia por residuos con
cadenas laterales voluminosas hidrofóbicas. La cadena lateral polar de His114, se sitúa
lateralmente a esta subcavidad pudiendo aceptar la cadena lateral de residuos polares. Esta
preferencia por el residuo P3 puede variar en los subtipos B*2706, B*2707 y B*2711 donde la
posición 114 está ocupada por Asp o Asn.
La subcavidad E aloja la cadena lateral del residuo P7. En HLA-A2 (Madden et al., 1993)
la cadena lateral de este residuo muestra una gran variabilidad conformacional dependiente de la
secuencia completa del péptido que le permite, según el caso, interaccionar con la molécula de
clase I o ser accesible al TCR. En la región intermedia del péptido los contactos con la molécula
de HLA-B27 son escasos y las cadenas laterales de los residuos P4, P5, P6 y P8 son en general
accesibles al contacto con el TCR.
I.7. HLA-B27 Y ESPONDILOARTROPATÍAS.
Con el término espondiloartropatías seronegativas, se integra a cinco subcategorías

clínicas: la espondilitis anquilosante (EA), la artritis reactiva (AR), la artritis psoriásica, la artritis
asociada a la enfermedad inflamatoria intestinal y las espondiloartropatías indiferenciadas. Estas
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enfermedades comparten entre otras características, la ausencia de factores reumatoides y una

predisposición genética asociada a la presencia de HLA-B27. Sus manifestaciones clínicas se
presentan como un conjunto de desordenes reumáticos y extraarticulares que solapan en muchos
de sus síntomas. La espondilitis anquilosante (EA), considerada como la manifestación más pura
de espondiloartropatía, es una enfermedad crónica que afecta principalmente al esqueleto axial.
La expresión de HLA-B27 no es una condición necesaria ni suficiente para desarrollar una
espondiloartropatía, pero sí supone un factor de riesgo, sobre todo en el caso de la EA
(Brewerton et al., 1973; Schlosstein et al., 1973) y en menor medida en la AR (Brewerton et al.,
1974). Evidencias indirectas sugieren además que otros genes pueden incrementar la
susceptibilidad a padecer enfermedad (Brown y Wordsworth, 1997).
La importancia que juegan los factores ambientales en el desarrollo de la EA, se
desconocen; pero en el caso de la AR, está bien documentada la implicación de bacterias
intracelulares obligadas o facultativas responsables de las infecciones de los epitelios urogenital
(Chlamidia trachomatis), entérico (Yersinia, Sigella, Salmonella o Campylobacter) y respiratorio
(Chlamidia pneumoniae). Los estudios realizados en ratas y ratones transgénicos refuerzan la
estrecha relación existente entre la expresión de HLA-B27, la flora bacteriana y el desarrollo de
artritis.
I.7.1. Posible papel patogénico de la presentación de péptidos por HLA-B27.
El mecanismo de asociación de HLA-B27 a las espondiloartropatías se desconoce. Entre las

diversas hipótesis que intentan explicar el papel patogénico de HLA-B27, tal vez la que está
apoyada por evidencias más convincentes es la teoría del péptido artritogénico (Benjamin y
Parham, 1990). Esta hipótesis postula que el evento patogénico primario en las
espondiloartropatías sería una estimulación antigénica externa (por ejemplo una infección
bacteriana) de una respuesta celular citotóxica contra un péptido restringido por HLA-B27. Estos
CTLs activados exógenamente reaccionarían cruzadamente con algún péptido propio presentado
por HLA-B27, lo que desencadenaría una reacción autoinmune. Las evidencia a favor de esta
hipótesis son más o menos circunstanciales.
(i) En humanos, ha sido demostrada la existencia de CTLs autorreactivos contra péptidos
del colágeno de tipo II en el líquido sinovial de pacientes con AR, (Gao et al., 1994), y de CTLs
específicos de péptidos bacterianos restringidos por HLA-B27 en pacientes con AR y EA
(Hermann et al., 1993, Duchman et al., 1996. Ugrinovic et al., 1997).
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(ii) En ratas transgénicas, la expresión de un elevado número de copias de HLA-B27, es

suficiente para el desarrollo de una enfermedad inflamatoria espontánea, con muchas
características similares a las espondiloartropatías humanas. El papel de las bacterias en este
modelo es evidente puesto que la enfermedad no se desarrolla en condiciones libres de gérmenes
(Hammer et al., 1990; Taurog et al., 1994; Breban et al., 1996). Recientemente también se ha
demostrado que la alteración del repertorio peptídico de HLA-B27 induce la ausencia de artritis
periférica en ratas transgénicas (Zhou et al., 1998). Esta es la evidencia más directa de un papel
crítico de los péptidos de HLA-B27 en la patogenia de la enfermedad asociada con este antígeno.
(iii) La sociación diferencial de los subtipos de HLA-B27 a EA. Este tema se desarrolla
en detalle en el siguiente apartado.
I.7.2. Distribución étnica y asociación a enfermedad de los subtipos de HLA-B27.
Se conocen hasta el momento quince subtipos de HLA-B27 que difieren entre uno y siete
residuos ubicados principalmente en el sitio de unión del péptido (Figura 6). Probablemente
todos ellos han derivado por diferentes mecanismos evolutivos de B*2705 (López-Larrea et al.,
1996). Sus distribuciónes étnicas y su asociación a enfermedad son variables (Tabla 1).
Entre las poblaciones euro-caucasoides el subtipo mayoritario es B*2705, presente en el
90% de los individuos B27+. Prácticamente el 10% restante son B*2702. A su vez este es el
subtipo predominante en judíos, donde representa el 60% de los individuos B27+ (González-
Roces et al., 1994). B*2709 es frecuente entre la población Sarda. B*2701, B*2708 y B*2710
son subtipos aparentemente minoritarios.
B*2703 detectado inicialmente entre población negra de Norteamérica es originario de
poblaciones del oeste africano.
B*2704 y B*2706 se encuentran en poblaciones asiáticas, donde el primero es mayoritario.
B*2707 es menos frecuente pero se encuentra también en poblaciones del sudeste asiático.
B*2705, B*2702, B*2704(López-Larrea et al., 1995; Nasution et al., 1997; Ren et al.,
1997) y B*2707 están claramente asociados a enfermedad. B*2706 y B*2709 (D’Amato et al.,
1995) no están asociados a enfermadad en poblaciones donde otros subtipos si lo están aunque se
han descrito dos casos de individuos B*2706 en China.
B*2703 se ha encontrado en algún individuo con EA (González-Roces et al., 1997), sin
embargo esta enfermedad es muy rara entre la poblacion del oeste de África, donde predomina
este subtipo, incluso entre los individuos B*2705 de la misma población, lo que sugiere que
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probablemente están implicados otros factores genéticos protectores (Brown et al., 1997).
Recientemente se ha encontrado co-segregación de EA con B*2708 en un estudio familiar
(Armas et al., 1999).
Los subtipos B*2701, B*2710, B*2711, B*2712. son subtipos poco frecuentes
encontrados en individuos aislados, lo que impide un tratamiento estadístico adecuado para
determinar su asociación a enfermedad. B*2713, B*2714 y B*2715 han sido descritos
recientemente como nuevos subtipos. El primero es una variante cuya mutación aparece en la
secuencia señal del exón 1 (Tabla 1).
α1 α2 α3
E
Subcavidad A C/F C/F C/F C/F C/F D D/E C/F E
Asoc. a
Subtipo 59 69 70 71 74 77 80 81 82 83 97 113 114 116 131 152 211
EA
(a)
B*2705 + Y A K A D D T L L R N Y H D S V A
(b)
B*2701 ¿? − − − − Y N − A − − − − − − − −
(c)
B*2702 + − − − − − N I A − − − − − − − − −
(d)
B*2703 + H − − − − − − − − − − − − − − − −
(e)
B*2704 + − − − − − S − − − − − − − − − E G
(f)
B*2706 − − − − − − S − − − − − − D Y − E G
(g)
B*2707 + − − − − − − − − − S H N Y R − −
(h)
B*2708 + − − − − − S N − R G − − − − − − −
(i)
B*2709 − − − − − − − − − − − − − − H − − −
(j)
B*2710 ¿? − − − − − − − − − − − − − − − E n.d
(k)
B*2711 ¿? − − − − − S − − − − S H N Y R − −
(l)
B*2712 ¿? − T N T − S N − R G − − − − − − n.d
(m)
B*2713 ¿? − − − − − − − − − − − − − − − − −
(n)
B*2714 # ¿? − − − − − − − − − − − − − − − −
(ñ)
B*2715 # ¿?
Tabla 1: Residuos polimórficos entre los subtipos de HLA-B27.

Los guiones indican identidad con el aminoácido presente en B*2705. (n.d; no determinado).
Referencias: a: (Ezquerra et al., 1985; Moses et al., 1995). b: (Rojo et al., 1987a; Choo et al., 1986). c: (Vega et al., 1985a;
Moses et al., 1995). d: (Rojo et al., 1987b; Choo et al., 1988). e: (Vega et al., 1985b; Rudwaleit et al., 1996). f: (Vega et al.,
1986; Vilches et al., 1994a). g: (Choo et al., 1991). h: (Hildebrand et al., 1994). i: (Del Porto et al., 1994). j: (Fernández-Viña et
al., 1996). k: (Hasegawa et al., 1997). l: (Balas et al., 1998). m: (Seurynck y Baxter-Lowe, 1998). n: (Hurley,C./ Nº
acceso.AF072763-64, presenta los cambios L95W; N97T; V103L). ñ: (Van den Berg-Loonen E.M./ Nº acceso Y16637-38.
Secuencia no publicada). # www.anthonynolan.com.
-19- INTRODUCCIÓN
69 71
74 77 80 83
70 82
81
59
97
6
11
4
11
3
11 152
131
Figura 6: Distribución de las posiciones polimórficas en los dominios α1 y α2 de la molécula de clase I HLA-
B27.
-21-
II. OBJETIVOS
-25-
III. MATERIALES Y MÉTODOS

MATERIALES Y MÉTODOS -27-
III. MATERIALES Y MÉTODOS
III.1. LÍNEAS CELULARES.
L
as células RMA-S pertenecen a una línea celular mutante derivada del linfoma de células
T de ratón RBL-5 (H-2b) inducido por el virus de Rauscher (Ljunggren y Kärre, 1985).
Estas células, son defectivas en proteínas TAP2 y muestran una baja expresión en
superficie de antígenos de clase I a 37ºC. Cuando se cultivan a temperaturas inferiores a 30ºC la
expresión en membrana se incrementa, y expresan moléculas inestables de MHC de clase I vacías
de péptido (Ljunggren et al., 1990b). La estabilidad, en estas condiciones, puede ser recuperada
añadiendo péptido exógeno. En esta tesis se han utilizado diferentes transfectantes de subtipos y
mutantes de HLA-B27 clonados previamente en el laboratorio.
III.2. ANTICUERPOS MONOCLONALES (mAb).
El anticuerpo ME1 (isotipo IgG1) (anti-HLA-B27+B7+B22) (Ellis et al., 1982), reconoce un

epítopo conformacional en el dominio α1 (El-Zaatari et al., 1990) que no es polimórfico entre los
subtipos de HLA-B27, y que no se altera tras la unión del péptido (Smith et al., 1996a). Se obtuvo
a partir de sobrenadante de cultivo del hibridoma secretor de dicho anticuerpo. Una vez verificada
su correcta actividad, el sobrenadante se filtró y almacenó a –20ºC con 0,02% azida sódica.
Como segundo anticuerpo, en citometría de flujo, se utilizó una dilución 1/100 de un mAb
comercial fluoresceinado (FITC, Fluorescein Isothiocianate-conjugated rabbit F(ab’)2-anti-mouse
IgG [H+L]) (Southern Biotechnology, Birmingham, Ala).
III.3. SÍNTESIS PURIFICACIÓN Y CUANTIFICACIÓN DE PÉPTIDOS.
III.3.1. Síntesis y purificación de péptidos y análogos no peptídicos.
Los péptidos se sintetizaron en fase sólida mediante un sintetizador múltiple de péptidos

AMS 422 utilizando la química F-moc. Tras la síntesis, se purificaron en HPLC de fase reversa
midiendo su absorbancia a 210 y 280 nm., empleando un equipo Waters LC 625 provisto de una
columna µ-Bondapack C18 (Waters) de 300 x 7,8mm. Se utilizó un gradiente de concentración
creciente de acetonitrilo a un flujo de 2ml/min durante 60 minutos. con: (A): H2O +TFA 0,1%
MATERIALES Y MÉTODOS -28-
(ácido trifluoroacético) y (B): acetonitrilo + TFA 0,1%. El gradiente, fue el siguiente: 0-5 minutos
con 100% de (A), 5-40 min hasta un 40% de (B), de 40-45 hasta 60% de (B) de 45-50 hasta el
100% de (B). La pureza de los picos purificados se confirmó mediante HPLC analítico en fase
reversa utilizando una columna Nova-Pack® C18 (Waters) 3,9 x 150mm a un flujo de 0,5ml/min y
el mismo gradiente de acetonitrilo-TFA. La correcta masa molecular se determinó por
espectrometría de masas mediante un espectrómetro VG Auto Spec.
Los análogos no peptídicos utilizados en esta tesis, fueron sintetizados en el Laboratory for
Organic Chermistry, Swiss Federal Institute of Technology. Zürich (Switzerland). Su
cuantificación y control de pureza, se analizó igual que el resto de péptidos.
III.3.2. Cuantificación.
La cuantificación de los péptidos y su correcta composición, se determinó mediante un

proceso previo de hidrólisis con ácido clorhídrico en atmósfera reductora de Nitrógeno, en
presencia de un control estandard de norleucina, durante 24h a 110ºC. El análisis posterior se llevó
a cabo mediante un analizador de aminoácidos (Beckman, Palo Alto, CA). Los péptidos se
conservaron en agua Milli-Q a -70ºC a una concentración final 1mM.
III.4. ENSAYO DE UNIÓN DE PÉPTIDOS.
El ensayo de unión de péptidos se realizó mediante un procedimiento cuantitativo (Galocha

et al., 1996 / Anexo 2), basado en la estabilización, por péptidos añadidos exógenamente, de las
moléculas vacías de HLA-B27 expresadas a 26ºC.
Los transfectantes se incubaron a 26ºC durante 18-24 h, a una concentración de 106
células/ml en placas estériles de 96 pocillos de fondo en V (NUNC) en 100µl de RPMI 1640,
25mM HEPES y 10% de FBS (Suero bovino fetal) en ausencia de péptido. Transcurrida la
incubación a 26ºC, las placas se lavaron dos veces con PBS estéril y se les añadió el péptido
diluido en medio RPMI 1640, 25mM HEPES sin suero, para obtener concentraciones finales
comprendidas entre 10-4M hasta 10-9M. Posteriormente las células se incubaron durante una hora
a 26ºC y, tras este periodo, a 37ºC durante 2h o 4h dependiendo del subtipo: B*2701, B*2702,
B*2703, B*2704 y los mutantes Y74, A81, D114 y E152 se incubaron durante 2h. B*2705,
B*2706, S77, Y116, D114Y116 se incubaron durante 4h. Estos tiempos se eligieron de forma
que la expresión de HLA-B27 era claramente superior a la expresión basal a 37ºC, pero en los
que en presencia de péptido la disociación y pérdida de expresión en superficie predominase
-29- MATERIALES Y MÉTODOS
sobre la asociación e inducción de la expresión.
III.4.1. Análisis por citometría de flujo.
Las células se lavaron dos veces con PBS para eliminar cualquier traza de péptido en el
sobrenadante y se incubaron nuevamente durante 30 minutos a 4ºC con 30-50 µl de anticuerpo
monoclonal ME1. Tras este período, se lavaron otras dos veces con PBS estéril y se añadieron de
30-50µl del segundo anticuerpo monoclonal fluoresceinado, dejando transcurrir otros 30 minutos a
4ºC. Transcurrida la segunda incubación, se lavaron dos veces con PBS estéril. y se fijaron con
100µl de paraformaldehído previamente a su análisis en un citómetro de flujo EPICS Profile II
Coulter donde se midió la fluorescencia lineal para un total de 5000. células.
III.4.2. Cálculo de la unión de péptidos.
La media de la fluorescencia lineal asociada a la expresión de HLA-B27 se representó en

función de las diferentes concentraciones de péptido. El análisis cuantitativo y comparativo de la
unión de los diferentes péptidos se realizó mediante el programa Origin MicroCal Software Inc.
Tras calcular la concentración molar de péptido a la cual se producía el 50% de la fluorescencia
máxima (C50). La concentración molar requerida de cada péptido para alcanzar el valor de
fluorescencia C50 del péptido utilizado como referencia o control, se denominó EC50. La unión
relativa se definió como la relación molar entre los valores EC50 de los péptidos comparados.
Los intervalos de afinidad se escogieron en función de los valores de afinidad obtenidos en
los ensayos de unión con los péptidos presentados in vivo. Así las afinidades se definieron como
sigue: (Afinidad alta: <5µΜ.), (Afinidad intermedia: 6µM-50µM ) y (Afinidad baja: >50µM). La
afinidad de péptidos mayor de 100µM no se midió en este ensayo, y refleja una unión marginal o
nula.
-31-
IV. RESULTADOS
RESULTADOS -33-
IV. RESULTADOS
IV.1. EFECTO DEL POLIMORFISMO DE HLA-B27 SOBRE LA ESPECIFICIDAD DE UNIÓN DE

PÉPTIDOS.
C
on la finalidad de determinar las bases moleculares que determinan el solapamiento de
repertorios peptídicos entre subtipos de HLA-B27, el estudio se centró en el análisis de
la especificidad peptídica de: (i) B*2704 y B*2706, (ii) B*2701 y (iii), B*2703.
B*2704 y B*2706 están relacionados estructuralmente pero desigualmente asociados a
enfermedad. B*2701 y B*2702 difieren de B*2705 en mutaciones distintas pero localizadas en la
misma región de la molécula. El polimorfismo de B*2703, afecta a una interacción conservada con
el extremo peptídico N-terminal.
Las diferencias entre estos subtipos se analizaron comparando las afinidades de unión in vitro
de ligandos naturales sintéticos de B*2705 (05.Pi) (Jardetzky et al., 1991) y B*2702 (02.Pi)
(Rötzschke et al., 1994). Las bases moleculares de estas diferencias se analizaran con mutantes
que mimetizaban los cambios puntuales entre los subtipos, y mediante análogos peptídicos a los
que se cambia en los residuos principales de anclaje PΩ o P2.
IV.1.1. Unión de péptidos a HLA-B*2705, B*2704 y B*2706. Modulación de la especificidad

por el residuo peptídico C-terminal. (Anexo 1)
B*2704 y B*2706, son los dos subtipos HLA-B27 restringidos a poblaciones asiáticas, muy
diferentes antigénicamente de B*2705 (López et al., 1994). B*2706 no está asociado a enfermedad
en poblaciones donde B*2704 si lo está. B*2704 difiere de B*2705 en dos cambios: D77S y
V152E. B*2706 tiene además dos cambios adicionales a los de B*2704, H114D y D116Y. Ambos
subtipos tienen además el cambio A211G, que por su localización, en el dominio α3, no afecta a la
unión del péptido.
Tanto los ligandos (05.Pi) como (02.Pi), se unieron a B*2705 con alta afinidad (EC50 ≤5µM),
(Tabla 2), lo que sugiere que el repertorio de B*2705 podría englobar una parte del repertorio
natural de B*2702.
El estudio con los análogos peptídicos en P2 mostró un descenso de la afinidad de unión,

RESULTADOS -34-
indicando que este anclaje era esencial para mantener la buena unión del péptido, sin embargo a
diferencia de lo que ocurre con los análogos de Ala2, el residuo Gln2 funcionaba como un residuo
subóptimo permitiendo una unión significativa, y por lo tanto compatible con la presencia de este
residuo entre los ligandos naturales de B*2705 (Tabla 3A).
La contribición del residuo P9 fue variable entre los diferentes análogos. Así, Lys en 05.P2
era mejor que en 05.P6 mientras que Tyr era equivalente a Arg y Leu en 02.P4 y 02.P6, y también
a Ala en 02.P4 pero no en 02.P6 (Tabla 3B). Esto indica que la tolerancia de determinados residuos
está influida por el resto de la secuencia del péptido. El estudio de la contribución de los diferentes
residuos debe realizarse con análogos que eviten, en lo posible, la interferencia de otras posiciones
(ver Anexo 5).
B*2704, unió eficientemente péptidos con residuo C-terminal alifático (Leu) o aromático
(Tyr) (EC50≤5µM) y peor aquellos con residuo básico (Tabla 2). Los análogos con Gln2 de
péptidos con residuos C-terminales alifáticos (Leu) se unieron a este subtipo mejor que a B*2705,
indicando que el anclaje C-terminal hidrofóbico es más fuerte que en B*2705. En cambio en
05.P6Q2 no se unió, lo que significa que la unión de Lys C-terminal es más débil que en B*2705
(Tabla 3B). La unión de los análogos de 02.P4 y 02.P6 con L9 (Tabla 3B) fue superior a la de los
péptidos correspondientes, indicando que Leu es mejor residuo C-terminal que Tyr para la unión a
B*2704.
B*2706 unió eficientemente péptidos con residuos C-terminales apolares (Leu, Phe), pero no
aquellos con Tyr o residuos básicos (Tabla 2). La unión relativa de los análogos con Gln2, que fue
buena para péptidos con Leu y Phe y mala para Lys o Tyr, confirmó estas preferencias (Tabla 3A)
La unión de análogos con L9 fue claramente superior que en los péptidos con Tyr C-terminal
(02.P4, 02.P6) lo que confirma las preferencias de B*2706 por Leu respecto a Tyr.
Estos resultados indican que B*2704 y B*2706 difieren de B*2705 sobre todo en su peor
tolerancia por residuos C-terminales básicos. Además la diferencia fundamental entre B*2704 y
B*2706, reside en la menor aceptación por este último de residuos con Tyr C-terminal.
IV.1.1.1. Efecto de las pérdidas y ganancias de residuos cargados en las subcavidades E/C/F.
El uso de mutantes que reproducen los cambios en B*2705 y B*2706, permitió el análisis del
papel que juegan las posiciones polimórficas que diferencian a estos subtipos. Estas mutaciones
determinan las propiedades electrostáticas de las subcavidades donde interacciona el péptido.
La eliminación de una carga negativa en la cavidad C/F, como ocurre con los mutantes S77 y
-35- RESULTADOS
Y116 no impidió la unión eficiente de los ligandos naturales, independientemente del residuo C-
terminal (Tabla 2). Además, en general, los péptidos con residuos C-terminales apolares se unieron
mejor a los dos mutantes que a B*2705. Una característica importante del mutante Y116 fue el
aumento notable de su preferencia por Leu como residuo C-terminal respecto a Tyr, como se
apreció con los análogos de 02.P4 y 02.P6.(Tabla 3B).
D114 y E152, al contrario que las mutaciones anteriores, suponen la ganancia de una carga
negativa. La unión de los ligandos naturales a estos mutantes mostró un empeoramiento general de
la unión relativa de los péptidos respecto a la unión a B*2705 (Tabla 2).
La doble mutación D114Y116, supone un balance neto de cargas neutro. Este mutante unió
bien los péptidos con residuos C-terminales tanto básicos, como alifáticos o aromáticos, y en
general las afinidades de unión al doble mutante se mostraron similares a las del mutante Y116,
indicando el efecto compensador de esta mutación sobre los efectos adversos de la mutación D114.
PÉPTIDO SECUENCIA B*2705 B*2704 B*2706 S77 Y116 E152 D114 DY
05.P2 RRIKEIVKK 0,8 10 100 0,5 0,1 6 60 0,1

05.P6 GRIDKPILK 2 20 70 1 1 20 5 0,3
05.P5 RRSKEITVR 2 10 30 1 3 20 40 3
05.P8 KRFEGLTQR 2 20 40 0,6 2 >100 90 2
05.P10 RRISGVDRY 3 5 40 0,8 5 >100 40 4

02.P6 KRGILTLKY 4 2 40 0,3 5 30 10 2
02.P2 GRLTKHTKF 4 4 4 0,9 1 5 8 0,4

02.P3 RRFVNVVPTF 2 2 1 0,5 0,4 3 4 0,5
05.P1 RRYQKSTEL 1 1 0,5 1 0,1 5 20 0,2
Tabla 2: Unión de ligandos naturales de B*2705 y B*2702, a subtipos y mutantes de HLA-B27.
La unión a cada variante de HLA-B27 está expresada en valores de EC50 (µM) que indica la concentración
requerida de péptido para obtener la mitad de la fluorescencia máxima (C50), asociada a HLA-B27 unido al
péptido de máxima afinidad entre los péptidos de las series 05.Pi y 02.Pi. Los péptidos con EC50 ≤ 5µM se
considera que tienen alta afinidad por ser este el rango en el que se unen los péptidos naturales presentados por
B*2702 y B*2705 respectivamente. EC50 ≥ 50 µM indica baja afinidad, 5 µM ≤ EC50 ≤ 50 µM afinidad intermedia,
EC50≥100µM, carencia de unión.
RESULTADOS -36-
Tabla 3A
Péptido Secuencia B*2705 B*2704 B*2706 S77 Y116 E152 D114 DY
05.P1 RRYQKSTEL 1 (1) 1 (2) 1 (0,1) 1 (2) 1 (0,05) 1 (3) 1 (20) 1 (0,4)
05.P1Q2 -Q------L 10 2 1 0,5 6 7 5 2,5
05.P1A2 -A------L 90 4 5 3 60 - - 7,5
05.P4 RRWLPAGDA 1 (5) 1 (7) 1 (9) 1 (1) 1 (2) 1 (30) 1 (20) 1 (3)
05.P4Q2 -Q------A - - - 40 20 - 2 3
05.P4A2 -A------A - - 8 60 20 - 2 13
05.P6 GRIDKPILK 1 (0,9) 1 (12) 1 (50) 1 (1) 1 (1) 1 (26) 1 (4) 1 (0,1)
05.P6Q2 -Q------K 11 - - 30 6 - 10 2
05.P6A2 -A------K - - - - - - - -
02.P2 GRLTKHTKF 1 (4) 1 (4) 1 (2) 1(0,9) 1 (0,6) 1 (6) 1 (6) 1 (0,2)
02.P2Q2 -Q------F 18 5 4 6 5 - - 2,5
02.P2A2 -A------F - - 40 8 17 - - 20
02.P4 KRYKSIVKY 1 (3) 1 (6) 1 (2) 1 (0,5) 1 (1) 1 (10) 1 (8) 1 (1)
02.P4Q2 -Q------Y 20 5 25 10 30 4 - 30
02.P4A2 -A------Y - - - - - - - -
02.P6 KRGILTLKY 1 (1) 1 (5) 1 (40) 1 (0,2) 1 (3) 1 (50) 1 (20) 1 (5)
02.P6Q2 -Q------Y - 10 - 40 13 - - -
02.P6A2 -A------Y - - - - - - - -
Tabla 3B
Péptido Secuencia B*2705 B*2704 B*2706 Y116 D114
05.P6 GRIDKPILK 1 (0,9) 1 (12) 1 (50)

La unión relativa está
05.P6A9 -R------A 8 0,6 0,04
expresada como el
cociente entre el EC50 del
02.P2 GRLTKHTKF 1 (4) 1 (4) 1 (2)
correspondiente análogo
02.P2R9 -R------R 1 5 30
y el C50 del ligando
natural.
02.P4 KRYKSIVKY 1 (3) 1 (6) 1 (2) 1 (1) 1 (8)
02.P4R9 -R------R 1 1 0,4 5 0,4 Los valores de C50 (µM)
02.P4L9 -R------L 0,7 0,3 0,2 0,01 0,4 del péptido sin cambios
02.P4A9 -R------A 1 1 0,4 0,04 1 aparecen indicados entre
paréntesis. Los guiones
02.P6 KRGILTLKY 1 (1) 1 (5) 1 (40) 1 (3) 1 (20) indican no unión del
02.P6R9 -R------R 1 2 - 3 0,4 péptido.
02.P6L9 -R------L 0,9 0,6 0,02 0,002 0,3
02.P6A9 -R------A 20 1 0,08 0,2 -
Tabla 3: Efecto de los análogos en P2 (Tabla 3A) y P9 (Tabla 3B) en la unión relativa a
subtipos y mutantes.
-37- RESULTADOS
IV.1.2. Unión de péptidos a B*2701 y B*2702. Efecto del polimorfismo sobre la especificidad
de los residuos en P2. (Anexo 2)
En este estudio, siguiendo una estrategia similar a la del apartado anterior, se determinó la
especificidad de unión de péptidos in vitro a B*2701 y B*2702. B*2701 es un subtipo poco
frecuente, cuya asociación a enfermedad se desconoce; se diferencia de B*2705 en los cambios
D74Y, D77N y L81A. El primero es un cambio único entre los subtipos conocidos de HLA-B27.
B*2702, que sí está asociado a enfermedad, se diferencia de B*2705 en los siguientes cambios:
D77N, T80I y L81A.
La unión de los péptidos 05.Pi y 02.Pi mostró que tanto B*2701 como B*2702 presentaban
preferencias similares por residuos C-terminales alifáticos (Leu) y aromáticos (Phe y Tyr). Los
residuos C-terminales básicos estaban desfavorecidos en la unión a B*2701 pero B*2702
también unía péptidos con Arg9 (05.P5, 05.P8) con afinidades compatibles con su posible
presentación in vivo (Tabla 4). Estos resultados sugieren que B*2701 y B*2702 comparten con
B*2705 una parte del repertorio peptídico, que incluye sobre todo residuos C-terminales
alifáticos o aromáticos.
Los análogos con Gln2 de los péptidos con residuos C-terminales básicos se unieron mal a
B*2702, pero esos mismos análogos de péptidos con Leu, Tyr o Phe C-terminal (05.P1Q2,
02.P4Q2, 02.P6Q2) se unieron de forma similar a los péptidos naturales, mostrando una mejor
unión relativa a B*2702 que a B*2705 (Tabla 5A). Estos resultados sugieren que los residuos
alifáticos y aromáticos, están más favorecidos en B*2702 que en B*2705, y que los péptidos con
Gln2 podrían formar parte del repertorio natural de B*2702, aunque no han sido aún
encontrados. Todos los análogos con Gln2, independientemente del residuo C-terminal, se
unieron a B*2701 con una eficiencia similar a la del péptido natural, indicando que las
contribuciónes de la Arg2 y de la Gln2 en B*2701 son equiparables.
La preferencia, tanto de B*2701 como de B*2702 por Leu, Phe y Tyr C-terminal, se
confirmó mediante los análogos con cambios en esta posición. La unión relativa de los análogos
con Leu C-terminal (02.P4L9 y 02.P6L9, originalmente Tyr9) mostraron una eficiencia de unión
similar, indicando que tanto Tyr como Leu son igualmente adecuados en ambos subtipos. Sin
embargo, la peor unión a B*2701 de los análogos con Ala9 de esos mismos péptidos, sugiere que
los residuos C-terminales Tyr y Leu contribuyen más fuertemente a la unión en B*2701 que en
B*2702 (Tabla 5B).
En general la unión de los péptidos naturales al mutante Y74 fue buena (Tabla 4), por
RESULTADOS -38-
tanto, la mala unión de algunos péptidos a B*2701 no era debida a esta mutación. Por el
contrario, la unión de los mismos péptidos al mutante A81 fue bastante peor, indicando que esta
mutación es probablemente responsable de la deficiente unión de muchos de los péptidos a
B*2701. El hecho de que algunos de los péptidos se unían bien a B*2702, que también posee el
cambio A81, sugiere la existencia de efectos compensadores de otros cambios, posiblemente I80,
en este subtipo (Tabla 4).
Al igual que con B*2701, los análogos con Gln2 se unieron bien al mutante Y74,
indicando que la preferencia de B*2701 por Gln2 es debida al efecto de esta mutación (Tabla
5A). Debido a que la posición Y74 se localiza fuera de la subcavidad B, este resultado indica que
la especificidad de esta subcavidad es modulada por polimorfismo existente fuera de ella.
Confirmando los resultados de unión in vitro, la secuenciación de los respectivos pooles de
péptidos demostró la presencia, tanto de Arg2 como de Gln2 entre los péptidos presentados in
vivo por B*2701 y por el mutante Y74 (Anexo 2).
Péptido Secuencia B*2705 B*2702 B*2701 Y74 A81
05.P1 RRYQKSTEL 1 8 5 0,7 10

05.P2 RRIKEIVKK 0,8 20 >100 0,8 9
05.P3 RRVKEVVKK 2 50 >100 2 20
05.P11 ARLFGIRAK 5 >100 >100 3 80
05.P6 GRIDKPILK 2 20 >100 1 20
05.P5 RRSKEITVR 2 20 >100 1 80
05.P7 FRYNGLIHR 4 6 40 0,6 20
05.P8 KRFEGLTQR 2 4 30 0,4 30
05.P10 RRISGVDRY 3 8 4 2 40
05.P4 RRWLPAGDA 4 6 >100 3 10
05.P9 RRFTRPEH 20 40 >100 20 70
02.P3 RRFVNVVPTF 2 1 0,9 0,5 2

02.P2 GRLTKHTKF 4 2 10 3 9
02.P4 KRYKSIVKY 4 2 1 1 20
02.P6 KRGILTLKY 4 1 0,6 3 7
Tabla 4: Unión de ligandos naturales de B*2705 y B*2702 a subtipos y mutantes

de HLA-B27.
Se indican valores de EC50 (µM).( ver pie de la tabla 2)
-39- RESULTADOS
Tabla 5: Péptido Secuencia B*2705 B*2702 B*2701 Y74 A81

Unión relativa de varios
análogos peptídicos con 05.P1 RRYQKSTEL 1 (1) 1 (4) 1 (5) 1 (1) 1 (12)
cambios en las posiciones 05.P1Q2 -Q------L 10 1 0,8 0,8 -
P2 (Tabla 5A) y P9 (Tabla 05.P1A2 -A------L 90 15 1,4 20 -
5B) a los B*2705, B*2702
y B*2701 y a los mutantes 05.P6 GRIDKPILK 1 (0,9) 1 (10) 1 (2) 1 (20)
Y74 y A81. 05.P6Q2 -Q------K 11 - 2 4
05.P6A2 -A------K - - - -
La unión relativa está
expresada como el cociente 05.P7 FRYNGLIHR 1 (2) 1 (5) 1 (20) 1(21) 1 (24)
entre el EC50 del 05.P7Q2 -Q------R 5 8 1,5 2 3
correspondiente análogo y
el C50 del ligando natural. 02.P2 GRLTKHTKF 1 (4) 1 (4) 1 (6) 1(0,8) 1 (9)
Entre paréntesis aparecen 02.P2Q2 -Q------F 18 7,5 0,5 2,5 -
Los valores de C50 (µM) del 02.P2A2 -A------F - - - - -
péptido sin cambios. Los
guiones indican no unión 02.P3 RRFVNVVPTF 1 (2) 1 (1) 1 (2) 1(1) 1 (3)
del péptido. 02.P3Q2 -Q-------F 3 3 1 1 10
02.P3A2 -A-------F 35 20 2,5 20 -
02.P4 KRYKSIVKY 1 (3) 1 (4) 1 (2) 1 (1) 1 (10)

02.P4Q2 -Q------Y 20 1 0,4 0,7 9
02.P4A2 -A------Y - 15 2,5 20 -
Tabla 5A
02.P6 KRGILTLKY 1 (1) 1 (1) 1 (0,7) 1 (1) 1 (15)
02.P6Q2 -Q------Y - 2 0,9 2 -
02.P6A2 -A------Y - 80 29 - -
Péptido Secuencia B*2705 B*2702 B*2701 Y74 A81

05.P6 GRIDKPILK 1 (0,9) 1 (10) 1 (2) 1 (20)
05.P6A9 -R------A 8 0,4 2 1,5
02.P2 GRLTKHTKF 1 (4) 1 (4) 1 (6) 1(0,8) 1 (9)

02.P2R9 -R------R 1 15 - 2,5 1
02.P3 RRFVNVVPTF 1 (2) 1 (1) 1 (2) 1(1) 1 (3)

02.P3R10 -R-------R 2 4 35 2 3
02.P3A10 -R-------A 2 2 3,5 3 7
02.P4 KRYKSIVKY 1 (3) 1 (4) 1 (2) 1 (1) 1 (10)

02.P4R9 -R------R 1 12,5 10 1 1
02.P4L9 -R------L 0,7 1 1,5 0,6 0,3
02.P4A9 -R------A 1 2,5 40 1 1
02.P6 KRGILTLKY 1 (1) 1 (1) 1 (0,7) 1 (1) 1 (15)

Tabla 5B
02.P6R9 -R------R 1 20 - 2 1,3
02.P6L9 -R------L 0,9 1 1,3 0,7 0,2
02.P6A9 -R------A 20 10 - 10 -
RESULTADOS -40-
IV.1.3. Unión de péptidos a B*2703. Papel del polimorfismo de la subcavidad A. (Anexo 3)
B*2705 y B*2703 se diferencian exclusivamente en el cambio Y59H, localizado en la

subcavidad A. Este residuo está implicado en la estabilización del extremo N-terminal del
péptido, y está conservado entre los subtipos de HLA-B27 a excepción de B*2703.
Para determinar los efectos de esta Unión relativa
Péptido Secuencia
B*2703 B*2705
mutación en la interacción con péptido,
ésta se estudió bajo dos puntos de vista. En (1) RRYQKSTEL 1 (2.10-6) 1 (2.10-6)
(2) ARYQKSTEL 1,5 2
primer lugar, mediante un ensayo de unión (3) RQYQKSTEL >>100 10
in vitro se determinaron las eficiencias de
unión a B*2705 y B*2703 de tres péptidos: Tabla 6: Afinidades de unión de tres péptidos a los
subtipos B*2705 y B*2703.
(1) RRYQKSTEL, un ligando natural de
ambos subtipos (Jardetzky et al, 1991; Los valores correspondientes al C50 (µM) del péptido
(1), que aparece entre paréntesis, indican la concentración
Boisgérault et al, 1996.) y dos análogos del en la cuál se alcanza la mitad de la máxima fluorescencia,
determinada mediante citofluorimetría. La unión relativa
mismo, (2) ARYQKSTEL y (3) de los análogos, indica el exceso molar de péptido
necesario para alcanzar el valor de C50
RQYQKSTEL (Tabla 6).
Los resultados indican que el cambio
de Arg por Ala en P1 tiene un efecto limitado y cualitativamente similar sobre la unión a ambos
subtipos. Sin embargo, el cambio Arg por Gln en P2 tiene un efecto mucho más dramático sobre
la unión a B*2703 que a B*2705. Esto muestra que el cambio Y59H en B*2703, además de los
efectos en la subcavidad A afecta a las interacciones en la subcavidad B, aumentando la
preferencia por Arg2 con relación a Gln2.
Los efectos de los cambios peptídicos sobre su unión a ambos subtipos, se analizaron
mediante una simulación de dinámica molecular basada en la estructura cristalográfica de HLA-
B27. Esta técnica permite predecir varios parámetros moleculares (distancias entre ligando y el
centro de masas de la proteína, fluctuaciones atómicas, áreas accesibles y no accesibles del
ligando, frecuencias de formación de enlaces de hidrógeno) que ayudan a interpretar las
características de la unión a HLA-B27 observadas experimentalmente (Rognan et al., 1994).
IV.1.3.1. Propiedades dinámicas vs afinidad de unión de péptidos.
Mediante la determinación de las variaciones en las distancias entre el péptido y un centro

de masas teórico de la molécula de HLA-B27, puede obtenerse una medida indirecta de la
-41- RESULTADOS
movilidad del péptido y, por tanto, de su estabilidad. Definiendo una serie de distancias: d1:
Distancia proteína-péptido; d2: proteína-(P1, P2, P3), d3: proteína-(P4, P5, P6, P7 y P8); d4:
Distancia entre la subcavidad A y el residuo P1, d5: Distancia subcavidad B-residuo P2; d6:
Distancia subcavidad D-residuo P3 y d7: Distancia subcavidad F-residuo P9, la modelización
permite determinar lo que sucede en la interacción de los diferentes péptidos a ambos subtipos.
Cuantitativamente, la parte central del péptido expuesta al TCR (residuos P4-P8) sufrió un
incremento de las distancias, similar en los tres péptidos unidos a ambos subtipos (Anexo 3,
Tabla 2: d3). El análisis de las distancias d4-d7 entre los anclajes y sus subcavidades
complementarias A, B, D y F mostró que el péptido (3), tanto unido a B*2703 como a B*2705
experimentaba una repulsión localizada en el residuo P9 (d7), muy alejada del lugar de la
mutación en la subcavidad A, así como una mayor distancia d5 para el complejo RQYQKSTEL-
B*2703. La distancia d4, era dependiente del residuo presente en P1, aunque para un mismo P1
siempre fue mayor en el subtipo B*2703. Por último, las distancias d6 fueron más variables
demostrando la flexibilidad de ésta (Anexo 3, Tabla2).
Estos datos indican que la mutación Tyr→His59 desestabiliza la subcavidad A, de modo
que en estas circunstancias, un mal anclaje en P2 causa una inestabilidad global del péptido en
varias posiciones, y de forma especial en su extremo C-terminal.
IV.1.3.2. Fluctuaciones atómicas, áreas accesibles y no accesibles.
Como era de esperar, la parte central del péptido expuesta al TCR mostró mayores
fluctuaciones que las posiciones de anclaje del péptido. En concordancia con los valores de
afinidad de unión in vitro, la comparación de las movilidades atómicas de los péptidos (1) y (2)
unidos a ambos subtipos no mostró diferencias significativas, pero la flexibilidad del péptido (3)
se incrementó, especialmente en el complejo de menor afinidad RQYQKSTEL-B*2703 (Anexo 3:
Figura 3). La magnitud de las fluctuaciones en el residuo P9, indican que cuando el anclaje en
P2 es débil, la inestabilidad se distribuye a otras posiciones de anclaje incluída, de forma
prominente, la posición C-terminal.
En consonancia con el resultado anterior, el análisis de las áreas accesibles frente a las no
accesibles, nuevamente mostró que la mayor accesibilidad de P9, se daba en el complejo
RQYQKSTEL-B*2703 (Anexo 3: Figura 4). Sin embargo, a pesar de la flexibilidad que mostró la
Gln2 (Anexo 3: Figura 3), este residuo permaneció inaccesible sugiriendo que, aunque la Gln2
no es por si misma un buen residuo de anclaje, aún conserva interacciones en la subcavidad B.
RESULTADOS -42-
IV.1.3.3. Análisis cualitativo y cuantitativo de los puentes de hidrógeno
La estabilidad de los puentes de hidrógeno establecidos entre HLA-B27 y el péptido, se

determinó mediante el cálculo de la frecuencia de formación de dichos enlaces. Se consideró
como un puente de hidrógeno fuerte aquél con una frecuencia mayor del 50%, medio cuando la
frecuencia estaba entre el 25% y el 50%, y débil si era inferior al 25%. Con estas premisas, el
número, distribución y frecuencia de los puentes de hidrógeno permitió distinguir cualitativa y
cuantitativamente, los péptidos (1) RRYQKSTEL, (2) ARYQKSTEL y (3) RQYQKSTEL (Anexo 3:
Figura 5). La modelización predijo un número de 25 enlaces para los péptidos (1) y (2) unidos a
ambos subtipos, y de la mitad cuando el péptido unido era (3). Asimismo, la distribución de los
enlaces débiles y fuertes se correspondió con las afinidades de unión in vitro, de forma que los
complejos formados por los péptidos (1) y (2) mostraron un número similar de enlaces fuertes en
ambos subtipos frente al reducido número de enlaces medios o fuertes encontrados para el
péptido (3). Estos resultados indican que la afinidad de unión de un péptido está directamente
relacionada con la cantidad y calidad de los enlaces de hidrógeno que establece el péptido con
diferentes residuos de la molécula de clase I.
-43- RESULTADOS
IV.2. RELACIÓN ENTRE LA UNIÓN DE PÉPTIDOS Y LA SELECCIÓN DE EPÍTOPOS

VIRALES POR CÉLULAS T. (Anexo 4)
El polimorfismo de las moléculas de clase I tiene una función clave en el reconocimiento

por las células T de los complejos MHC-Péptido, puesto que determina la presentación o no de
un péptido antigénico, modula su afinidad y estabilidad de unión, y puede alterar la
conformación final del epítopo reconocible por el TCR. En este estudio se trató de determinar el
papel que juega el polimorfismo de HLA-B27, en la presentación y en el reconocimiento por
células T de péptidos derivados del virus de Epstein-Barr (EBV), que son inmunogénicos sólo en
el contexto de determinados subtipos de HLA-B27.
IV.2.1. Unión de péptidos virales a diferentes subtipos de HLA-B27, y su relación con la

inmunogenicidad.
Se estudió la unión de tres péptidos derivados del EBV, restringidos por diferentes
subtipos de HLA-B27. EBNA3C (258-266) (Brooks et al., 1993) es restringido por los subtipos
B*2705 / B*2702 / B*2704; LMP2 (236-244) es restringido por B*2704 (Brooks et al., 1993) y
EBNA3B (243-253) es restringido por B*2702 (Brooks et al., 1998) (Tabla 7). Aunque todos se
unieron a los tres subtipos, EBNA3B se unió mejor a B*2705 que a B*2702, y LMP2 se unió con
igual afinidad a B*2705 y B*2704. Por tanto, no existe una correlación entre la eficiencia de
unión in vitro de un péptido viral a un subtipo de HLA-B27, y su inmunogenicidad en el
contexto de dicho subtipo. La unión relativa tampoco se correspondió con sus patrones de
restricción; así en el caso de LMP2 la unión a B*2702 fue 30 veces mejor que la unión de
EBNA3B y 7,5 veces mejor que la unión de EBNA3C a B*2705 (Tabla 7). Estos resultados
indican que la unión y la inmunogenicidad de un péptido, están determinadas por factores
distintos al de su afinidad por el subtipo HLA que actúa como elemento de restricción.
Los valores entre Péptido Restricción Secuencia B*2705 B*2702 B*2704

paréntesis corresponden al
C50 µM del péptido que
mejor unión presentaba LMP2 B*2704 RRRWRRLTV 1 (0,4 µM) 1 (1 µM) 1 (0,4 µM)
(LMP2). El resto de EBNA3C B*2705 / 02 / 04 RRIYDLIEL 7,5 3 12,5
valores corresponde al EBNA3B B*2702 RRARSLSAERY 15 30 50
exceso molar necesario de
péptido al necesario para
alcanzar el valor de C50 . Tabla 7: Unión de péptidos de EBV a tres subtipos de HLA-B27 que actúan como
elementos de restricción.
RESULTADOS -44-
La unión de los tres péptidos virales a otros subtipos de HLA-B27 (B*2705, B*2703 y
B*2706) fue buena en general (Anexo 4, Tabla 3), lo que indica que el polimorfismo entre los
subtipos B*2701-B*2706, no afecta críticamente a la unión de los péptidos estudiados. Sin
embargo, para LMP2 las diferencias de afinidad por diferentes subtipos se hicieron más patentes
mediante el uso de análogos con Ala2 (Anexo 4, Tabla4). La unión relativa de LMP2A2 fue más
baja para B*2705 / 03 / 01 que para su elemento de restricción (B*2704) y para B*2706 y
B*2702. Este resultado confirma que la inmunogenicidad de LMP2, exclusivamente en B*2704
no está relacionada con su mayor afinidad por este subtipo.
IV.2.2. Reconocimiento de péptidos de EBV por CTLs restringidos por HLA-B27.
En estos experimentos se analizó la capacidad de CTLs específicos de péptido, y

restringidos por un subtipo determinado, para reconocer dicho péptido en el contexto de otros
subtipos. La capacidad de los tres péptidos de EBV, para ser reconocidos por diferentes CTLs
restringidos por B*2705, B*2704 y B*2702 se resume en la Tabla 8.
De 10 clones restringidos por B*2705 específicos de EBNA3C, tres reconocieron al péptido
también en el contexto de B*2702. De igual forma, cuatro de los cinco clones restringidos por
B*2702 contra el mismo péptido lo reconocieron en el contexto de B*2705, pero ninguno de los
quince lo reconocieron unido a B*2704. Los clones restringidos por B*2702 específicos de
EBNA3B, también reconocían al péptido, unido tanto a B*2702 como a B*2705 pero no a
B*2704. De los cuatro clones restringidos por B*2704 específicos de LMP2, ninguno reconoció
al péptido unido ni a B*2705 ni a B*2702. Estos resultados muestran que B*2705 y B*2702,
pueden actuar como elementos de restricción equivalentes, al menos para algunos CTLs. Sin
embargo, B*2704 muestra un grado mucho mayor grado de disparidad funcional.
IV.2.3. El motivo Arg2, anclaje principal de los péptidos unidos a HLA-B27, no es esencial
para mantener la capacidad antigénica del péptido.
En estos experimentos se analizó el papel del residuo principal de anclaje de los péptidos
en HLA-B27, en mantener la capacidad antigénica del epítopo viral.
El análisis realizado con el péptido EBNA3C y sus análogos con Gln2 y Ala2 mostró
diferencias en la afinidad de unión a los subtipos que actuan como elementos de restricción para
este péptido, en función del residuo presente en P2 y del subtipo (Figura 7A). No obstante, los
CTLs restringidos por B*2705 reconocieron tanto al péptido como a sus análogos. Los CTLs
-45- RESULTADOS
restringidos por B*2702 reconocieron al análogo con Ala2 mucho peor.

El mismo análisis realizado con los análogos del péptido EBNA3B y sus análogos en P2
mostró una unión similar del análogo con Gln2 a B*2702, sin embargo el análogo con Ala2
aunque se unió bastante peor, fue reconocido con igual eficacia por los CTLs restringidos por
B*2702 específicos de EBNA3B. (Figura 7B).
Estos resultados mostraron que el residuo de anclaje principal Arg2 es un requisito
fundamental para obtener una buena unión los péptidos a HLA-B27, pero no es esencial para
mantener la estructura antigénica del péptido.
RESULTADOS -46-
Tabla 8: Clon Donante Célula Diana Nº clones
Reconocimiento por CTLs restringidos B*2705 B*2702 B*2704

por HLA-B27 de péptidos derivados de
EBNA3C
EBV.
RTc10 B*2705 65 3 2 7
Los valores indican el % de lisis RTc37 B*2705 51 60 1 3
específica a una relación Efector:Diana Total 10
de 4:1. Las células diana se incubaron EBNA3C
durante 30 minutos con una LYc39 B*2702 9 55 0 1
concentración de péptido 10-6M. En Kor c69 B*2702 44 53 0 4
todos los casos el fondo fue inferior al Total 5
5%. En la columna derecha aparece el EBNA3B
número de clones que tenían el mismo
LYc40 B*2702 72 76 0
patrón de reactividad. En negrita y
NWc20 B*2702 50 64 0 Total 4
para mayor claridad, se marcan los
casos en los que la reactividad es LMP2
claramente positiva. DHc21 B*2704 0 3 35 4
Total 4
Figura 7:
PÉPTIDO SECUENCIA B*2702 B*2705 B*2704
Unión y reconocimiento de dos A
EBNA3C RRIYDLIEL 3 3 5
péptidos virales y sus análogos en P2
EBNA3CA2 -A------- − − −
por CTLs específicos de péptido.
EBNA3CQ2 -Q------- 20 100 −
A/ Arriba; unión del péptido EBNA3C
y sus análogos, a los tres subtipos que 80 100
EBNA 3C
actúan como sus elementos de EBNA 3CA2 LY c25 AL c12
EBNA 3CQ2 80
restricción. Debajo, a la izquierda,
% de lisis específica
60 SIN PÉPTIDO
lísis de una línea celular 60

linfoblastoide autóloga, por un CTL 40
40
específico del péptido, provenientes de
un donante B*2702+(LYc25), y 20
20
sensibilizada a varias concentraciones
0 0
con los péptidos anteriores. Relación -11 -10 -9 -8 -7 -6 -5 -11 -10 -9 -8 -7 -6 -5
10 10 10 10 10 10 10 10 10 10 10 10 10 10
Efector : Diana=4:1. A la derecha un
experimento similar en el que diana y Concentración de péptido (M)
efector (Alc12) eran de un individuo B
50 PÉPTIDO SECUENCIA B*2702
B*2705.+ Relación E:D=2:1. EBNA 3B
EBNA 3BA2 LY c29
40 EBNA 3BQ2 EBNA3B RRARSLSAERY 20
% de lisis específica
SIN PÉPTIDO
EBNA3BA2 -A--------- 100
B/ Unión del péptido EBNA3B y sus 30
EBNA3BQ2 -Q--------- 20
análogos al subtipo que actúa como
20
su elemento de restricción, (B*2702).
A la izquierda, se muestra la lisis de 10
una línea celular linfoblastoide
0
autóloga por el clon restringido y
-11 -10 -9 -8 -7 -6 -5
específico de péptido LYc29. Relación 10 10 10 10 10 10 10
E:D = 4:1. Concentración de péptido (M)
-47- RESULTADOS
IV.3. MODULACIÓN DE LA ESPECIFICIDAD EN LAS POSICIONES DE ANCLAJE P1, P3 Y

PΩ, POR EL POLIMORFISMO DE HLA-B27. (Anexo 5)
IV.3.1. Especificidad de B*2705, B*2704 y B*2706 por los residuos en P1, P3 y P9.
Para determinar la contribución de las posiciones de anclaje secundario P1 y P3 y del

anclaje primario P9, a la unión de péptidos a HLA-B27, se utilizaron tres series de nonámeros de
poli-Alanina en los que conservando el anclaje principal Arg2, cada una de las tres posiciones
fue sustituida por diferentes aminoácidos. La unión de cada análogo (EC50), se cuantificó con
base a la unión del péptido control RRYQKSTEL, un ligando natural de B*2705, B*2704 y
B*2706. La contribución relativa de cada residuo, se calculó como la unión relativa del análogo
correspondiente respecto al péptido ARAAAAAAA (ARA7) (Figs. 8A, 8B y 8C). Este péptido, se
unió con más afinidad a B*2704 y B*2706 (10 y 9 µM respectivamente) que a B*2705 (30 µM)
lo que significa que el esqueleto de poli-Alanina interacciona más fuertemente en los dos
primeros.
Residuo P1:
El residuo mas favorecido en B*2705 fue R (EC50 de RRA7= 9 µM), cuya contribución al
anclaje respecto a Ala1 fue aproximadamente 3. K, H, G, I, M y los residuos aromáticos fueron
aproximadamente equivalentes a Ala y los residuos ácidos, polares, y L y V redujeron
claramente la afinidad.
En general, la especificidad de B*2704 por residuos en P1 fue similar a B*2705 en lo
referente al efecto negativo de los residuos ácidos, polares y alifáticos. Una diferencia fue la
mayor preferencia de este subtipo por G (EC50 de GRA7= 6 µM) que por R.
B*2706 se diferenció claramente de B*2704, en que sólo D estaba muy desfavorecido. La
contribución a la unión de los residuos básicos R, K, H, los polares, Q, G y Y fue mayor en
B*2706 que en los otros dos subtipos. Estos resultados indican que B*2705, B*2704 y B*2706 a
pesar de tener una misma subcavidad A, muestran diferencias en sus preferencias por el residuo
P1.
Residuo P3:
Los residuos en esta posición mostraron un amplio rango de afinidades de unión a B*2705.
El más favorecido fue W (EC50 =5µM), y en general se apreció una preferencia por los residuos
apolares. H, N, y Y fueron equivalentes a Ala y los residuos ácidos, T, Q, G y P estaban
desfavorecidos.
RESULTADOS -48-
B*2704 se asemejó a B*2705 en general. Las principales diferencias con B*2705 fueron
que Ala no era peor que otros residuos alifáticos de mayor tamaño y que N era peor que Ala en
B*2704, pero no en B*2705.
La especificidad de B*2706 por los residuos en P3 mostró importantes diferencias con
B*2704. Así, H, R, y los residuos polares estaban especialmente favorecidos respecto a Ala en
B*2706, y G, P y los residuos ácidos estaban menos desfavorecidos. Además, los residuos
apolares alifáticos y los aromáticos eran más adecuados que Ala, pero Y estaba menos
favorecida que muchos otros residuos, entre los que se incluían los aromáticos. Ala por si misma
estaba entre los mejores residuos de B*2704, pero era peor que muchos otros en B*2706.
Estos resultados indican que B*2704 y B*2706 difieren entre si, y también de B*2705, en las
preferencias por el residuo P3.
Residuo P9:
El número de aminoácidos que se estudió en esta posición se limitó a los residuos básicos
y apolares, por ser este el tipo de residuos C-terminales mayoritariamente presentado por
B*2705. Adicionalmente se incluyó Pro, un residuo C-terminal presente entre los péptidos de
HLA-B73, que muestra la misma preferencia que HLA-B27 por Arg2.
Como era esperado, tanto los residuos básicos como los apolares se unieron en general
bien a B*2705, pero no de forma equivalente. Entre los residuos aromáticos Y estaba favorecido,
pero no F ni W. Asimismo, P estaba desfavorecida.
En B*2704, F, W y P también estaban desfavorecidos, además de los residuos básicos y Y.
Por último, en B*2706, y al igual que en B*2704, ni los residuos básicos, ni Y, W o P eran
adecuados, pero B*2706 mostró una mayor preferencia que B*2704 por los residuos alifáticos y
F. Estos resultados indican que una de las principales diferencias entre la especificidad de
B*2704 y B*2706 por los residuos C-terminales, radica en la mejor aceptación de F por B*2706.
IV.3.2. La unión de un péptido es el resultado de la contribución aditiva de varios residuos de

anclaje.
Para determinar si la afinidad de unión de un péptido es simplemente la suma de las

contribuciones individuales de cada uno de los residuos de anclaje, o está influida por efectos
cooperativos más complejos, se analizó la unión de dos ligandos naturales RRYQKSTEL y
KRYKSIVKY y de distintos análogos de poli-Alanina en los que se conservaron una o varias de
las posiciones P1, P3, P7 y P9. Para calcular el EC50 de todos los análogos se utilizó como
-49- RESULTADOS
referencia el péptido RRYQKSTEL

Primeramente, se midió en qué medida la introducción de esas posiciones de anclaje
incrementaba o hacía decrecer la unión respecto a ARA7. Después se calculó la relación entre la
unión relativa de cada ligando, o análogo portador de multiples posiciones de anclaje del ligando
natural, y la suma de las uniones relativas de cada análogo de poli-Alanina, con uno sólo de los
residuos de anclaje. Si la contribución de los residuos individuales es aditiva, esta relación debe
ser 1. Si existen efectos interactivos entre los residuos de anclaje, esta relación se desviará de
forma significativa de ese valor. Para tener en cuenta el error experimental, los valores de esa
relación entre 1,5 (1,5:1) y 0,67 (1:1,5) se consideró que implicaban contribución aditiva.
Como se aprecia en la (Figura 8D_a), el EC50 de la mayor parte de los péptidos portadores
de varios anclajes del péptido RRYQKSTEL, (P1, P3, P7, P9) es resultado, en cuatro de cinco
casos, del valor aditivo de sus correspondientes análogos portadores de un simple residuo. De
manera similar el EC50 de los análogos con múltiples posiciones de anclaje del péptido
KRYKSIVKY es, en cuatro de cinco casos, el resultado de la contribución de los análogos con
uno o pocos residuos de anclaje (Figura 8D_b), con un único caso (KRAAAAAAY, relación 0,6)
que mostró una ligera desviación del rango 0,67-1,5.
Estos resultados indican que en general, la eficiencia de unión de un péptido es
simplemente una función aditiva de la contribución de los anclajes individuales; no obstante los
efectos interactivos mútuos de las cadenas laterales pueden en ocasiones afectar a la unión.
El papel que juegan las posiciones P4, P5, P6 y P8, se determinó a partir de la relacion
EC50(ligando natural)/EC50(análogoP1-P2-P3-P4-P9) que mostró unos valores de 10/15=0,67 y
7,5/4,3=1,7 para RRYQKSTEL y KRYKSIVKY respectivamente. Este resultado muestra que su
contribución a la unión es variable y dependiente del péptido.
RESULTADOS -50-
Leyendas para las figuras 8A,8B,8C y 8D. (Ver página siguiente).
Figuras 8A, 8B y 8C. Figura 8D.
Unión relativa de diferentes análogos de poli- Relación entre la unión de los péptidos (a)
Alanina a B*2705, B*2704 y B*2706.: RRYQKSTEL y (b) KRYKSIVKY. con distintos
análogos en las posiciones de anclaje:
Cada análogo aparece representado en el eje de Las barras negras indican la unión relativa
abscisas por el código de una letra del residuo respecto al análogo ARA7, expresada como la
introducido en la secuencia del péptido ARA7 en relación molar entre el EC50 de ARA7 y el de cada
posición P1, P3 o P9. El péptido de referencia péptido (abscisas). En los residuos cuyo efecto fue
RRYQKSTEL (EC50: 8A=3 µM; 8B=4 µM; detrimental respecto a Ala (T7, K1), el descenso
8C=0,3 µM ) está marcado con un asterisco (*). de la unión relativa se expresó como: 1-unión
La unión relativa de cada análogo (eje de relativa. Las barras blancas indican el valor
ordenadas, en escala logarítmica) indica la aditivo de las uniones relativas de los análogos de
relación entre el EC50 de ARA7 (8A=30 µM; poli-Ala portadoras de sustituciones sencillas en
8B=10 µM; 8C=9 µM) y el del análogo P1, P3, P7 o P9. El efecto de V7 no se analizó de
correspondiente. Debido a que la concentración forma separada; en su lugar se utilizó el análogo
máxima que se utilizó de péptido fue 100 µM, la ARAAAAVAY. Teniendo en cuenta el error
unión relativa menor que 0.3, que indica carencia experimental en la determinación de los valores de
de unión en este ensayo (EC50>100 µM), no EC50, los valores representados por las barras
puede medirse. En la gráfica se le asignó un valor negras y blancas se consideraron iguales, cuando
de 0,25 por motivos de representación. su relación se encontraba entre 0.67 (1:1.5) y 1.5
(1.5:1). Los valores que excedieron esos margenes
aparecen marcados con un asterísco (*).
-51- RESULTADOS
B*2705 A B*2704 B
10 10
P1
1 1
0,1 0,1
K H R D E S T N Q G A V I L M F Y W * K H R D E S T N Q G A V I L M F Y W *
10 10
P3
1 1
0,1 0,1
H R D E S T N Q G A V I L M F Y W P * H R D E S T N Q G A V I L M F Y W P *
10 10
P9
1 1
0,1 0,1
K R A V I L M F Y W P * K R A V I L M F Y W P *
B*2706 C D
100
RRYQKSTEL
10
P1 RRAAAAAAA
ARYAAAAAA a
ARAAAATAA
ARAAAAAAL
1 0 2 4 6 8 10 12 14 16
ARYAAATAA
0,1
*
ARYAAAAAL
K H R D E S T N Q G A V I L M F Y W *
100 ARAAAATAL
ARYAAATAL
P3
10 RRYAAATAL
1 KRYKSIVKY
KRAAAAAAA
ARYAAAAAA b
0,1 ARAAAAAAY
H R D E S T N Q G A V I L M F Y W P ARAAAAVAY
*
100 0 2 4 6 8 10 12 14 16
KRYAAAAAA
P9
10 KRAAAAAAY
*
ARYAAAAAY
1 ARYAAAVAY
KRYAAAVAY
0,1
K R A V I L M F Y W P *
RESULTADOS -52-
IV.3.3. Distribución de los residuos P1, P3 y PΩ entre los ligandos naturales de B*2705.
Conocida la contribución al anclaje de cada residuo, se procedió al estudio comparativo de

su distribución entre 54 ligandos naturales de B*2705 (Tabla 10), con el propósito de determinar
las reglas que rigen el uso de residuos en las posiciones de anclaje, por el repertorio peptídico
natural de este subtipo. En función de la eficacia de unión de cada uno de los residuos, respecto
al péptido de referencia ARA7, se establecieron cinco niveles, siendo el nivel 1 el de los residuos
más favorecidos. (Tabla 9).
Rango Nivel P1 P3 PΩ
<10 µΜ 1
44% ( 24/54 ) 85% ( 45/53 )
86% ( 44/51 )
11-20 µΜ 2 -
21-40 µΜ 3 (ARA7)
14% ( 7/51 )
41-80 µΜ 4
48% ( 26/54 )
15% ( 8/53 )
>80 µΜ 5 -
Tabla 9: Distribución porcentual de los residuos P1, P3 y P9 entre los ligandos naturales de B*2705.
Los resultados indican que las posiciones P3 y P9, utilizan residuos favorables (niveles 1 y
2) en el 85% de los casos, pero pueden acomodar también residuos desfavorables. La posición
P1, es más permisiva y acomoda residuos desfavorables (niveles 4 y 5) en el 48% de los casos.
Adicionalmente se siguen las siguientes normas de uso:
Entre los, nonámeros y decámeros con PΩ subóptimo (niveles 3 a 5) (cinco nonámeros y
dos decámeros) todos tienen un anclaje óptimo en P3 (nivel 1), independientemente del residuo
presente en P1. De igual modo, todos los péptidos de estos tamaños, con un anclaje subóptimo
en P3 (cinco nonámeros y tres decámeros) tienen un PΩ bueno (nivel 1), independientemente del
residuo presente en P1. Este resultado indica que la presencia de un anclaje subóptimo en P3 o
en P9, siempre se compensa con un buen anclaje en la otra posicion. Dieciocho de los 30
péptidos con un mal residuo de anclaje en P1 (niveles de 3 o >3), tienen tanto en P3 como en P9
un buen residuo de anclaje (niveles 1 y 2) y todos, como mínimo, un buen anclaje al menos en
una de estas dos posiciones. Siete de los péptidos, que muestran un mal anclaje en P1 y P3 o P1
y P9 tienen en el residuo restante uno de nivel 1. Por lo tanto, un mal residuo de anclaje en P1
requiere un residuo óptimo al menos en una de las otras dos posiciones.
Entre los péptidos de tamaño no-canónico (octámeros, undecámeros y dodecámeros), las

-53- RESULTADOS
tres posiciones estudiadas mostraron buenos anclajes (niveles 1 y 2), lo que sugiere que este tipo
de ligandos, es más restrictivo en el tipo de residuo que puede ocupar sus posiciones P1, P3 y
PΩ, aunque el número de ligandos conocidos de estos tamaños es aún limitado.
Estas reglas, estudiadas en B*2705 tambien se cumplen con los escasos ligandos conocidos de
B*2704 y B*2706 (Anexo 5, Tabla 2).
RESULTADOS -54-
Valoración Valoración del

Secuencia Referencia. Secuencia Referencia.
del residuo residuo
Octámeros Decámeros
RRFFPYYV 1-1----1 [1] KRFEETGQEL 4-1------1 -Este estudio-

RRFTRPEH 1-1----X [2] NRFAGFGIGL 5-1------1 -Este estudio-
RRQDILDLWI 1-5------1 HIV (*)
Nonámeros GRFNGQFKTY 4-1------1 [7]
RRYDRKQSGY 1-2------1 [6]
ARLQTALLV 3-1-----1 -Este estudiob GRWPGSSLYY 4-1------1 [6]
RRYQKSTEL 1-2-----1 [2] GRKTGQAPGY 4-X------1 [6]
SRTPYHVNL 4-4-----1 -Este estudio- GRILSGVVTK 4-2------1 [6]
RRLPIFSRL 1-1-----1 [3] RKGGNNKLIK 1-5------1 [6]
GRHGVFLEL 4-2-----1 -Este estudio- LRDNIQGITK 5-5------1 -Este estudio-
RRIYDLIEL 1-2-----1 [4] (*) KRWIILGLNK 4-1------1 HIVd (*)
RRYPDAVYL 1-2-----1 [5] (*) RRFVNVVPTF 1-1------4 -Este estudio-
GRFGSGMNM 4-1-----1 [6] KRWQAIYKQF 4-1------4 [6]
GRTFIQPNM 4-4-----1 [6] RRIKEIVKKH 1-2------X [3]
LRFQSSAVM 5-1-----1 [6]
RRSKEITVR 1-3-----1 [2] Undecámeros
FRYNGLIHR 3-2-----1 [2]
KRFEGLTQR 4-1-----1 [2] RRYLENGKETL 1-2-------1 [7]
HRAQVIYTR 3-3-----1 [6] RRMGPPVGGHR 1-1-------1 [3]
SRYWAIRTR 4-2-----1 [2] (*) WRLGSSDILNY 2-1-------1 -Este estudio-
RRFMPYYVY 1-1-----1 [3]
SRVKLILEY 4-2-----1 -Este estudio- Dodecámeros
RRFFPYYVY 1-1-----1 [1, 7]
RRVLVQVSY 1-2-----1 [6] RRFVNVVPTFGK 1-1--------1 [6]
RRISGVDRY 1-2-----1 [2, 3]c
RRIKEIVKK 1-2-----1 [2] (b)
RRVKEVVKK 1-2-----1 [2] Descrito previamente como octámero (ARLQTALL) por
secuenciación de Edman [Rötzschke et al., 1994]. También
ARLFGIRAK 3-1-----1 [2,3]
encontrado como nonámero en B*2709 (ARLQTALLV)
GRIDKPILK 4-2-----1 [2] [Fiorillo et al., 1997].
GRFEGTSTK 4-1-----1 [6]
(c)
GRAFVTIGK 4-3-----1 HIV (*) Descrito también como nonámero en B*2701 [García et
IRLRPGGKK 4-1-----1 HIV (*) al., 1997c] y como decámero (RRISGVDRYY) en B*2703
RRWLPAGDA 1-1-----3 [2] [Boisgérault et al., 1996 ] y B*2710 [García et al., 1998].
GRLTKHTKF 4-1-----4 [3, 7] (d)
Existe también una variante natural de este péptido con el
KRFKEANNF 4-1-----4 -Este estudio-
cambio L6M.
RRFGDKLNF 1-1-----4 [3]
[1] Paradela et al., 1998. [2] Jardetzky et al., 1991. [3]
KRFSFKKSF 4-1-----4 [3]
Rötzschke et al., 1994. [4] Brooks et al., 1993. [5] van
TRYPILAGH 5-2-----X [3]
Binnendijk et al., 1993. [6] Fiorillo et al., 1997. [7]
KRVVINKDT 4-2-----X [8] (*) Boisgérault et al., 1996. [8] Ugrinovic et al., 1997.
a
Tabla 10: Ligandos naturales de B*2705 y valoración de los residuos P1, P3 y PΩ.
(a)
Los péptidos marcados con un asterisco son de origen bacteriano o viral (*). El resto pertenecen a
proteínas endógenas celulares. En negrita se indican los valores asignados a cada residuo. X:
valoración no analizada. Los péptidos derivados del HIV se obtyuvieron del HIV Molecular Immunology
Database of Los Angeles National Laboratory. (http://hiv-web.lanl.gov/).
-55- RESULTADOS
IV.4. UNIÓN DE ANÁLOGOS NO PEPTÍDICOS A HLA-B27. (Anexo 7)
Como una primera aproximación al posible uso de ligandos no-peptídicos como

antagonistas en la respuesta inmune mediada por CTLs, en este estudio se analizaron las
propiedades de unión de varios de estos
ligandos a HLA-B27. Para ello se alteró la H2N OH
Aua: 11-Amino undecanoico.
región central, que comprende los residuos P4-
P8, en varios ligandos naturales de B*2705 O O O
(Tabla 11). Se pretendía con ello, conservar O O O

HB3
las propiedades de unión del péptido natural a
O O O O
la molécula de clase I, y simultaneamente
O O O O
alterar su región central, reconocida por el
HB4
TCR.
Figura 9: Estructura química de los tres espaciadores
En los análogos no peptídicos utilizados, no peptídicos utilizados en los análogos. Aua: ácido
la parte central fue sustituida por espaciadores 11-amino undecanoico. HB: (R)-3-Hidroxibutirato.
no peptídicos de diferente naturaleza química

y longitud (Figura 9). El diseño de estos ligandos se realizó por técnicas de simulación de
dinámica molecular, y su unión a HLA-B27 se analizó mediante un ensayo de estabilización de
péptidos in vitro. Asimismo, la eficiencia de unión a B*2705, medida por este ensayo, se
compararó con el parámetro de desnaturalización térmica (Tm) obtenido mediante dicroísmo
circular.
IV.4.1. Reemplazamiento de la parte central de epítopos naturales con un espaciador

monofuncional.
El ácido 11-amino undecanoico (Aua) es un espaciador monofuncional, que únicamente

enlaza los residuos P3 y P9, pero no establece interacciónes con la molécula de clase I por
carecer de cadenas laterales. En los cuatro análogos analizados con este espaciador, se apreció
una pérdida general de afinidad respecto al péptido natural, tanto en el ensayo de unión in vitro
como en su estabilidad térmica. Sin embargo las diferencias observadas por este último criterio
fueron más acusadas (Tabla 11).
La unión de los análogos de -Aua- a B*2704, fue muy ineficiente cuando el residuo P9 era
básico, pero apenas se alteró cuando dicho residuo era apolar. Este resultado indica la
importancia de un buen anclaje en P9 para la unión del análogo con este tipo de espaciador, y el
RESULTADOS -56-
papel decisivo de las interacciones secundarias entre el péptido y B*2704, cuando P9 es un mal
anclaje para este subtipo.
IV.4.2. Reemplazamiento de la parte central de epítopos naturales con espaciadores

bifuncionales.
En base a los resultados anteriores, se ensayaron dos tipos de espaciadores bifuncionales

formados por oligómeros de (R)-3-hidroxibutirato (HB), uno trimérico -HB3- y otro tetramérico
-HB4. Estos espaciadores, además de enlazar P3 y P9 forman polímeros químicamente estables, y
pueden adoptar plegamientos conformacionalmente similares a los de los péptidos en estado
libre (Plattner et al., 1993). Adicionalmente, poseen grupos metilo capaces de interaccionar en
las subcavidades del sitio de unión del péptido. Con estos espaciadores se construyeron los
correspondientes análogos del ligando de HLA-B27 QRLKEAAEK, y una variante con Ala1,
ARLKEAAEK, con objeto de paliar posibles problemas en el ensayo de unión derivados de la
eventual ciclación de la Gln N-terminal.
Ambos análogos mostraron eficiencias de unión in vitro muy diferentes (Tabla 11). El
análogo (12) con -HB4- se unió 15 veces mejor que el (11) con -HB3-. La presencia del
espaciador -HB4- siempre mejoró la unión respecto al péptido natural (7). Sin embargo, los
valores de Tm que mostraron los análogos estudiados fueron similares (Péptidos 11 y 12, Tabla
11). Estos resultados indican que la introducción de grupos -HB4- en la parte central del
espaciador, mejora la unión a B*2705 considerablemente, pero no afecta de forma significativa a
su estabilidad térmica.
IV.4.3. Modelado molecular de la unión de análogos con espaciadores no peptídicos a

B*2705.
Mediante la modelización, se predicen diferencias claras entre el péptido natural

QRLKEAAEK y los análogos con espaciador no peptídico (Anexo 7, Figuras 2 y 5). En primer
lugar, el número de contactos establecidos por el análogo con -Aua- era menor, lo que explica la
menor afinidad de los análogos con este espaciador respecto al péptido natural. La menor
longitud del análogo con -HB3- impide la interaccion óptima con las subcavidades A y F, lo que
no sucede con el análogo con -HB4- cuya mayor longitud le permitía incrementar el número de
interacciones en ambos extremos, que son suplementadas por los contactos adicionales de los
grupos metilo. Por tanto, la modelización teórica de las interacciones con HLA-B27 confirmó, al
-57- RESULTADOS
menos cualitativamente, las diferencias experimentales y proporcionó una posible interpretación

molecular de estos resultados.
Secuencia EC50 (a)

Péptido Tm (ºC)(b)
P1-P2-P3 -Espaciador- P9 B*2705 B*2704
1(c) RRR WRRLT V 1,2 0,8 52,8 ± 0,7

2 RRR -Aua- V 4 1 42,9 ± 0,3
3(d) SRY WAIRT R 3 1,4 46,3 ± 0,5
4 SRY -Aua- R 8,6 100 39,5 ± 0,2
5(e) GRA FVTIG K 1,8 6,4 61,9 ± 0,3
6 GRA -Aua- K 7 >100 48,1 ± 0,4
7(f) QRL KEAAE K 10 62,8 ± 0,7
8 QRL -Aua- K 46,5 ± 0,2
9 QRL -HB3- K 40
10 QRL -HB4- K 2,5
11 ARL -HB3- K 20 63,2 ± 0,6
12 ARL -HB4- K 1,6 62,1 ± 0,7
Tabla 11: Valores de EC50 y Tm de los péptidos naturales y sus análogos no peptídicos.
(a) EC50: Concentración de ligando a la (c) Proteína latente de membrana del

cuál la fluorescencia de HLA-B27 en las EBV (236-244), (Brooks et al., 1993).
células RMA-S, es la mitad de la
fluorescencia máxima obtenida con el (d) Nucleoproteína del virus Influenza A
péptido natural. (383-391), (Huet et al., 1990).
(b) Tm: Punto medio del valor térmico de (e) Glicoproteína 120 del virus del SIDA
desnaturalización del heterodímero (314-322), (Jardetzky et al., 1991).
formado por la cadena pesada de
B*2705, la β2m y el ligando. (f) Proteína DnaK de E. coli (260-268),
(Rognan et al., 1995).
-59-
V. DISCUSIÓN
DISCUSIÓN -61-
V. DISCUSIÓN
V.1. POLIMORFISMO DE HLA-B27 Y SOLAPAMIENTO DE REPERTORIOS PEPTÍDICOS

ENTRE SUBTIPOS.
V.1.1. Influencia del polimorfismo de HLA-B27 sobre la especificidad por el residuo C-

terminal del péptido. Diferencias entre B*2704 y B*2706.
L
a teoría del péptido artritogénico implica que los subtipos asociados a enfermedad,
deben de ser capaces de presentar un mismo péptido unido selectivamente a los
subtipos asociados a enfermedad. Por esta razón, es particularmente importante
conocer el grado de solapamiento de los repertorios peptídicos unidos a los diferentes subtipos
de HLA-B27, y las diferencias entre los repertorios de los subtipos asociados diferencialmente a
enfermedad. Contrariamente a lo que ocurre en la subcavidad B, cuya estructura es común entre
los subtipos de HLA-B27 y está optimizada para unir péptidos con Arg2, la mayor parte del
polimorfismo de esta molécula se concentra en las subcavidades C y F, lo que se traduce en
distintas especificidades por el residuo C-terminal.
B*2705 une péptidos con residuos C-terminales básicos, alifáticos o aromáticos. Muchos
de los péptidos presentados por B*2702 se unen in vitro y probablemente también in vivo a
B*2705 (García et al., 1997b). Este solapamiento de repertorios peptídicos entre ambos subtipos
concuerda cualitativamentecon los patrones de reactividad cruzada de CTLs alorreactivos
(López et al., 1994). Por tanto B*2705 y B*2702 son un ejemplo de dos subtipos asociados a
EA, con un grado importante de solapamiento de sus repertorios peptídicos. Puesto que B*2702
no une péptidos con residuos C-terminales básicos, éstos probablemente no están implicados en
la patogénesis de la EA.
A pesar de las similitudes estructurales entre B*2704 y B*2706, sólo el primero está
asociado a enfermedad (López-Larrea et al., 1995), y sus especificidades por el residuo C-
terminal muestran marcadas diferencias.
B*2704 une preferentemente in vitro, péptidos con residuos C-terminales alifáticos y
aromáticos, similares a los presentados por B*2702 in vivo. Algunos péptidos con residuos C-
terminales básicos también se unen a B*2704 in vitro, sin embargo tales péptidos no se han
DISCUSIÓN -62-
detectado entre los ligandos naturales de este subtipo.

B*2706 por su parte, discrimina en mayor medida que B*2704 entre los residuos C-
terminales polares y apolares, lo que se concreta en una mayor preferencia que B*2704 por Leu
y Phe y menor por residuos básicos y Tyr. Ello sugiere que el repertorio de péptidos que B*2706
comparte con otros subtipos, incluye principalmente a los péptidos con Leu y Phe C-terminales.
Las diferencias de especificidad observadas in vitro entre B*2704 y B*2706 se
correlacionan con las que muestran in vivo, como se deriva de la secuenciación de los pooles de
péptidos eluídos de ambos subtipos (García et al., 1997b).
El aumento de la preferencia por residuos C-terminales apolares tras la eliminación de los
dos residuos ácidos Asp77 y Asp116, explica las especificidades C-terminales de B*2704 y
B*2706. No obstante, la ausencia de uno sólo de estos residuos en B*2704, no es suficiente para
impedir totalmente la unión de péptidos con residuos C-terminales básicos.
La preferencia que muestra B*2706 por Leu y Phe, y la unión ineficiente de Tyr C-
terminal, es probablemente debida al cambio D→Y116. El papel de esta posición ha sido
analizada en dos estudios previos en los que se analizaban mutaciones distintas, pero en ambos
tanto Leu como Phe eran los dos residuos C-terminales más adecuados, cuando D116 era
mutado. El cambio de Asp por Phe disminuía la aceptación de residuos C-terminales básicos
(Parker et al., 1994). Esta especificidad se explicaría por la incapacidad de Phe para formar
puentes de hidrógeno. En el otro estudio (Fiorillo et al., 1995), B*2709 cuyo residuo 116 es His,
era incapaz de unir péptidos de poli-Alanina con Arg o Tyr C-terminal pero sí podía unir Lys.
Puesto que B*2709 tampoco se asocia a EA, este estudio junto con los de B*2706 sugiere que el
residuo tiene un papel clave en determinar la susceptibilidad a EA.
La introducción de residuos ácidos en las posiciones 114 y 152, no altera la especificidad
de la subcavidad C/F debido a su localización, pero afectan notablemente a la unión in vitro de
los péptidos estudiados. Estos resultados sugieren que es posible alterar la especificidad por
péptidos unidos sin alterar las preferencias por los anclajes primarios, debido probablemente a la
modulación de las interacciones con residuos de anclaje secundarios (por ejemplo P7).
En el caso concreto de E152 (B*2710), este subtipo es muy distinto antigénicamente de
B*2705, puesto que es el que presenta una menor reactividad cruzada (Calvo et al., 1990). Sin
embargo, el análisis del repertorio peptídico natural de B*2710 reveló una sorprendente
homología con el de HLA-B27 (García et al., 1998 / Anexo 8). Por tanto el efecto de la mutación
E152 es mucho mayor sobre el reconocimiento por los TCR que sobre la especificidad de unión
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de péptidos. Estudios de modelización sugieren que ésto es debido a que el residuo 152 en HLA-
B27 es accesible al TCR (García et al., 1998 / Anexo 8; Figura 5).
Cuando se compara la unión de muchos de los péptidos a B*2704, S77 y E152, se observa
que la mutación S77 compensa el efecto negativo del residuo E152. De igual modo, las
afinidades de unión similares a Y116 y al doble mutante D114Y116 muestran una compensación
de la mutación Y116 sobre la mutación D114. Estos efectos compensatorios que modulan la
unión de péptidos, se correlacionan con resultados previos en los que se observaron efectos
compensatorios de las mutaciones en el reconocimiento por CTLs alorreactivos (López et al.,
1992; Villadangos et al., 1994).
Estos efectos compensadores, podrían suponer una ventaja evolutiva en el polimorfismo de
HLA-B27. Debido a que dos mutaciones generadas mediante conversión génica, un mecanismo
evolutivo frecuente en este sistema (López de Castro, 1989; Parham et al., 1995), tienen un
efecto menos disruptivo que una mutación puntual.
La ausencia de Asp116, y la menor capacidad para unir péptidos con C-terminal Tyr, son
características que comparten B*2706 y B*2709 y que diferencian a estos subtipos de otros
asociados a enfermedad: B*2705, B*2702 y B*2704. Esta correlación podría sugerir que un
posible péptido artritogénico debería tener Tyr lo que restringiría en gran medida el número de
candidatos. B*2707, aunque tampoco presenta el motivo Tyr C-terminal (Tieng et al., 1997) sí
está asociado a enfermedad. Sin embargo, es posible que este subtipo pudiera presentar péptidos
con Tyr C-terminal en niveles no detectables por secuenciación de Edman.
V.1.2. El polimorfismo en la cavidad C/F determina parcialmente la especificidad de la

subcavidad B.
Los resultados derivados del estudio realizado con B*2701, B*2702 y los mutantes que
mimetizan sus cambios, todos localizados en la cavidad C/F, pusieron de manifiesto la
preferencia de B*2701 por péptidos con residuo Leu, Tyr y Phe C-terminal de forma similar a
B*2702 (Rötzschke et al., 1994).
Estas preferencias se explican por la mayor hidrofobicidad de la cavidad C/F de ambos
subtipos, respecto a B*2705. Adicionalmente, muchos de los péptidos secuenciados de B*2701
son compartidos por otros subtipos asociados a enfermedad, lo que es compatible con una
posible asociación de B*2701 a EA. De hecho uno de los pocos individuos tipados como
B*2701+, padecía esta enfermedad. La principal diferencia entre B*2701 y B*2702 reside en las
DISCUSIÓN -64-
preferencias por el residuo en P2. Este residuo, que está conservado entre los subtipos de HLA-
B27, es Arg2; la Gln2 aunque compatible con la unión de péptidos in vitro a varios subtipos, es
un residuo sobóptimo (García et al., 1997a; Villadangos et al., 1995; Galocha et al., 1996 /
Anexo 1; Parker et al., 1994; Fukazawa et al., 1994; Raghavan et al., 1996). Sin embargo,
B*2701 es capaz de unir in vitro y presentar in vivo péptidos tanto con Gln2 como con Arg2 con
eficiencia similar. Esta característica singular de B*2701 radica en el cambio D→Y74, como se
deduce de la presencia de Gln2 y Arg2 entre los péptidos que unen in vivo tanto B*2701 como
en el mutante Y74 (Anexo 2).
El efecto que ejerce la mutación Y74, situada en la subcavidad C/F, sobre la especificidad
de la subcavidad B, tiene su explicación en el residuo Lys70. Este residuo, casi exclusivo de
HLA-B27, se localiza próximo a la subcavidad B, pero no interviene en las interacciones con el
residuo P2. En B*2705, su cadena lateral se orienta hacia el exterior de la subcavidad B
(Madden et al, 1992) estableciendo un puente salino con el residuo Asp74. En B*2701, la
mutación Y74 impide la formación de ese enlace permitiendo la reorientación de la cadena
lateral de la Lys70 hacia la subcavidad B, donde puede interaccionar con residuos peptídicos de
Gln2.
Estudios recientes realizados en nuestro laboratorio (Krebs et al. 1999 / en revisión), han
confirmado experimentalmente el papel crítico de la Lys70 en la especificidad de B*2701 por
Gln2. En estos estudios, la mutación de Lys70 a Ala70 en B*2701, revierte la especificidad a
Arg2 exclusivamente. Adicionalmente, los estudios de modelización molecular sugieren que la
especificidad dual de B*2701 por Arg2 y Gln2 se debe a la capacidad de Lys70, en este subtipo,
para adoptar dos estados rotaméricos distintos dependiendo del residuo P2. Como se ha dicho, si
P2 es Gln, Lys70 se orienta hacia la subcavidad B para interaccionar con Gln2; si P2 es Arg,
Lys70 se reorienta en una conformación diferente hacia fuera de la subcavidad B, preservando el
mismo modo de interacción de la Arg2 en esta subcavidad, que en B*2705.
La mala unión general de muchos de los péptidos al mutante A81 se explica porque la
ausencia de Leu81 impide las interacciones con los residuos C-terminales apolares o con la
porción alifática de los básicos (Madden et al., 1992). Finalmente, la mejor unión de algunos
péptidos a B*2701 o B*2702 que al mutante A81, sugiere la existencia de efectos
compensatorios de los otros cambios.
V.1.3. Análisis del efecto del polimorfismo de la subcavidad A sobre la unión de péptidos.
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HLA-B*2703 se diferencia de B*2705 en un solo aminoácido, Y59H, ubicado en la

subcavidad A. Esta mutación es la responsable de que B*2703 presente un subconjunto de los
péptidos presentados por B*2705 (López et al, 1994; Villadangos et al, 1994) lo que hace
interesante el estudio del efecto que tiene esta mutación en la unión de péptidos.
En la estructura cristalográfica de HLA-B*2705 (Madden et al, 1992), las cadenas laterales
de los aminoácidos Tyr7 y Tyr171 establecen puentes de hidrógeno con el extremo N-terminal
del péptido. Ambas cadenas interaccionan adicionalmente, por mediación de una molécula de
agua, con las cadenas laterales de los residuos cercanos Tyr59, Glu45 y Tyr171. (Figura 6 /
Anexo 3)
En B*2703, se produce la distorsión de esa red de enlaces. La molécula de agua desaparece
y el extremo N-terminal del péptido se une a la His59, en lugar de a Tyr7. Como consecuencia,
se pierden el enlace directo con Tyr171 y cinco interacciones mediadas por la molécula de agua.
La desaparición de la molécula de agua que enlaza la subcavidad A con Glu45 en la subcavidad
B, probablemente refuerza la interacción de este residuo con Arg2.
En el caso en que P2 es Gln, los enlaces en la subcavidad B de B*2705 se debilitan,
principalmente con Thr24 y Glu45 y se generan nuevos reordenamientos conformacionales en
las interacciones con P1. Gln2 es más tolerado en B*2705, debido a que Tyr59 aún puede unirse
a Tyr7. Adicionalmente el enlace Cα−Ν del péptido unido, sufre una rotación que establece un
nuevo puente de hidrógeno con Glu63 sin perder el enlace con Tyr7. La cadena lateral de Gln2
establece además puentes de hidrógeno con Glu45 y Tyr99 reforzando las interacciones en la
subcavidad B. Estas interacciones no se producen en B*2703, como explica la baja afinidad de
péptidos con Gln2 a este subtipo (Figuras 7 y 8 / Anexo 3).
Tanto en B*2705 como en B*2703, la presencia de Gln2 induce una desestabilización del
extremo C-terminal. Esta situación ya detectada en otros péptidos (Rognan et al., 1994), sugiere
la posible función estabilizadora de la región N-terminal para el resto del péptido.
En los péptidos analizados, el residuo de Arginina en P1 es accesible a la formación de dos
puentes salinos con Glu63 y Glu163, sin embargo esto no supone una ventaja significativa sobre
la unión in vitro del análogo con Alanina. La cadena lateral de Alanina puede interaccionar con
residuos apolares conservados de la subcavidad A como (Met5 y Trp167), lo que explicaría la
similar afinidad de unión de péptidos tales como RRYQKSTEL y ARYQKSTEL. No obstante, hay
estudios que indican la preferencia de B*2703 por residuos básicos (Colbert et al., 1994) y la
DISCUSIÓN -66-
presencia mayoritaria de éstos entre los péptidos que une in vivo (Boisgérault et al., 1996;
Griffin et al., 1997) que no pueden explicarse mediante este modelo, aunque es posible la
formación de puentes salinos entre varios rotámeros de la cadena lateral básica de P1 y los
residuos cargados negativamente cercanos a la subcavidad A.
En conclusión, el efecto del cambio Y59→H presente en B*2703 tiene varios efectos
simultáneos que consisten en: (i) una disrupción de la red de puentes de hidrógeno que se
establecen en la subcavidad A, (ii) reordenamientos de las interacciones en la subcavidad B y
(iii) debilitamiento general de las interacciones que se producen con el extremo C-terminal del
péptido. Estos efectos pueden afectar en gran medida al conjunto de péptidos presentados por
B*2703 y hacer la unión de éstos más dependiente de la presencia de residuos básicos en P1.
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V.2. RELACIÓN ENTRE LA UNIÓN DE PÉPTIDOS Y LA SELECCIÓN DE EPÍTOPOS POR

CÉLULAS T.
Los resultados de este estudio muestran: (i) la moderada influencia del polimorfismo en la
unión de péptidos de EBV restringidos por HLA-B27, (ii) la inexistencia de correlación entre la
unión promiscua de los péptidos virales a varios subtipos y su antigenicidad y/o
inmunogenicidad en el contexto de un subtipo particular, (iii) el motivo de anclaje Arg2, no es
necesario para mantener la estructura antigénica del péptido.
La moderada incidencia que muestra el polimorfismo entre los subtipos B*2701-B*2706,
en la unión de péptidos de EBV, que poseen residuos C-terminales alifáticos o aromáticos, es
consistente con el predominio de este tipo de residuos entre los ligandos naturales de los seis
subtipos (García et al., 1997a; Jardetzky et al., 1991; Boisgérault et al., 1996; Rötzschke et al.,
1994; García et al., 1997b). En general, no existe una correlación entre la unión a un subtipo y su
inmunogenicidad en el contexto del mismo. Este es el caso del péptido EBNA3B, restringido por
B*2702 y de LMP2, restringido por B*2704, que muestran una buena unión a todos los subtipos,
en algunos casos mejor incluso que al subtipo por el que están restringidos.
A pesar de que el desarrollo de una respuesta mediada por CTLs requiere habitualmente
una alta afinidad al elemento de restricción (Sette et al., 1994), en el estudio presente no se
aprecia una correlación directa entre la afinidad de unión a un subtipo y su inmunogenicidad en
el contexto del mismo. La inmunogenicidad parece correlacionarse mejor con la estabilidad del
complejo MHC-péptido (Van der Burg et al., 1996; Levitsky et al., 1996). En un trabajo reciente
(Brooks et al., 1998), EBNA3B, cuya unión in vitro es tan buena a B*2705 como a su elemento
de restricción B*2702, mostró una unión más estable a B*2702 que a B*2705 que se
correlacionó con la ausencia de reconocimiento del péptido en el contexto de B*2705. Por lo
tanto, las diferencias de estabilidad, no evidentes en el ensayo in vitro, pueden ser las
responsables de la inmunogenicidad de un péptido en el contexto de un subtipo y no de otros.
Aunque múltiples factores contribuyen a limitar el número de péptidos inmunogénicos en
una respuesta antiviral, tales como la afinidad, la acción de los proteosomas, el transporte
mediado por TAP, el repertorio de células T y la supresión de la respuesta de células T por otros
péptidos inmunodominantes (Deng et al., 1997); en este estudio los tres péptidos virales se unían
significativamente a todos los subtipos y además eran inmunogénicos, al menos en el contexto
de un subtipo, reduciendo las posibles variables, exclusivamente al de la capacidad de los
repertorios de células T para reconocer la estructura del complejo péptido-MHC.
DISCUSIÓN -68-
El hecho de que la estructura del complejo péptido-MHC depende del subtipo, es evidente
en la ausencia de correlación entre la unión de un péptido a varios subtipos, y su reconocimiento
en el contexto sólo de algunos. Así, los CTLs restringidos por B*2704 para el péptido LMP2 no
reconocían al péptido en el contexto de B*2702 ni de B*2705, confirmando observaciones
previas (Brooks et al., 1993); los CTLs restringidos por B*2705 o B*2702 no reconocían al
péptido EBNA3C unido a B*2704; los CTLs restringidos por B*2705 o B*2702 no reconocían al
péptido en el contexto de B*2704, y la mayoría de los efectores contra B*2705 no reaccionaban
de forma cruzada con B*2702.
El reconocimiento por CTLs activados de un péptido restringido por un subtipo, implica un
cambio en la estructura del epítopo tras la unión del péptido a diferentes subtipos, bien debido a
un cambio conformacional del propio epítopo, o bien a que el polimorfismo entre subtipos altera
la estructura del complejo o la interacción con el TCR. Esta última posibilidad es probablemente
la responsable de la ausencia de reactividad cruzada entre B*2704 y B*2705 o B*2702. La razón
de esto es que B*2704 difiere de los otros dos subtipos en el cambio E152→V. Esta mutación
que no parece afectar mucho a la presentación in vivo de los mismos péptidos naturales que
B*2705, ni altera su conformación, tiene sin embargo efectos drásticos en el reconocimiento por
el TCR (García et al., 1998 / Anexo 8).
Por lo tanto, el polimorfismo de HLA-B27 modula el reconocimiento por células T
mediante factores adicionales a la simple afinidad de unión de péptidos. Las diferencias mayores
entre subtipos residen en su diferente modulacion de la inmunogenicidad y antigenicidad de los
péptidos unidos, más que en su diferente especificidad de unión de péptidos.
La modulación de la antigenicidad e inmunogenicidad de un péptido en el contexto de
diferentes subtipos, tiene claras implicaciones en la patogenia de HLA-B27. La hipótesis que
sugiere la unión selectiva de un péptido artritogénico a los subtipos asociados a enfermedad tiene
ahora otra alternativa adicional, consistente en que dicho péptido artritogénico pueda unirse a
varios subtipos, pero sólo ser relevante en el contexto de algunos.
En este estudio, péptidos que carecían del motivo Arg2 podían ser reconocidos por CTLs
restringidos por el péptido con Arg2, lo que implica que su estructura antigénica reconocida no
era alterada tras eliminar un motivo de anclaje principal. Evidencias adicionales como la
reacción cruzada de CTLs con péptidos carentes de motivos canónicos (Malarkannan et al.,
1996), la secuenciación de péptidos carentes de Arg2 en B*2701 (García et al., 1997c / Anexo 2)
y en B*2705 de ratas transgénicas (Simmons et al., 1997) y la demostración de que los péptidos
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con Gln2 se unen in vitro a muchos subtipos de HLA-B27, sugiere que estos podrían constituir
una fracción menor del conjunto total de péptidos en subtipos diferentes a B*2701. Por tanto, la
búsqueda de posibles péptidos artritogénicos, en particular autopéptidos, no debería basarse
exclusivamente en los motivos canónicos. Péptidos con motivos no canónicos, debido a su baja
afinidad y escasa presentación in vivo, podrían eludir la autotolerancia mejor que los péptidos
con Arg2 y convertirse en dianas de CTLs autorreactivos generados tras una infección
artritogénica.
DISCUSIÓN -70-
V.3. LA ESPECIFICIDAD PEPTÍDICA DE LOS SUBTIPOS DE HLA-B27 ES MODULADA EN

MULTIPLES POSICIONES DE ANCLAJE.
La variabilidad de los residuos en P1, P3 y PΩ determina en gran medida las propiedades de

unión del péptido, pero la contribución de cada una de las posiciones está jerarquizada según el
orden P9>P3>P1. Adicionalmente, el hecho de que muchos de los residuos sean inapropiados en
cualquiera de estas tres posiciones indica que la unión del péptido depende tanto de los efectos
positivos como de los negativos.
La exploración de los residuos presentes entre los ligandos naturales de B*2705 revela un
predominio de los residuos más adecuados en las posiciones P3 y P9; no obstante, la presencia de
un residuo subóptimo en una de estas posiciones es tolerada, siempre y cuando se compense con la
presencia en la otra posición de anclaje de un residuo óptimo. En el análisis de la distribución de
residuos entre los ligandos naturales de B*2705 no se aprecian excepciones a esta regla, sugiriendo
que si se excluyen los factores implicados en el procesamiento y transporte, aún insuficientemente
caracterizados (van Endert et al., 1995; Uebel et al., 1997; Daniel et al., 1998; Peh et al., 1998), la
limitación del número de ligandos naturales se basa en este tipo de restricciones.
El residuo P1 es el más permisivo de los tres, y su contribución a la unión es menor, pero esta
permisividad está condicionada por la presencia de un buen anclaje en P3 o P9. Teniendo en cuenta
que la contribución aditiva de las tres posiciones, junto con la posición P2 (Arg2), da cuenta de la
mayor parte de la afinidad del péptido natural, la predicción de epítopos naturales puede reducirse
al estudio de los residuos P1, P3 y P9 obviando el papel de los residuos de las posiciones centrales,
cuya menor contribución permite su sustitución por espaciadores no peptídicos que no alteran en
gran medida su afinidad (Rognan et al., 1995; Krebs et al., 1998 / Anexo 6; Poenaru et al., en
prensa / Anexo 7). A pesar de que no se conocen muchos ligandos naturales de tamaños distintos a
los canónicos, de nueve o diez residuos, la unión de ligandos con tamaños no canónicos sólo parece
posible cuando presentan buenos anclajes en las tres posiciones P1, P3 y PΩ.
Un aspecto relevante de la comparación entre B*2705 y B*2704 reside en las diferentes
especificidades por PΩ. En concordancia con su ausencia in vivo (García et al., 1997b) y su mala
unión in vitro (Tanigaki et al., 1994; Galocha et al., 1996 / Anexo 1), los residuos PΩ básicos no
están favorecidos en B*2704. Adicionalmente, los residuos C-terminales Y y F aunque no están
favorecidos, son presentados de forma natural por B*2704 (García et al., 1997b) probablemente
debido a que la estabilización por los otras posiciones de anclaje es suficiente para permitir la unión
de ligandos con estos residuos. Por lo tanto, el solapamiento de repertorios peptídicos de B*2705 y
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B*2704, probablemente consiste sobre todo en péptidos con residuos C-terminales alifáticos, y
aquellos con Y y F que además poseen en P3 residuos apolares.
Para entender la base molecular de su diferente asociación a enfermedad, es fundamental
analizar las diferencias entre B*2704 y B*2706. Las diferencias de B*2706 con B*2704 se
localizan en posiciones que pueden influir directamente en la interacción con los residuos P3 y P9
de los péptidos unidos. Los resultados obtenidos concuerdan plenamente con los estudios previos
de secuenciación que muestran la mayor preferencia de B*2706 por residuos C-terminales
alifáticos y F, así como la ausencia de Y en PΩ (García et al, 1997b). Además, en los estudios in
vitro, los residuos alifáticos están más favorecidos que Y en B*2706, pero no en B*2704 (Galocha
et al., 1996 / Anexo 1). La ausencia de Y se explicaría por el mejor ajuste en B*2706 de los
residuos alifáticos voluminosos y F que de Y, de forma que los péptidos con Y competirían en
desventaja para unirse in vivo a B*2706.
B*2704 y B*2706, muestran además otras diferencias en la preferencias por P3 y P1. Lo más
destacado es la distinta especificidad por el residuo P3, especialmente una mejor aceptación de R,
N y Q por B*2706 y la peor de A respecto a otros residuos. Estas diferencias son probablemente
debidas a la presencia del residuo D114 en lugar de H114. Las diferencias en el residuo P1, entre
subtipos que comparten una subcavidad A común, sugiere la existencia de efectos a larga distancia
de posiciones polimórficas alejadas de esta subcavidad.
La diferente especificidad de B*2704 y B*2706 en múltiples posiciones de anclaje implica
que su asociación diferencial a enfermedad puede no correlacionarse exclusivamente con la
incapacidad de B*2706 para unir Tyr C-terminal, sino también por la modulación de la
especificidad por los residuos en P1 y sobre todo en P3. Por lo tanto B*2704 y B*2706, aunque
comparten ligandos comunes pueden diferir en los repertorios de péptidos que presentan y muchos
péptidos con Arg2 y residuo C-terminal compatible con la unión tanto a B*2704 como a B*2706
pueden sin embargo unirse exclusivamente a un subtipo.
DISCUSIÓN -72-
V.4. UNIÓN DE ANÁLOGOS NO PEPTÍDICOS A HLA-B27.
La supresión de la reactividad por CTLs, puede lograrse mediante la utilización de

ligandos modificados que al reaccionar con el TCR induzcan anergia, un fenómeno llamado
antagonismo. Debido a los numerosos detalles conocidos de las interacciones entre un péptido y
la molécula del MHC, el reemplazamiento en un péptido antigénico de la parte central
reconocida por el TCR, por espaciadores orgánicos no peptídicos que conserven los residuos de
anclaje a la molécula de clase I, es posiblemente una buena estrategia para diseñar ligandos que
funcionen como antagonistas de péptidos antigénicos. La ventaja de tales compuestos sobre los
antagonistas peptídicos, para su utilización in vivo, reside en su alta resistencia a la acción de
proteasas y sus mejores propiedades farmacocinéticas (Ishioka et al., 1994).
La modificación de la porción central del péptido con espaciadores no peptídicos, debe
mejorar en lo posible tanto su afinidad de unión como su estabilidad.
En los análogos estudiados con espaciador de -Aua- se observa una disminución de la
afinidad, respecto al péptido natural, dependiente del subtipo al que se une. Su naturaleza
monofuncional, permite la unión covalente entre los residuos P3 y P9 pero no el establecimiento
de contactos adicionales en las subcavidades centrales de la molécula de clase I. La ausencia de
grupos funcionales hace a estos análogos muy dependientes del buen anclaje en P9 que queda
claramente reflejada en los valores de baja afinidad que muestran los análogos con P9 básico
unidos a B*2704.
Los espaciadores bifuncionales formados por trímeros y tetrámeros de -HB-, además de
servir de enlace entre P3 y P9, poseen grupos funcionales metilo capaces de establecer contactos
adicionales en el surco de unión del péptido. Sin embargo, los contactos sólo son posibles de
forma óptima cuando la longitud del espaciador es apropiada, permitiendo el contacto de ambos
extremos del análogo con las subcavidades A y F; en este sentido el análogo con -HB3- no
cumple este requisito, una característica que lo diferencia claramente del análogo con el
espaciador de -HB4-, que si lo cumple.
El incremento de afinidad medido in vitro, es debido al anclaje adicional que proporcionan
los dos grupos metilo del espaciador -HB4-, éstos interaccionan con las subcavidades C y E. El
mayor número de interacciones determina una unión de este análogo superior a la del ligando
natural. En este sentido la utilización del estereoisómero (R) no es trivial, puesto que la
conformación estereoisomérica (R o S) de los sustituyentes es importante para mejorar la
afinidad (Poenaru et al., en prensa /Anexo 7).
-73- DISCUSIÓN
En este estudio se observaron discrepancias en los valores comparativos de afinidad entre

ligandos de HLA-B27 y sus análogos no peptídicos dependiendo de que se midiera su unión in
vitro (EC50) o su estabilidad térmica (Tm). Estas discrepancias se explican porque el ensayo de
unión in vitro, está muy influído por la cinética de asociación del péptido a la molécula de MHC,
mientras que la Tm es una medida de la estabilidad del complejo y se relaciona directamente con
la cinética de disociación del péptido.
RESUMEN Y DISCUSIÓN GENERAL:
Si el papel patogénico de HLA-B27 reside en su función presentadora de péptidos, el

conocimiento de las pautas que determinan el solapamiento de repertorios peptídicos entre
subtipos, así como el reconocimiento de dichos péptidos en función del subtipo al que están
unidos, son cuestiones fundamentales.
En esta tesis se han definido algunos aspectos importantes de la modulación del repertorio
peptídico por el polimorfismo de HLA-B27. Se ha analizado la relación entre la unión de
péptidos y su inmunogenicidad y antigenicidad, y se han estudiado algunos aspectos de la unión
de ligandos no peptídicos a HLA-B27.
El polimorfismo de HLA-B27 modula la unión de péptidos a tres niveles:
En primer lugar, el polimorfismo de las posiciones localizadas en la subcavidad C/F afecta

directamente a la especificidad por el residuo C-terminal, que es un anclaje principal a HLA-
B27. En consecuencia, limita o impide la aceptación de residuos C-terminales básicos en
múltiples subtipos. Además introduce una importante diferencia entre B*2704 y B*2706, dos
subtipos asociados diferencialmente a EA, en cuanto a que restringe la aceptación de Y C-
terminal en este último subtipo.
En segundo lugar, algunas posiciones polimórficas localizadas en una determinada

subcavidad modulan la especifidad por residuos peptídcos que interaccionan en subcavidades
distintas. En esta tesis se han analizado dos efectos contrapuestos. El poliformismo de B*2703,
localizado en la subcavidad A, fortalece la interacción de Arg2 en la subcavidad B y afecta a la
estabilización del extremo C-terminal del péptido. Por otra parte, la mutación D74Y en B*2701,
localizada cerca de la subcavidad C/F, favorece la interacción de Gln2 en la subcavidad B por un
efecto indirecto mediado por la Lys70.
DISCUSIÓN -74-
En tercer lugar, el polimorfismo de B27 modula la especifidad en posiciones secundarias

de anclaje. Esto es particularmente relevante, ya que indica que la asociación diferencial de
B*2704 y B*2706 a EA, no se correlaciona solamente con la aceptación de Y C-terminal, sino
con una modulación más compleja que incluye, adicionalmente, otras posiciones de anclaje. Las
interrelaciones entre los repertorios peptídicos de los dos subtipos se hacen más complejas por el
hecho de que las diversas posiciones de anclaje pueden tolerar en mayor o menor medida
residuos desfavorecidos, que son compesados por la presencia de buenos anclajes en otras
posiciones.
El estudio efectuado con péptidos virales pone de manifiesto que más allá de las
diferencias y similitudes en la especifidad de unión de péptidos, las diferencias funcionales entre
subtipos dependen de la modulación adicional que ejerce el polimorfismo sobre la
inmunogenicidad y antigenicidad de los péptidos unidos. En este estudio se demuestra que no
existe una correlación entre la eficiencia con la que un péptido se une HLA-B27, y su capacidad
para estimular una respuesta inmune o de ser reconcido por CTLs activados. Estos datos están de
acuerdo con los conceptos de que la estabilidad del complejo MHC-péptido es el determinante
crítico de la inmunogenicidad, y con que un CTL activado puede reconocer un péptido unido con
muy baja afinidad a MHC si la conformación del epítopo está conservada.
Finalmente, se han explorado las propiedades de unión a HLA-B27 de ligandos no
peptídicos en los que los residuos P4-P8 fueron sustituidos por varios espaciadores orgánicos. Se
ha demostrado que estos ligandos se unen a HLA-B27 con una afinidades que pueden ser
superiores a la del péptido natural, dependiendo de la naturaleza química del espaciador. Estos
estudios abren una vía a un ulterior análisis sobre el posible uso de estos compuestos en la
modulación de la respuesta citotóxica restringida por HLA-B27.
-75-
VI. CONCLUSIONES
CONCLUSIONES -77-
VI. CONCLUSIONES
Los subtipos B*2704 y B*2706, asociados diferencialmente a enfermedad, difieren en la

menor preferencia de B*2706 por Tyr C-terminal y en su especificidad por residuos de anclaje
secundario, en particular en P3.
B*2701 es el único subtipo conocido de HLA-B27 que une de forma significativa péptidos
con Gln2 in vivo. La mutación Y74 es la responsable de esta característica y su efecto es
indirecto a través de la Lys70.
Por lo tanto un residuo polimórfico (D74Y) puede ejercer efectos sobre la especificidad por
residuos del péptido que interaccionan en regiones alejadas (cavidad B). Estos efectos están
mediados a través de un residuo conservado (Lys70).
El cambio Y59→H en B*2703 tiene varios efectos simultáneos (i) ruptura de la red de puentes
de hidrógeno en la subcavidad A, (ii) reordenamiento de las interacciones en la subcavidad B y
(iii) debilitamiento general de las interacciones con el extremo C-terminal del péptido. Estos
efectos hacen a B*2703 más dependiente del anclaje en P1.
La unión promiscua de los péptidos virales a HLA-B27 no se correlaciona con su

antigenicidad e inmunogenicidad en el contexto de subtipos particulares. El polimorfismo de
HLA-B27, probablemente influye en la inmunogenicidad peptídica modulando la estabilidad
más que la afinidad. El motivo canónico Arg2 no es necesario para mantener la estructura
antigénica de los epítopos peptídicos analizados.
Las restricciones al número de ligandos naturales de B*2705 se basan en gran medida en la

coexistencia compensada de residuos óptimos y subóptimos en las posiciones de anclaje P1, y
sobre todo P3 y P9. Éstas posiciones muestran una contribución jerárquica y aditiva a la
afinidad del péptido. Entre los ligandos naturales de longitud no canónica es necesaria la
presencia de buenos anclajes en las tres posiciones estudiadas.
Los análogos de péptidos antigénicos modificados en su región central mediante

espaciadores no peptídicos de tipo bifuncional pueden mejorar la afinidad de unión a la
molécula de clase I.
-79-
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VIII. ANEXOS
ANEXOS -93-
VIII. ANEXOS
-Anexo 1- -Anexo 5-
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presented by HLA-B27 to the differentially differentially associated to ankylosing
disease-associated B*2704 and B*2706 spondylitis is modulated at multiple anchor
subtypes, and to mutants mimicking their positions. (aceptado en Arthritis and
polymorphism. Tissue Antigens. 48: 509- Rheumatism).
518.
-Anexo 2- -Anexo 6-
García, F., Galocha, B., Villadangos, J.A, Krebs, S., Lamas, J.R., Poenaru, S.,
Lamas, J.R., Albar, J.P., Marina, A., Folkers, G., López de Castro, J.A.,
López de Castro, J.A. (1997). HLA-B27 Seebach, D., Rognan, D. (1998).
(B*2701) specificity for peptides lacking Substituting nonpeptidic spacers for the T
Arg2 is determined by polymorphism Cell Receptor-binding part of class I Major
outside the B pocket. Tissue Antigens. 49: Histocompatibility Complex-binding
580-587. peptides. J.Biol. Chem. 273: 19072-19079.
-Anexo 3- -Anexo 7-
Rognan, D., Krebs, S., Kuonen, O., Poenaru, S., Lamas, J.R., Folkers, G.,
Lamas, J.R., López de Castro, J.A., López de Castro, J.A., Seebach, D.,
Folkers, G. (1997). Fine specificity of Rognan, D. (1998). Nonapeptide analogues
antigen for two clas I major containing (R)-3-hydroxybutanoate and β-
histocompatibility protein alleles (B*2705 homoalanine oligomers: synthesis and
and B*2703) differing in one amino acid. binding affinity to a class I MHC protein.
J.Comput. Aid. Mol. Des. 11: 463-478. (enviado a J. Med. Chem).
-Anexo 4- -Anexo 8-
Lamas, J.R., Brooks, J.M. Galocha, B. García, F., Rognan, D., Lamas, J.R.,
Rickinson, A.B., López de Castro, J.A. Marina, A., López de Castro, J.A. (1998).
(1998). Relationship between peptide An HLA-B27 polymorphism (B*2710) that
binding and T-cell epitope selection: a study is critical for T-cell recognition has limited
with subtypes of HLA-B27. International effects on peptide specificity. Tissue
Immunology. 10: 259-266. Antigens. 51:1-9.
ANEXO -1-
ANEXO -2-
ANEXO -3-
Journal of Computer-Aided Molecular Design, 11 (1997) 463–478. 463
KLUWER/ESCOM
© 1997 Kluwer Academic Publishers. Printed in The Netherlands.
J-CAMD 410
Fine specificity of antigen binding to two class I major histocompatibility

proteins (B*2705 and B*2703) differing in a single amino acid residue*
Didier Rognana,**, Stefan Krebsa, Oliver Kuonena, José R. Lamasb,

José A. López de Castrob and Gerd Folkersa
a
Department of Pharmacy, Swiss Federal Institute of Technology, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
b
Centro de Biologia Molecular Severo Ochoa, Universidad Autonoma de Madrid, Facultad de Ciencas, E-28049 Madrid, Spain
Received 10 March 1997

Accepted 26 May 1997
Keywords: MHC; HLA-B27; Drug design; Molecular dynamics simulations
Summary
Starting from the X-ray structure of a class I major histocompatibility complex (MHC)-encoded protein
(HLA-B*2705), a naturally presented self-nonapeptide and two synthetic analogues were simulated in
the binding groove of two human leukocyte antigen (HLA) alleles (B*2703 and B*2705) differing in a
single amino acid residue. After 200 ps molecular dynamics simulations of the solvated HLA–peptide
pairs, some molecular properties of the complexes (distances between ligand and protein center of
masses, atomic fluctuations, buried versus accessible surface areas, hydrogen-bond frequencies) allow
a clear discrimination of potent from weak MHC binders. The binding specificity of the three nonapep-
tides for the two HLA alleles could be explained by the disruption of one hydrogen-bonding network
in the binding pocket of the HLA-B*2705 protein where the single mutation occurs. Rearrangements
of interactions in the B pocket, which binds the side chain of peptidic residue 2, and a weakening of
interactions involving the C-terminal end of the peptide also took place. In addition, extension of the
peptide backbone using a β-Ala analogue did not abolish binding to any of the two HLA-B27 subtypes,
but increased the selectivity for B*2703, as expected from the larger peptide binding groove in this
subtype. A better understanding of the atomic details involved in peptide selection by closely related
HLA alleles is of crucial importance for unraveling the molecular features linking particular HLA alleles
to autoimmune diseases, and for the identification of antigenic peptides triggering such pathologies.
Introduction presentation to MHC proteins are presently accumulating

at an incredible pace. The huge amount of molecular
Major histocompatibility complex (MHC)-encoded details have made human leukocyte antigen (HLA) pro-
class I proteins play a major role in the immune surveil- teins very interesting drug design targets for two reasons.
lance of intracellular pathogens by presenting antigenic First, it is likely that the three-dimensional (3D) structures
peptides to cytotoxic T-lymphocytes (CTLs) at the surface of all class I and class II alleles are very similar, and that
of infected cells [1]. In the last decade, tremendous re- the MHC binding mode is rather conserved for most of the
search efforts have been made to delineate the molecular presented peptides, within each HLA class [5,6]. Reliable
aspects of antigen presentation to CTLs. Three major 3D pictures of MHC–peptide complexes are now accessible
breakthroughs in this field were the description of the and can be interpreted with respect to biological data [7–
first class I MHC crystal structure [2], the identification 10]. Second, the expression of certain MHC alleles is asso-
of allele-specific motifs for naturally bound peptides [3], ciated with either resistance or susceptibility to human
and the prominent role played by MHC-encoded TAP immunological diseases like ankylosing spondylitis [11],
heterodimers for antigen transport [4]. Starting from these diabetes [12], rheumatoid arthritis [13] or malaria [14].
three major observations, experimental data on antigen One of the strongest linkages known to date between
*Dedicated to Prof. D. Seebach on the occasion of his 60th birthday.

**To whom correspondence should be addressed.
464
the expression of one class I HLA allele and susceptibility common HLA-B*2705 allele [33,34]. Positively charged
to a pathology is that of HLA-B27 to inflammatory dis- residues (Lys, Arg and His) at P1 have been proposed to
eases of the joints called spondyloarthropathies [15,16]. be one of the main characteristics of this subset common
For example, more than 95% of patients suffering from to both subtypes as the replacement of Ser1 by Arg re-
ankylosing spondylitis are HLA-B27 positive, while this stored the binding of a B*2705-restricted viral epitope to
MHC type is only expressed in 7% of the healthy popula- HLA-B*2703 [35]. In addition, basic residues were pre-
tion [11]. Interestingly, among the 11 HLA-B27 alleles dominant among self-peptides naturally bound to B*2703
(HLA-B*2701 to HLA-B*2711) reported to date, at least [23]. Additional interactions given by basic side chains
two are not associated with spondyloarthropathies: HLA- could compensate for the weaker interaction of the pep-
B*2706 [17,18] and HLA-B*2709 [19]. All subtypes differ tide N-terminus to B*2703 pocket A. However, this is not
among each other only at a few residues, mostly located a stringent requirement because amino acids other than
in the peptide binding groove. Arg/Lys at P1 (Ala for example) are compatible with a
Deciphering the molecular parameters responsible for good binding to this allele [28].
the binding of antigenic peptides to the different HLA- To rationalize these data, molecular dynamics (MD)
B27 subtypes is an absolute prerequisite for better under- simulations of both alleles in complex with three different
standing their differential association with susceptibility peptides were undertaken to delineate similarities and dif-
to spondyloarthropathy, and to identify the sequence of ferences in MHC binding, which may explain specificity
potential arthritogenic peptides [15] that may trigger the variations.
disease. Sequencing of peptides naturally presented by the
different alleles [20–26] shows that Arg at position 2 (P2) Materials and Methods
is a conserved motif for peptides binding to all subtypes.
Gln2 is an additional motif among B*2701-bound pep- Coordinates setup
tides [25], but is a suboptimal residue (not found in vivo) Starting coordinates were taken from the crystal struc-
for other subtypes [27–30]. Two other anchoring positions ture of HLA-B*2705, solved at 2.1 Å resolution [32] and
could be disclosed from the frequency of occurrence of deposited in the Brookhaven Protein Databank [36] with
amino acids in peptides naturally bound to B*2705. Hy- the entry 1HSA. In order to save computational time,
drophobic amino acids are preferred at P3, and hydro- only the antigen-binding α1–α2 domains were taken into
phobic as well as positively charged residues can be found account in the study. This approximation was previously
at P9. Other positions are more variable and probably shown not to alter the accuracy of MD simulations
indicate a less important binding role. These observations [9,37,38] because only limited interactions exist between
are compatible with the crystal structure of one allele the α1-α2 part and the other two domains (α3 and β2m)
(HLA-B*2705) in complex with a peptide pool [31,32]. As that do not significantly contact antigenic peptides in the
for all other class I alleles crystallized to date, bound binding groove. This observation has been validated by
ligands are mainly nonapeptides strongly hydrogen- the crystal structure of one class I MHC protein lacking
bonded in a sequence-independent manner at their N- the membrane-proximal α3 domain, for which a con-
and C-termini to both ends of the MHC binding groove. served 3D fold of the α1–α2 antigen-binding domain was
The central part of the peptide (from P4 to P8) bulges out reported [39]. The C-terminal residue of the α2 domain
of the binding groove (Fig. 1) [32]. Some peptide side (Thr182) was protected by an N-methyl group to avoid
chains (P2, P3 and P9) are responsible for the allele speci- unrealistic electrostatic interactions. The HLA-B*2703
ficity of the recognition process, by binding to comple- subtype was obtained from the HLA-B*2705 crystal
mentary pockets of the MHC. Notably, the conserved structure by mutating Tyr59 into His, without changing
Arg2 of B27-bound peptides is perfectly centered in a the direction of the side chain. All MHC-bound nonamers
polar subsite (pocket B) composed of MHC polymorphic were built from the peptide (ARAAAAAAA) modeled in
residues (Tyr7, His9, Thr24, Glu45, Cys67). HLA-B*2705 is the original crystal structure [32] by substituting the cor-
the only B27 subtype that has been crystallized up to responding residue for alanine without altering the direc-
now. Furthermore, although peptide binding motifs have tion of the side chains. Six crystal water molecules were
been described for various HLA-B27 subtypes, the exact explicitly taken into account, as they are located in the
peptide repertoire selected by each allele is still under peptide binding cleft and bridge the binding of the pep-
investigation, and the exact contribution of individual tide to the protein X-ray structure. Polar hydrogen atoms
amino acids at the nine peptide positions to the various were then added and the complexes were centered in a 7.5
subtypes remains largely unknown. Å thick shell of TIP3P water molecules [40] without posi-
HLA-B*2703 contains a single point mutation tional constraint on solvent atoms. Any water atom closer
(Tyr59→His) in a subsite (pocket A) responsible for the than 1.75 Å to any solute atom was discarded, so that
binding of the peptide N-terminal residue. HLA-B*2703 approximately 1500 water molecules were added to each
probably selects a subset of peptides presented by the MHC–peptide binary complex.
465
Parametrization of the N-terminal b-alanine monomer parameter set [41]. Inner and outer dielectrics were as-
The N-terminal β-alanine was parametrized for signed values of 2.0 and 1.0 (vacuum) or 80 (water envi-
AMBER 4.0 [41] using a previously described procedure ronment). An ionic strength of 0.145 M and an ion exclu-
[42]. Briefly, atomic coordinates for β-alanine were ob- sion radius (Stern layer) of 2.0 Å were used according to
tained from the SYBYL biopolymer dictionary [43] and previously reported solvent calculations [51]. A probe
optimized by semiempirical quantum mechanics (MOPAC radius of 1.8 Å was utilized for computing the surface at
6.0) using the PM3 Hamiltonian [44]. Potential-derived which the electrostatic potential was extrapolated.
atomic charges were then computed on this geometry by
a single-point SCF calculation at the MNDO level [45]. Peptide synthesis
As new atom types were not defined, nonexisting force Peptides 1 and 3 were synthesized as previously de-
constants have been assigned according to available scribed [28]. Peptides 2 and 4 were synthesized by auto-
AMBER values for closely related bond, angle and di- mated, multiple solid-phase peptide synthesis with a robot
hedral types. They were incorporated into the parm91 system (Syro, MultiSynTech, Bochum, Germany) using
parameter set. an Fmoc/tBu strategy. For side-chain protection, Tyr(tert-
butyl), Ser(tert-butyl), Thr(tert-butyl), Glu(tert-butyl),
Molecular mechanics and dynamics simulations Gln(trityl), Arg(2,2,3,5,5-pentamethyl-chromansulfonyl)
All computations were performed on a CRAY J90 and Lys(tert-butyloxy-carbonyl) were used. The N-ter-
using the AMBER 4.0 program [41] and the united-atom minal residues were obtained using single couplings with
representation of the parm91 parameter set. Since explicit diisopropylcarbodiimide/1-hydroxy-benzotriazole activa-
water molecules were taken into account, a dielectric tion, 10-fold excess and a coupling time of 1 h on the 2-
constant of 1 was used for all calculations. To avoid chlorotritylchloride resin. The peptides were cleaved with
splitting dipoles, nonbonded interactions were calculated trifluoroacetic acid/thioanisole/thiocresol (20:1:1) within
within a residue-based cutoff of 10 Å. The solvent atoms 3 h, collected by centrifugation and lyophilized from
were first relaxed by 1000 steps of steepest descent energy water.
minimization, the solute being held fixed. The solvated They were then purified by reversed-phase HPLC
complex was then fully minimized by 1000 steps of steep- (Merck-Hitachi, Darmstadt, Germany) on a nucleosil 5
est descent, followed by a conjugate gradient minimiza- µM/C18 column (125 × 3 mm) at a flow rate of 600 µl/min.
tion procedure until the rms gradient of the potential The absorbance was measured at 220 nm. The solvent
energy was less than 0.25 kcal mol−1 Å−1. The minimized system used consisted of 0.1% trifluoroacetic acid in
coordinates were thereafter used as a starting point for an water (A) and 0.1% trifluoroacetic acid in acetonitrile (B).
MD simulation at constant temperature. Initial velocities A linear gradient from 10 to 60% B in 30 min was ap-
were taken from a Maxwellian distribution at 50 K and plied. The peptides were purified to homogeneity by a
an integration step of 2 fs was used. The system was second HPLC on a versapack 10 µm C18 column (300 ×
progressively heated from 50 to 297 K during the first 7.8 mm) at a flow rate of 2 ml/min with the same buffer
picosecond, the temperature being held at 297 K for the system, and a linear gradient from 0 to 40% B in 35 min
rest of the simulation by coupling the system to a heat followed by a 40–60% B linear gradient for 20 min. Fur-
bath [46] using a temperature coupling constant of 0.05 thermore, the peptides were analyzed by ion spray mass
ps. All bond lengths were constrained to their equilibrium spectrometry on a triple-quadrupole mass spectrometer
values using the SHAKE algorithm [47] with a bond API III with a mass range of m/z = 10–2400 equipped
length tolerance of 2.5 × 10−4 Å. Coordinates, energies and with an ion spray interface (Sciex, Thornhill, ON,
velocities were collected and saved every 250 steps (0.5 ps) Canada), and quantified by amino acid analysis using a
for 200 ps. The analyses of MD trajectories were achieved 6300 amino acid analyser (Beckman, Palo Alto, CA,
using in-house routines and the CARNAL module of U.S.A.).
AMBER [41].
Peptide binding assay
Calculation of electrostatic interaction energies The quantitative assay used has been described previ-
Electrostatic free energies were computed by solving ously [29]. Briefly, RMA-S transfectants expressing
the linear form of the Poisson–Boltzmann equation using B*2705 or B*2703 were used. These are murine cells with
the finite-difference method [48,49] of the DelPhi program impaired TAP-mediated peptide transport and low sur-
[50,51]. Peptides, MHC proteins and MHC–peptide com- face expression of (empty) class I MHC molecules, which
plexes were centered in three-dimensional boxes with can be induced at 26 °C [52] and stabilized at the cell
resolutions of 2.0, 1.20 and 1.10 grid points per Å, re- surface through the binding of exogenously added pep-
spectively. For each calculation, 90% of the box was filled tides. These cells were incubated at 26 °C for 24 h. After
with the corresponding molecule. Atomic radii and this, they were incubated for 1 h at 26 °C with 10−4–10−9
charges were taken from the AMBER 4.0 united-atom M peptides, transferred to 37 °C and collected for flow
466
B
C
P4 P6 P8 P9
P2
P1 P5
A P7
P3 F
E
D
Fig. 1. Orientation of a canonical nonapeptide (ball-and-stick model) in the binding groove of HLA-B27 (cyan ribbons) [32]. Peptide positions
are labeled at the Cα atoms from 1 (P1) to 9 (P9). MHC specificity pockets (A to F) are displayed according to the usual nomenclature [72]. The
figure has been obtained with the MOLSCRIPT [73] and Raster3D [74] programs.
microcytometry (FMC) analysis with the ME1 mAb histone peptide was also studied, in order to investigate
(IgG1, specific for HLA-B27, B7 and B22) [53] after 4 h the influence of pocket B–P2 interactions that may also
for B*2705, or after 2 h for B*2703. The determinant participate in the peptide discrimination [28].
recognized by ME1 is not affected by bound peptides or
by HLA-B27 polymorphism (data not shown). The bind- Dynamical properties of MHC–peptide complexes
ing of a given peptide was measured as its C50. This is its Monitoring instantaneous rms deviations (rmsd’s) of
molar concentration at 50% of the fluorescence obtained protein atoms from the starting structure is usually per-
with that peptide at 10−4 M. Peptides with C50 ≤ 5 µM formed to ascertain the reliability of MD simulations [54].
were considered to bind with high affinity, as these were For both alleles complexed to peptides 1–3, similar rmsd
the values obtained for most of the natural B27-bound values were observed (about 1.7 Å for backbone atoms;
ligands. C50 values between 5 and 50 µM were considered
to reflect intermediate affinity. C50 ≥ 50 µM indicated low
TABLE 1
affinity. Peptides having C50>100 µM were assumed not
RELATIVE BINDING OF THREE NONAPEPTIDES TO TWO
to bind. The binding of peptide analogues was measured HLA-B27 SUBTYPES
as the concentration of the peptide analogue required to
Peptide Sequence Relative bindinga
obtain the fluorescence value at the C50 of the unchanged
peptide. This was designated as EC50. Relative binding B*2703 B*2705
was expressed as the ratio between the EC50 of the pep- 1 RRYQKSTELb 1 (2×10−6) 1 (2×10−6)
tide analogue and the C50 of the corresponding unchanged 2 ARYQKSTEL 1.5 2
peptide. 3 RQYQKSTEL >>100 10
a
Data are expressed as the molar excess of peptide analogue, relative
Results and Discussion to the wild-type peptide 1, at which HLA-B27 fluorescence (meas-
ured by FMC analysis with an anti-B27 monoclonal antibody) on
A naturally bound nonapeptide (1) from the human RMA-S cells was half the maximum obtained with peptide 1. The
histone H3 protein was taken as reference for its equal molar concentration of peptide 1 at 50% maximum fluorescence
(C50) is given in parentheses.
binding to both subtypes (Table 1). The Ala1 analogue (2) b
Human histone H3 peptide: a self-peptide, naturally bound to HLA-
was chosen for its unexpected high affinity for both sub- B*2705 [20] and to B*2703 [23]. Dominant anchor residues are dis-
types [28,35]. Finally, the Gln2 analogue 3 of the human played in boldface.
467
data not shown), indicating that protein distortion upon protein cmass (Table 2). An examination of d2 and d3
ligand binding cannot account for the different binding intermolecular distances for the weak binder 3 clearly
affinities of these peptides. Stable rmsd values (1–1.5 Å) shows that MHC-anchoring amino acids only are pro-
were also observed for bound peptides. Interestingly, they gressively expelled from the binding groove. The dissocia-
remain in the same range as that observed for different tion is more significant when compound 3 is complexed
peptides co-crystallized with the same MHC host protein to HLA-B*2703, which relates well with the observed
[55,56]. One exception concerns the weakest binder (pep- binding data (Table 1). The TcR-binding region (P4–P8)
tide 3 to HLA-B*2703), for which larger distortions (up is similarly bulging out (at least quantitatively) of the
to 2.5 Å) were observed and still increasing after 200 ps binding cleft for all the six studied complexes (d3 dis-
simulation. tance, Table 2). An even more precise analysis has been
To follow a possible dissociation of peptides 1–3 from done by evaluating the inter-cmass distance between
the two HLA-B27 alleles, the distance between ligand and individual MHC anchor residues and their complemen-
protein center of mass (cmass) was monitored. For bind- tary pocket (A, B, D and F; d4–d7 distances, Table 2).
ing peptides (1, 2), whatever the B27 subtype, this inter- Surprisingly, the repulsion noticed for peptide 3 in com-
molecular distance increases during the warm-up phase plex with both alleles seems to be located at the
from 8 to 8.5 Å and remains constant for the rest of the P9–pocket F interaction level (d7 = 7.3 Å), far from where
simulation (Fig. 2). The weak binder (peptide 3) exhibits protein and peptide single-point mutations occur. Interest-
a slight but continuous increase of the intermolecular ingly, the critical d5 distance, illustrating the strength of
distance, suggesting a partial dissociation of the ligand the most important interaction between the invariant Arg2
from the binding groove. This phenomenon was signifi- and pocket B, is higher (5.1 ± 0.4 Å) for the less stable
cantly enhanced for the less stable complex (3a: peptide complex (3a) than for other pairs (Table 2). The different
3 in complex with HLA-B*2703). However, localization d4 distances reported here, especially for peptides 1 and
of the dissociating peptide amino acids is not possible 3 and peptide 2, are related to the size of the correspon-
with this analysis. For example, TcR-binding residues ding P1 side chain (Arg versus Ala). It indicates that the
may bulge even more out of the peptide binding site and Arg1 side chain is pointing away from its binding subsite
induce similar shifts in the intermolecular distance be- (pocket A) and therefore induces higher d4 inter-cmass
tween center of masses. distances. However, for a given P1 side chain, higher d4
Therefore, this analysis was extended by computing the distances are always observed for HLA-B*2703. This
cmass of bound peptide substructures (MHC anchors: P1, indicates that the Tyr59→His mutation found in the latter
P2, P3, P9; TcR anchors: P4, P5, P6, P7, P8) for each allele is detrimental for a stable and strong binding of P1
MD conformation and the distance relating it to the side chains to pocket A of the protein. The highest stan-
1a, 1b
10.0
2a, 2b
3a, 3b
9.5
9.0
Distance, Å
8.5
8.0
7.5
7.0
0 50 100 150 200
Time, ps
Fig. 2. Time course of the distance (in Å) between the center of mass of peptides 1–3 and that of the host HLA-B27 subtype (a: B*2703; b:
B*2705).
468
2.0
1a, 1b
1.8 2a, 2b
3a, 3b
1.6
1.4
rmsf, Å
1.2
1.0
0.8
0.6
P1 P2 P3 P4 P5 P6 P7 P8 P9
Pn
Fig. 3. Rms atomic fluctuations of peptides 1–3 when bound to an HLA-B27 protein (a: B*2703; b: B*2705). Pn represents the peptide position
(from 1 to 9).
dard deviations are found for the P3–pocket D interac- HLA-B*2705 protein [38,57]. This positive effect probably
tion (d6, Table 2). The 0.6 Å variations, observed in such results from two correlated components: (i) the existence
nonbonded distances, correspond to the alternative estab- of additional contacts to pocket D, a pure enthalpic ef-
lishment of strong and weak hydrophobic contacts, which fect; and (ii) a reduced flexibility of the MHC-bound P3
may be explained by the topology of the binding groove. side chain, a favorable entropic effect.
Pocket D is a hydrophobic subsite open to the central
part of the binding cleft, and partially filled by hydro- Atomic fluctuations
phobic side chains [20]. The significantly higher variance Atomic fluctuations of MHC-bound peptides were com-
of the d6 distance (Table 2) suggests that this interaction puted from mean conformations, time-averaged over the
is the most flexible one and that different local conforma- last 50 ps (Fig. 3). As expected, MHC anchors are much
tions at P3 are compatible with a good occupancy of less flexible than the TcR-binding middle part. If atomic
pocket D. Retrospectively, it explains why the P3–pocket mobility of the bound ligand is considered, it is not poss-
D interaction may be important for an optimal peptide ible to depict real differences in the binding of peptides 1
binding to HLA-B*2705. Bulky hydrophobic nonnatural and 2 to the two subtypes. However, the C-terminal an-
side chains (α- and β-naphthylalanine, cyclohexylalanine) chor residue clearly tends to be more flexible when the
have been shown to significantly enhance binding to the corresponding ligand does not strongly bind to the B27
TABLE 2
DISTANCE BETWEEN PROTEIN AND PEPTIDE CENTER OF MASSES
Distance (Å) Peptide
1a 1b 2a 2b 3a 3b
d1 08.2 ± 0.3 08.5 ± 0.3 08.3 ± 0.3 08.2 ± 0.4 09.3 ± 0.9 09.1 ± 0.7
d2 05.9 ± 0.3 05.9 ± 0.3 05.5 ± 0.3 05.6 ± 0.4 07.3 ± 0.5 06.6 ± 0.5
d3 11.5 ± 0.4 12.1 ± 0.5 12.3 ± 0.5 10.7 ± 0.5 12.0 ± 0.6 12.3 ± 0.6
d4 03.6 ± 0.3 02.9 ± 0.4 02.3 ± 0.3 01.5 ± 0.5 03.4 ± 0.4 02.8 ± 0.3
d5 04.7 ± 0.2 04.7 ± 0.3 04.7 ± 0.3 04.4 ± 0.3 05.1 ± 0.4 04.7 ± 0.3
d6 04.9 ± 0.6 04.8 ± 0.5 05.3 ± 0.5 05.0 ± 0.7 04.6 ± 0.5 05.2 ± 0.6
d7 02.5 ± 0.4 02.6 ± 0.3 02.9 ± 0.3 03.4 ± 0.4 07.3 ± 0.6 04.8 ± 0.5
d1: protein–peptide; d2: protein–MHC anchors (P1–P3, P9); d3: protein–TcR anchors (P4–P8); d4: pocket A–P1; d5: pocket B–P2; d6: pocket
D–P3; d7: pocket F–P9.
469
2.0
1a, 1b
2a, 2b
3a, 3b
1.5
Accessible / Buried
1.0
0.5
0.0
P1 P2 P3 P4 P5 P6 P7 P8 P9
Pn
Fig. 4. Ratio of accessible to buried surface area for relaxed MD time-averaged conformations. Surface areas were calculated with the MS program
[75] using a 1.4 Å probe radius. High ratios were truncated to a value of 2.0. Pn represents the peptide position (from 1 to 9).
subtype. The highest flexibilities are observed for the weakens the interactions to MHC pocket B that has been
weakest binder (peptide 3 to B*2703), especially at the designed to accommodate an arginine side chain [32].
important anchoring positions (P2, P3 and P9). It is logi- However, the P2 amino acid is more flexible when the
cal to find that the mutation at P2 (for peptide 3) corresponding peptide is complexed to HLA-B*2703
30
>50%
25-50%
25
H-bonds Number
20
15
10
0
1a 1b 2a 2b 3a 3b
Complex
Fig. 5. MHC–peptide H-bonding frequency for peptides 1–3 in complex with HLA-B27 subtype (a:B*2703; b: B*2705). H-bonds have been
geometrically defined by an acceptor (A) to donor (D) distance less than 3.25 Å and a D-H..A angle greater than 120°. Interactions were
statistically monitored throughout the simulations for a total of 400 conformations per MHC–peptide complex. Two categories of H-bonds were
defined: strong ones with frequencies higher than 50% and medium ones with occurrences between 25 and 50%.
470
Glu45
Thr24
Tyr59 His59
His9
Glu63
P2
P1
Tyr7
Tyr171 Tyr99
Trp167
Met5 Tyr159
Fig. 6. Crystal structure of HLA-B*2705 [32]. The view is focused on MHC pocket A (Met5, Tyr7, Tyr59, Glu63, Tyr159, Trp167, Tyr171) and pocket
B (His9, Thr24, Glu45, Tyr99) side chains interacting via H-bonds (direct H-bonds: green broken lines; water-mediated H-bonds: yellow broken lines)
with the P1–P2 positions of a bound peptide. The following color coding has been used: carbon, white (protein) or orange (peptide); nitrogen,
blue; oxygen, red; sulfur, yellow. Bound water molecules are shown as cyan balls. Arrows indicate the direction of the H-bonds (from the donor
to the acceptor). HLA-B*2703 was obtained by mutating Tyr59 into His (SYBYL Biopolymer module) [43]. The side-chain χ2 dihedral was just
modified here in order to bring the Nε atom as close as possible to the bound water molecule. However, whatever the rotamer chosen, a direct
H-bond to a water molecule is not possible. The interatomic distance between the peptide N-terminus and Tyr59 (OH) or His59 (Nε2) atoms is 4.31
and 5.35 Å, respectively. Figures 6–8 have been obtained by using the rendering program Raster 3D [74].
(compare 3a and 3b, Fig. 3). Again, the most striking ible and buried surface areas of each HLA-bound peptide
differences are not observed at the variable amino acids residue (Fig. 4). Only position 9 of peptide 3 in complex
of the peptides (P1, P2) but at the C-terminal anchor with B*2703 was much more accessible than the others.
(P9), a feature already noticed for other MHC–peptide Otherwise, the main anchor P2 was similarly buried what-
complexes [9]. One may hypothesize that the N-terminal ever the peptide and the host HLA protein. This means
tripeptide (P1-P2-P3) determines the stability of peptide– that a partial dissociation was only observed for one
MHC interactions over the whole length of the binding position (P9) in one complex (3a) and that the previously
groove by controlling the conformational space accessible reported higher flexibility of Gln2 for the same peptide–
to the bulging middle part and, consequently, the binding MHC complex did not correspond with a release of the
capacity of the following C-terminus. However, atomic P2 side chain from pocket B. It may however influence
flexibilities of the P1–P3 and P4–P8 parts are not interre- the quality and frequency of hydrogen bonds between the
lated. It is also possible that these differences are related Gln2 side chain and pocket B of both B27 alleles. The
to the short time scales (200 ps) used for simulating the influence of secondary anchor positions is more difficult
complexes and that much longer simulations are needed to ascertain. P3 is similarly buried for all MHC–peptide
to see significant molecular differences at positions P1 complexes. P6 (Ser) and P7 (Thr) positions are probably
and P2 of the peptide ligand. Nanosecond MD simula- accessory anchor positions that marginally bind, in some
tions of macromolecules are nowadays feasible [58,59], conformations, to the central part of the peptide binding
but still remain unrealistic as a structure–activity relation- groove (pockets C/E). This observation is not incompat-
ship tool for comparing a series of ligands in their pro- ible with the high atomic fluctuations of P6-P7 amino
tein-bound state. acids (Fig. 3), as their side chains are directed towards the
binding groove but without reaching its floor. P4 (Gln),
Accessible versus buried surface areas P5 (Lys) and P8 (Glu) residues are potential candidates
Whether peptide flexibility correlates with dissociation for TcR recognition because of their concomitant atomic
from the binding cleft was addressed by looking at access- flexibility and surface accessibility.
471
Glu63 Glu45
His59 Thr24
P2
His9
Tyr7
P1
Tyr99
Trp167 Tyr159
Tyr171
Met5
Fig. 7. MD model of complex 3a, focused on MHC pockets A–B (see the legend to Fig. 6). A mean conformation was averaged from the last 100
conformers and submitted to 500 steps of steepest descent, followed by 1500 steps of conjugate-gradient energy relaxation.
Qualitative and quantitative analysis of peptide–MHC H- clear distinction between peptides 1 and 2 and the Gln2
bonds analogue (peptide 3, Fig. 5). The stability of protein–
Reporting the number of MHC–peptide H-bonds as peptide H-bonds was assessed by computing the frequency
well as their frequencies during the simulation allows a of occurrence of the interaction throughout the MD tra-
Glu45
Tyr59
Glu63
Thr24
His9
P2
P1
Tyr7
Glu163
Tyr171 Tyr99
Trp167
Met5 Tyr159
Fig. 8. MD model of complex 3b, focused on MHC pockets A–B (see the legend to Fig. 6). The mean conformation was obtained as described
in Fig. 7.
472
TABLE 3 for complexes 1a, 1b, 2a and 2b, consistent with the simi-
MHC–PEPTIDE H-BONDS WITH A FREQUENCY HIGHER lar binding efficiencies of peptides 1 and 2 to both sub-
THAN 50%
types. On the other hand, a reduced number of medium
Pn atom HLA-B27 1a 1b 2a 2b 3a 3b and/or strong H-bonds (peptide 3 in complex with the
P1 N Tyr7 (OH) 1 1 1 two alleles) correlates with the decreased binding of this
59
His (NE2) 1 1 1 peptide. The weakest binding potency (peptide 3 to
B*2703) could effectively be qualitatively and quantitat-
Glu45 (OE2) 3
ively related to the distribution of intermolecular H-
Glu63 (OE1) 1 1 1
bonds. Not only the number but also the quality of the
Glu63 (OE2) 1 1 MHC–ligand interactions correlates well with the binding
Glu163 (OE2) 3 potency.
NE Glu 163
(OE2) 1 × × 1 To accurately localize the interactions that may explain
NH2 Glu63 (OE1) × × 3 peptide specificity variations, all H-bonds with frequencies
higher than 50% were identified for the six complexes
Glu63 (OE2) × × 3
(Table 3). The first noticeable difference between the two
O Tyr159 (OH) 1 1 1 1
HLA-B27 alleles is the H-bonding network between the
P2 N 63
Glu (OE1) 1 1 MHC residues involved in binding to the peptide P1
Glu63 (OE2) 1 1 position. In HLA-B*2705, two amino acid side chains are
NE Glu45 (OE2) 3 × × H-bonded to the peptide N-terminus (Tyr7/Tyr171 in the
Glu63 (OE1) 3 × × crystal structure, Tyr7/Glu63 in the MD models) (Table 4,
× × × ×
Figs. 6–8). Both side chains are fixed by a subtle water-
OE1 99
Tyr (OH) 3
relayed H-bond network involving proximal MHC side
NE2 His9 (NE2) × × × × 3
chains (Tyr59, Glu45, Tyr171). Tyr59 is directly bound to
Glu45 (OE2) × × × × 3 Tyr171, and indirectly to Tyr7, Glu45 and Glu63. The single
NH1 His9 (NE2) 1 1 1 × × point mutation occurring for HLA-B*2703 (Tyr59→His)
24
Thr (OG1) 3 × × perturbs this network. The bound water molecule disap-
NH2 24
Thr (OG1) 1 1 1 × × pears and the peptide N-terminus binds to His59 and no
Glu45 (OE1) 1 1 1 × ×
more to Tyr7 (Table 3, Fig. 7). The consequence on the
H-bond balance is a loss of one direct MHC–MHC inter-
Glu45 (OE2) 1 1 1 × ×
action (His59 cannot interact with Tyr171) and five water-
Glu63 (OE1) 3 × × mediated interactions for complex 3a (Fig. 7). The result-
P3 N 99
Tyr (OH) 1 1 1 1 ing conformational change may be well accommodated as
P6 OG Ala69 (O) 1 far as P2 is strongly bound to pocket B (His9, Thr24,
Thr73 (OG1) 1 Glu45) and the resulting H-bonds are strong enough to
P8 O Trp147 (NE1) 1 1 1
maintain the peptide in the binding groove (P2=Arg). If
P2 is not an arginine (peptide 3), the resulting interaction
OE1 Lys 146
(OE1) 1
to pocket B (Thr24 and Glu45 notably) is much weaker
P9 N Asp77 (OD1) 1 1 1 1 1 and the conformational rearrangement at P1 is important
OXT 84
Tyr (OH) 1 (see the three new H-bonds for the P1 position in com-
Thr143 (OG1) 1 1 1 plex 3a, Fig. 7). The Arg to Gln change at the P2 posi-
Lys 146
(NZ) 1 1 1 tion of the bound peptide is better tolerated by HLA-
B*2705 (complex 3b, Fig. 8) as the Tyr59 side chain is still
Empty boxes indicate interactions that are common to at least two
able to fix the position of Tyr7. During the MD simula-
complexes, whereas filled boxes represent unique MHC–peptide hy-
drogen bonds. The absence of a specific side chain is featured by a tion, the N-terminal Cα-N bond of the bound peptide has
cross. rotated to gain a new H-bond to Glu63. However, it is
still bound to Tyr7 as in the reference structure. Import-
jectory (400 conformations). A frequency higher than 50% antly, the Gln2 side chain is bound to Glu45 and Tyr99,
was chosen to characterize strong H-bonds. Medium in- thus providing additional interactions to pocket B when
teractions were assigned a frequency between 25 and 50%. compared to complex 3a (Fig. 8). The quality of the
About 25 H-bonds have been identified for peptides 1 interaction between Gln2 and pocket B is, however, much
and 2 in complex with B*2703 and B*2705 while 50% less inferior to that observed for peptide analogues 1 and 2
could be found for the Gln2 analogue with the two sub- bearing an optimal Arg residue (Table 4), thus explaining
types (Fig. 5). The distribution of strong and medium H- the reduced binding affinity of peptide 3 for HLA-
bonds correlates well with the binding potency of the B*2705.
peptide. A similar number of strong H-bonds were found For the set of peptides studied here, the advantage of
473
2.0
2a
2b
4a
4b
1.5
Accessible/buried
1.0
0.5
0.0
P1 P2 P3 P4 P5 P6 P7 P8 P9
Pn
Fig. 9. Accessible versus buried surface areas of peptides 2 and 4 in complex with B*2703 (a) and B*2705 (b) alleles (see the legend to Fig. 4).
Arg over Ala at P1 could be quantified by the gain of However, the present model cannot fully explain recent
two water accessible salt bridges to Glu63/Glu163 (Table 3). data, indicating that basic residues are overrepresented at
However, this does not correspond to a higher binding the P1 position of B*2703-bound natural ligands [23].
affinity of the Arg analogue when compared to the Ala1 From a purely statistical point of view, various rotamers
peptide. An Ala side chain is much easier to desolvate of basic P1 side chains could develop a salt bridge with at
and optimally interacts with conserved apolar residues of least three negatively charged amino acids located at the
pocket A (Met5, Trp167), thus explaining a rather similar rim of pocket A (Glu58, Glu63, Glu163), and thus stabilize
binding affinity of peptides 1 and 2 to both subtypes. the MHC–peptide complex.
30
> 50%
25- 50%
25
20
H-Bonds
15
10
0
2a 2b 4a 4b
Complex
Fig. 10. Intermolecular hydrogen bonds for peptides 2 and 4 in complex with B*2703 (a) and B*2705 (b) alleles (see the legend to Fig. 5).
474
TABLE 4
MHC–PEPTIDE INTERACTION ENERGIES CALCULATED FROM THE LINEAR POISSON–BOLTZMANN EQUATION AND
AMBER FORCE-FIELD CALCULATIONS
Peptide ∆G0coul a
∆G0reac b
∆G0elec c
∆Helec d
∆Hvdw e
∆Gtot f
∆Htot g
1a −499 487 −12 −87 −90 −102 −177

1b −542 498 −44 −79 −97 −141 −176
2a −359 340 −19 −72 −77 −96
0− −149
2b −389 335 −54 −75 −80 −134 −155
3a −306 334 −28 −44 −68 −40
0− −112
3b −371 380 −09 −62 −67 −58
0− −129
a
∆G0coul: Coulombic component of MHC–peptide electrostatic interaction energy (charge–charge, charge–dipole, dipole–dipole interactions). ∆Gcoul 0
= ∆G0coul(P–L) − ∆G0coul(P) − ∆G0coul(L) [50], where P–L describes the protein–ligand complex, P the protein and L the ligand.
b
∆G0reac: corrected self-reaction field component of MHC–peptide electrostatic interaction energies (energy required to transfer a molecule from
a continuum dielectric (vacuum) to another (water). ∆G0reac = ∆G0reac(P–L) − ∆G0reac(P) − ∆G0reac(L). As the contribution of the protein–ligand complexes
(∆G0reac(P–L)) and of the isolated protein (∆G0reac(P)) could be omitted from the calculation without affecting the reliability of the results [61], this
component corresponds here to the free energy of peptide desolvation (−∆G0reac(L)).
c
∆G0elec: total electrostatic interaction energy (∆G0coul + ∆G0reac).
d
∆Helec: AMBER electrostatic interaction energy (ε = 4rij).
e
∆Hvdw: AMBER van der Waals interaction energy. ∆Hvdw = A/r12 − B/r6, where r is the distance between atom pairs and A and B are atom-type-
dependent parameters.
f
∆Gtot: total interaction energy (∆G0elec + ∆Hvdw).
g
DHtot: total AMBER interaction enthalpy (∆Helec + ∆Hvdw).
MHC–peptide interaction energies respect to that observed for the Arg1 analogue. It may be
Interaction energies were extrapolated for all six ener- noticed that the free electrostatic interaction energies
gy-minimized time-averaged conformations (Table 4) by (∆G0elec, Table 4) computed by the continuum electrostatics
summing up the van der Waals nonbonded interaction method were also in rather good qualitative agreement
energy (calculated with the AMBER 4.0 force field) and with the binding data reported in Table 1. Hence, the
the electrostatic component (calculated by solving the three peptides are highly polar and interact mainly via H-
linear form of the Poisson–Boltzmann equation), as re- bonds and salt bridges.
cently described [60]. As both ligands and protein struc- For an even more realistic ranking of highly polar li-
tures are very similar for all complexes, distortion ener- gands than those presented here, free energy perturbation
gies as well as translational/rotational entropy losses upon [62] is probably the method of choice. Unfortunately, the
binding were neglected here. Moreover, the self-reaction enormous amount of CPU time that would be necessary
field energy component of the electrostatic interaction for this computation precludes its systematic use in fast
energy was limited to the contribution of the isolated screening of a set of congeneric molecules. Synthesis and
peptide (free energy of desolvation) and calculated from in vitro binding assays in this case provided a faster and
the bound-peptide coordinates extracted from the MHC– experimentally determined answer.
peptide binary complexes. It has recently been shown that MD simulation of MHC–peptide complexes could
neglecting the protein contribution to the self-reaction relate observed binding potencies and allele specificity to
field energy is indeed possible and does not alter the simple molecular criteria (inter-cmass distances, atomic
reliability of the obtained results [61]. fluctuations, accessible surface areas, distribution and
Our computational protocol is able to properly rank
the binding of the three peptides 1–3 to both MHC al- TABLE 5
leles. Peptide 3 clearly interacts much weaker than the INFLUENCE OF A P1 β-AMINO ACID ON THE HLA-B27
other two peptides 1 and 2, whatever the MHC allele. SUBTYPE SELECTIVITY OF A MODIFIED HLA-B27
The weakest interaction energy was observed for binding LIGAND
of 3 to B*2703, and is thus in agreement with binding Peptide Sequence EC50 (µM)a
data (Table 1). Force-field interaction enthalpies (calcu- number
B*2703 B*2705
lated by summing up both AMBER van der Waals and
electrostatic components, using a dielectric permittivity of (P1-RYQKSTEL)
2 P1=Ala 3.0 04.0
4rij) were much less related to the observed binding data,
4 P1=Balb 7.5 20
as peptide 2 was always disfavoured with regard to pep-
tide 1 (Table 4). Notably, taking into account the peptide
a
Concentration of the peptide (in µM) at which HLA-B27 fluor-
escence (measured by FMC analysis with an anti-B27 monoclonal
desolvation energy by the continuum eletrostatics method antibody) on RMA-S cells was half the maximum obtained with the
permits to compensate for the weakest Coulombic interac- wild-type peptide (peptide 1, Table 1).
tions provided by peptide 2 (P1=Ala) to both alleles, with b
Bal: β-alanine (H2N-CH2-CH2-CO).
475
Glu45
Thr80
Asp77
Leu95 Leu81
Glu63 Thr24 Tyr84
His59 His9
Gln4 Lys5
Leu9
Arg2
Ser6
Glu8
Bal1 Tyr3 Thr7
Tyr7
Asp116
Tyr123 Thr143
Tyr171 Trp167 Glu163
Lys146
Tyr99
Tyr159 His114
Trp147
Leu160 Leu156 Val152
Fig. 11. Energy-minimized time-averaged MD model of complex 4a. The MHC protein backbone is displayed as a solid cyan tube, with peptide-inter-
acting side chains. The bound peptide 4 is represented by sticks. The following color coding has been used: carbon, white (protein) or green (peptide);
nitrogen, blue; oxygen, red; sulfur, yellow. Bound water molecules are shown as cyan balls. Yellow broken lines indicate MHC–peptide H-bonds.
location of intermolecular H-bonds). A single point muta- analyses [28], this minor change strengthens even more
tion in the HLA binding groove is sufficient to break an the binding role of the dominant anchor P2 side chain
H-bond network in the vicinity of the peptide N-terminus. (Arg) for one allele (HLA-B*2703) and explains why
As previously suggested on the basis of peptide binding changing P2 to Gln has more detrimental effects in pep-
Glu45
Thr80
Tyr59 Asp77
Thr24
Leu81
Glu63 Tyr84
Gln4
Lys5 Leu95 Glu8
Ser6
Thr7 Leu9
Arg2 His9
Bal1 Tyr3 Asp116

Tyr7 Ty123
Trp167
Ty171 Thr143
Tyr99 Lys146
Glu163 Trp147
His114
Tyr159 Val152
Leu156
Leu160
Fig. 12. Energy-minimized time-averaged MD model of complex 4b (see the legend to Fig. 11).
476
tide binding for HLA-B*2703 than for HLA-B*2705, 9 and 10). Interestingly, the weak binding of the β-Ala
where compensatory stabilization of the MHC–peptide peptide to B*2705 could also be related to a partial disso-
complex is still possible by H-bonded MHC side chains. ciation of the C-terminus from its complementary pocket
Interestingly, the most spectacular consequence of pro- F (Fig. 9), far away from the peptide mutation site. The
tein/peptide variability affects an area far away (10 Å) present data, in agreement with previous MD simulations
from the location of the point mutations. It concerns the of different MHC–peptide complexes [9], suggest that the
stability of the interaction between the peptidic C-ter- expulsion of the C-terminus from pocket F could be the
minal residue and its complementary pocket F, which has very first event in the dissociation of weak binding pep-
recently been shown to play a decisive role in linking tides from class I MHC binding grooves. The modified P1
particular B27 alleles to spondyloarthropathies [24,26]. position is, however, significantly more buried when the
host protein is the B*2703 allele (Fig. 9). A qualitative
Protein-based design and quantitative analysis of intermolecular hydrogen
Relating the structure of B27 subtypes to the sequence bonds also supports the reported binding data. A total of
of their naturally bound peptides is a crucial step in 15 H-bonds could be depicted for complex 4b (peptide 4
identifying potential immunodominant epitopes that may in complex with B*2705), whereas 26 interactions have
discriminate alleles and confer susceptibility or resistance been found for complex 4a (peptide 4 in complex with
to autoimmune diseases. One striking feature concerns the B*2703, Fig. 10). However, this analysis was unable to
single point mutation (Tyr59His) distinguishing HLA- explain the reduced affinity of the β-Ala compound for
B*2705 from HLA-B*2703, which is unique among HLA B*2703, when compared to that of the natural Ala ana-
proteins. It is believed that B*2703 selects a subset of the logue 2 (Table 4). The slight differences seen in the epi-
peptides presented by HLA-B*2705 [34]. Recent studies tope stabilization assay are certainly too subtle for the
have identified some peptides that are naturally presented short MD runs reported here. They probably result from:
by both subtypes, and at least one natural B*2705 ligand (i) the absence of a side chain at position P1 of ligand 4;
(the undecamer RRYLENGKETL) is not presented by and (ii) a weaker binding contribution of the bulging
B*2703 [23,63]. The only difference between both alleles P4–P8 part, for which higher atomic fluctuations (data
concerns the position 59 located in pocket A which inter- not shown) and less nonbonded contacts (see the high
acts with the N-terminal amino acid of the bound peptide solvent accessibility of the P5 and P8 residues for ligand
(Fig. 6). As pocket A is slightly wider for HLA-B*2703, 4, Fig. 9) have been noticed. Energy-minimized time-
extending the peptide backbone towards His59 by replacing averaged conformations of both complexes (Figs. 11 and
the natural P1 residue by a β-amino acid should theoreti- 12) clearly depict significant differences in the MHC
cally allow a better discrimination of both alleles. This pocket A (Tyr59, Trp167, Tyr171), which deviates dramati-
structural change should be much better accommodated by cally from the starting crystal coordinates for B*2705
HLA-B*2703 (H-bond between His59 and the N-terminus only (rmsd values from all pocket A atoms of 1.5 and 2.5
of the P1 β-amino acid) than by HLA-B*2705, for which Å for B*2703 and B*2705, respectively). The major con-
a steric clash with the Tyr59 side chain may be expected. formational alterations upon Bal1 binding were observed
Starting from the self-peptide 1 (RRYQKSTEL) nat- for the Tyr59-Trp167-Tyr171 triad (rmsd values of 1.7 and
urally presented by HLA-B*2705 [20] and B*2703 [23], 2.7 Å for B*2703 and B*2705, respectively)sl. As pre-
Ala and Bal (β-alanine) were substituted for the natural dicted, the Tyr59 side chain was shifted away from the
Arg at P1 (Table 5). The Ala1 peptide analogue was here peptide N-terminus and is now interacting via a water
taken as a reference for its strong binding to both sub- molecule with the β-alanine terminal ammonium (Fig.
types. The two ligands were synthesized and tested for 12). In contrast, the β-amino acid can directly interact
their binding to B*2703 and B*2705. As expected from with the larger pocket A of B*2703 through three H-
the topology of the binding cleft, only the Bal analogue bonds to His59 (mutated position), Glu63 and Glu163 (Fig.
could discriminate between the two subtypes, with a bet- 11). Another significant difference in the binding of pep-
ter binding to HLA-B*2703 (Table 5). tide 4 to both alleles concerns the C-terminal amino acid,
To rationalize the experimental binding data, the non- which has nearly lost, upon binding to B*2705, all H-
natural ligand 4 was simulated a posteriori, in complex bonds to the polar side chains of pocket F (Tyr84, Thr143,
with both alleles, using exactly the same conditions as Lys146; compare Figs. 11 and 12). The incorporation of a
those employed for simulating the natural MHC–peptide β-amino acid at P1 has modified the above described H-
complexes (see the section Computational procedures). bond network between MHC side chains and the peptide
Using two of the previously described molecular parame- N-terminus. The bound water molecule located in pocket
ters (accessible versus buried surface area of the bound A of HLA-B*2705 (recall Fig. 6) has either disappeared
ligand, intermolecular H-bonds) as quality control of the (B*2703, Fig. 11) or has been shifted towards the extreme
complex stability, peptide 4 was indeed found to be much left end of the binding groove (B*2705, Fig. 12).
better accommodated by B*2703 than by B*2705 (Figs. More importantly, these results show that the incor-
477
poration of a β-amino acid in the peptide sequence does its application to the rationalization of peptide specificity
not abrogate binding to HLA-B27 subtypes. Peptide 4 is for closely related HLA alleles and the design of non-
one of the very first ligands for which the backbone natural ligands with increased specificity for one HLA-
modification of an anchor residue does not abolish class B27 subtype. Identifying the molecular rules, fine tuning
I MHC binding. Up to now, only a retro-inverso (NH- peptide selection by HLA alleles is a crucial step for
CO instead of CO-NH) and a reduced peptide bond better understanding the peptide–HLA interactions that
(CH2-NH instead of CO-NH) pseudopeptide analogue of may confer either susceptibility or resistance to immuno-
an HLA-A2-binding peptide have been proposed as suc- logical diseases associated with particular HLA alleles.
cessful P1 modifications [64,65]. However, a β-amino acid
at P1 presents the advantage to preserve the backbone Acknowledgments
direction of the peptide ligand and the H-bonding capac-
ity of the first peptide bond (to Glu63 and Tyr159), so that D.R. wishes to thank the computational center of the
less 3D conformational changes of the MHC binding cleft ETH Zürich for generous allocation of computer time on
are necessary to accommodate the modified ligand. The the CRAY J90 and PARAGON machines. This work was
recently described X-ray structure of an MHC–peptide– supported by the Schweizerischer Nationalfonds zur
TcR ternary complex [66] suggests that the latter feature Förderung der wissenschaftlichen Forschung (Project No.
may be of particular importance for a proper recognition 31-45504.95) and by Grant SAF 94-0891 from the Plan
of the MHC–ligand pair by a TcR. Furthermore, it opens Nacional de I+D to J.A.L.C. J.R.L. is a fellow of the
the door to the incorporation of β-amino acids at other Basque Government.
anchor positions, notably P2, P3 and P9. Potential TcR-
binding amino acids have already been replaced by vari- References
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13 Wordsworth, B.P., Lanchbury, J.S., Sakkas, L.I., Welsh, K.I.,
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17 López-Larrea, C., Sujirachato, K., Mehra, N.K., Chiewsilp, P.,
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ANEXO -4-
ANEXO -5-
ARTHRITIS & RHEUMATISM
Vol. 42, No. 9, September 1999, pp 1975–1985
© 1999, American College of Rheumatology 1975
MODULATION AT MULTIPLE ANCHOR POSITIONS OF THE

PEPTIDE SPECIFICITY OF HLA–B27 SUBTYPES DIFFERENTIALLY
ASSOCIATED WITH ANKYLOSING SPONDYLITIS
JOSÉ R. LAMAS, ALBERTO PARADELA, FERNANDO RONCAL, and JOSÉ A. LÓPEZ DE CASTRO
Objective. To investigate the rules governing pep- peptide repertoires are limited by the allowed residue
tide binding to HLA–B*2705, and to B*2704 and combinations described in this study. The differential
B*2706, which are 2 subtypes differentially associated association of B*2704 and B*2706 with spondylarthro-
with ankylosing spondylitis. pathy correlates with differences in their peptide spec-
Methods. Poly-Ala analogs carrying the HLA–B27 ificity at multiple anchor positions. However, it is now
motif Arg-2, and substitutions at anchor positions P1, possible to predict the peptide features that determine
P3, or P⍀, were used to determine a binding score for this differential binding to both subtypes.
each residue at each position. Binding was assessed in a
quantitative epitope stabilization assay, where the cell HLA class I proteins bind endogenous peptides
surface expression of HLA–B27 was measured by flow and present them at the cell surface for recognition by
cytometry as a function of peptide concentration. cytotoxic T lymphocytes. These peptides, generally rang-
Results. Peptide anchor residues contributed ad- ing in size from 8 to 12 amino acids but with a predom-
ditively to B*2705 binding. About 15% of the natural inance of nonamers and decamers, bind to the class I
B*2705 ligands used a deficient P3 or P⍀ anchor, but molecule through interactions involving the peptide
never both, indicating that detrimental anchoring at one main chain, both peptide ends, and various peptide side
of these positions is always compensated by a good chains. These interact in cavities or pockets of the
anchor at the other one. About 50% of the B*2705 peptide-binding site, which are formed by amino acid
ligands used suboptimal P1 residues. However, this was residues of the class I molecule. The structure of these
compensated with optimal P3 and/or P⍀ anchoring. pockets is modulated by HLA polymorphism, which
Peptides that were longer than decamers used good affects the size and polarity of the pockets, and this
anchor residues at the 3 positions, suggesting more determines the peptide-binding specificity of each class I
stringent binding requirements. B*2704 and B*2706
allotype (1).
differed in their residue specificity at P1, P3, and P⍀.
Typically, the peptide repertoire bound to a given
The rules derived for B*2705 also applied to the known
class I molecule shows limited diversity at some peptide
ligands of these 2 subtypes.
positions (P) (2). These so-called main anchor residues
Conclusion. The B*2705, B*2704, and B*2706
interact with the HLA molecule and have a significant
contribution to peptide affinity. However, only ⬃30% of
Supported by grant no. SAF97/0182 from the Plan Nacional
de I⫹D, grant no. PM95-002 from the Spanish Ministry of Education,
the nonamers carrying the right main anchor residues
and an institutional grant from the Fundación Ramón Areces to the will actually bind a given class I molecule (3). This is due
Centro de Biologı́a Molecular Severo Ochoa. Dr. Lamas is a fellow of to the significant influence of auxiliary anchor positions.
the Basque Government.
José R. Lamas, Alberto Paradela, José A. López de Castro, Thus, the peptide specificity of an HLA class I molecule
PhD: Consejo Superior de Investigaciones Cientı́ficas, and Univer- cannot be understood without knowing the suitability of
sidad Autónoma de Madrid, Madrid, Spain; Fernando Roncal: different amino acid residues at these auxiliary positions.
Pharmacia-Consejo Superior de Investigaciones Cientı́ficas, Centro
Nacional de Biotecnologı́a, Madrid, Spain. This is also essential for the prediction of putative
Address reprint requests to José A. López de Castro, PhD, ligands.
Centro de Biologı́a Molecular Severo Ochoa, Universidad Autónoma The peptide-binding specificity of HLA–B27 has
de Madrid, Facultad de Ciencias, Cantoblanco, 28049 Madrid, Spain.
Submitted for publication February 22, 1999; accepted in received much attention because of the strong associa-
revised form May 4, 1999. tion of this molecule with ankylosing spondylitis (AS)
1976 LAMAS ET AL
and reactive arthritis (4–6). Among other mechanisms, prediction of putative HLA–B27 ligands. Third, we
it has been proposed that an autoimmune response demonstrated that B*2704 and B*2706 differ in their
triggered by bacterial infections against a self peptide residue specificity at the 3 positions, P1, P3, and P⍀.
presented by HLA–B27 could be a primary pathogenetic This provides a novel understanding of the functional
event (7). This hypothesis is supported by recent studies differences of the 2 subtypes that are differentially
in transgenic rats (8), and by the differential association associated with AS.
of HLA–B27 subtypes with AS. Multiple HLA–B27
subtypes, including those that are predominant in whites
MATERIALS AND METHODS
(B*2705) and Asians (B*2704), are associated with this
disease (9). However, B*2709 (10) and B*2706 (11–13) Synthetic peptides. Peptides were synthesized in an
are less or not associated with AS. Thus, the peptide AMS 422 Multiple Peptide Synthesizer (Abimed, Langelfeld,
specificity of HLA–B27 and its alteration by subtype Germany) using Fmoc chemistry, and purified by reverse-
phase high-performance liquid chromatography. The correct
polymorphism becomes highly relevant to understand composition and quantitation of the peptides was determined
the differential association of closely related subtypes by amino acid analysis, as previously described (28). Peptides
with AS. Presumably, an arthritogenic peptide should be were stored as stock solutions at 4°C in water.
selectively presented by the various disease-associated Cell lines and monoclonal antibodies (mAb). RMA-S
subtypes to autoimmune T cells that are putatively is a mutant cell line of the Rauscher virus–induced murine T
involved in the pathogenesis of spondylarthropathies. cell lymphoma RBL-5 (H-2b), which has impaired transporter-
associated antigen-processing (TAP)–mediated peptide trans-
The main anchor positions of HLA–B27–bound port (29,30) and low surface expression of class I major
peptides are P2 and the C-terminal residue (P⍀). Aux- histocompatibility complex antigens that can be induced at
iliary anchor positions include P1, P3, and P7 (14,15). 26°C (31). RMA-S transfectant cells expressing B*2705,
Arg-2 is the main anchor motif for all HLA–B27 sub- B*2704, or B*2706 plus human ␤2-microglobulin have been
types, and the overwhelming majority of natural HLA– previously described (32,33). The expression levels of B*2705
and B*2706 at 26°C were the same, and that of B*2704 was
B27 ligands have this residue. C-terminal residues are ⬃30% lower. These transfectants were grown in RPMI 1640
more variable, being basic, aliphatic, and aromatic in medium containing 25 mM HEPES buffer and 10% fetal calf
B*2705, B*2703, and B*2710 (14,16–19), and aliphatic/ serum (FCS; all from Life Technologies, Paisley, UK).
aromatic with subtype variability in B*2701, B*2702, HMy2.C1R (C1R) is a human lymphoblastoid cell line that has
B*2704, B*2706, B*2707, and B*2709 (16,20–23). Se- low expression of its endogenous class I antigens. Transfec-
tants of these cells, with high expression of B*2705, were
quence studies of subtype-bound peptide repertoires cultured in Dulbecco’s modified Eagle’s medium with 7.5%
have revealed the main anchor motifs and the residues heat-inactivated FCS. The mAb ME1 (␣-HLA–B27 ⫹ B7 ⫹
occurring naturally at other peptide positions, but pro- B22) (34) was used as undiluted culture supernatant.
vide little information about the relative suitability of Peptide-binding assay. The quantitative epitope stabi-
residues at a given position. Very few studies, all limited lization assay used has been previously described (32). Briefly,
RMA-S transfectant cells were incubated at 26°C for 24 hours
to B*2705 and B*2703 (18,24–27), have addressed the in 96-well plates in RPMI 1640, 25 mM HEPES buffer, and
role of auxiliary anchor residues in determining the 10% FCS. After incubation, plates were washed with sterile
peptide specificity of HLA–B27. phosphate buffered saline, and peptides diluted in RPMI/
In this study, we have systematically explored the HEPES medium without FCS were added at a final concen-
specificity of B*2705, B*2704, and B*2706 for P1, P3, tration ranging from 10–4 to 10–9M. Cells were then incubated
for 1 hour at 26°C, transferred at 37°C, and collected for flow
and P⍀ residues using series of poly-Ala nonamer cytometric analysis after 4 hours. This time point was chosen
analogs carrying Arg-2. The following issues were ad- because there was a significant difference between the HLA–
dressed. First, we evaluated the relative suitability of B27–associated fluorescence in the presence of a peptide
residues at each of the 3 positions for binding to B*2705. ligand relative to its absence. In addition, peptides differing in
This allowed us to rank the contribution of different their dissociation rates are more easily distinguished at this
time point. For B*2704, whose peptide-induced stabilization
residues at the various positions, providing a novel after this time was too low, cells were collected after 2 hours at
understanding of the peptide specificity of the “proto- 37°C. At this time point, the difference between the HLA–
type” HLA–B27 molecule. Second, we demonstrated B27–associated fluorescence in the presence or in the absence
that binding of a given ligand to B*2705 is usually an of a suitable ligand was comparable with that for B*2705 or
additive function of the contribution of the different B*2706 at 4 hours.
HLA–B27–associated fluorescence on RMA-S trans-
anchor residues, implying that interactive effects among fectant cells was plotted as a function of peptide concentration.
amino acid residues at different peptide positions do not Binding was calculated as follows. First, a natural HLA–B27
play, in general, a significant role. This allows a reliable ligand (RRYQKSTEL) was chosen as reference, and its molar
PEPTIDE SPECIFICITY OF B*2705, B*2704, AND B*2706 1977
concentration at 50% of the maximum fluorescence obtained

with that peptide (C50) was calculated. Second, the molar
concentration of each other peptide required to obtain the
fluorescence value at the C50 of the reference peptide was
found by interpolation, and this was designated as the EC50.
EC50 values of ⱕ5 ␮M indicated high affinity, since these
values were generally obtained with natural HLA–B27 ligands.
EC50 values ⬎5 ␮M and ⬍50 ␮M were considered to reflect
intermediate affinity. EC50 values ⱖ50 ␮M indicated low
affinity. Peptides with an EC50 ⬎100 ␮M were considered not
to bind, since their affinity was below the detection limits of
this assay (32). The binding-promoting effect of substitutions
at P1, P3, or P9 was calculated as the binding of the corre-
sponding poly-Ala peptide carrying each substitution plus
Arg-2, relative to the ARAAAAAAA (ARA7) peptide. This
was expressed as the ratio between the EC50 of ARA7 and that
of each analog. All calculations were carried out with the
Origin program (MicroCal Software, Northampton, MA).
Flow cytometric analysis was carried out as previously de-
scribed (28).
Isolation and sequencing of B*2705-bound peptides.
Natural B*2705 ligands were isolated by acid extraction of
immunoaffinity-purified B*2705 from C1R transfectant cell
lysates as previously described (35). Peptides were sequenced
by quadrupole ion trap mass spectrometry using a nanospray
interface as described elsewhere (36). Assignment of residues
with the same mass (for example, I/L, Q/K) was done on the
basis of unambiguous matching with known human sequences
in the protein database.
RESULTS
Specificity of B*2705 for peptide anchor resi-
dues. The role of the P1, P2, and P⍀ anchor positions in
binding to B*2705 was analyzed with 3 series of poly-Ala
nonamers carrying Arg-2 and most of the amino acid Figure 1. Relative binding of poly-Ala peptide analogs to B*2705.
residues at P1 or P3. A more restricted series, mainly Each analog (x-axis) is represented by the 1-letter code of the amino
including basic, aliphatic, and aromatic residues, was acid residue introduced at P1, P3, or P9 into the ARAAAAAAA
(ARA7) sequence. The reference peptide RRYQKSTEL (EC50 of 3
used for P⍀ (P9). The contribution of each residue was ␮M) is designated by an asterisk. Binding of each analog was measured
measured as the ratio between the EC50 of the corre- as described in Materials and Methods and its relative binding (y-axis,
sponding poly-Ala analog and that of ARA7. This logarithmic scale) was expressed as the ratio between the EC50 of
peptide bound to B*2705 with an EC50 of 30 ␮M, ARA7 (30 ␮M) and that of the analog. Since the maximum amount of
peptide tested was 100 ␮M, relative binding lower than 0.3, which
reflecting the contribution of the peptide main chain, indicates lack of binding in this assay (EC50 ⬎100 ␮M), could not be
Arg-2, and Ala side chains. measured. For representation purposes only, a value of 0.25 was
P1. The most favored residue at position P1 was assigned to these analogs. Data are the mean of at least 2 independent
Arg, so that the RRA7 peptide bound ⬃3-fold better experiments.
than ARA7 (Figure 1). H and aromatic (Y, W, F)
residues were roughly equivalent to Ala (relative binding
0.7–1.5). A few residues, including K, G, I, and M, were residue was W (relative binding 6), followed by F and
slightly less favored than Ala (relative binding 0.6). some aliphatic (L, M) residues (relative binding 3 or
Finally, acidic (D, E), polar (S, T, N, Q), and some higher). Other aliphatic (V, I), some polar (N, S), H, and
aliphatic (L, V) residues were detrimental (relative Y residues were similar to Ala (relative binding 0.7–1.5).
binding ⱕ0.4). A number of chemically diverse residues, including T
P3. The binding efficiency of P3 poly-Ala analogs and especially R, and acidic (D, E), Q, G, and P residues
spanned a wide range (Figure 1). The most favored were detrimental.
1978 LAMAS ET AL
Table 1. Natural ligands of B*2705 and binding scores of their P1, P3, and P⍀ residues*
Ligand Binding score Ref. number Ligand Binding score Ref. number
Octamers IRLRPGGKK 4-1-----1 HIV‡

RRFFPYYV 1-1----1 35 RRWLPAGDA 1-1-----3 14
RRFTRPEH 1-1----X 14 GRLTKHTKF 4-1-----4 16,17
Nonamers KRFKEANNF 4-1-----4 This study
ARLQTALLV 3-1-----1 This study† RRFGDKLNF 1-1-----4 16
RRYQKSTEL 1-2-----1 14 KRFSFKKSF 4-1-----4 16
SRTPYHVNL 4-4-----1 This study TRYPILAGH 5-2-----X 16
RRLPIFSRL 1-1-----1 16 KRVVINKDT 4-2-----X 46‡
GRHGVFLEL 4-2-----1 This study Decamers
RRIYDLIEL 1-2-----1 44‡ KRFEETGQEL 4-1------1 This study
RRYPDAVYL 1-2-----1 45‡ NRFAGFGIGL 5-1------1 This study
GRFGSGMNM 4-1-----1 23 RRQDILDLWI 1-5------1 HIV‡
GRTFIQPNM 4-4-----1 23 GRFNGQFKTY 4-1------1 17
LRFQSSAVM 5-1-----1 23 RRYDRKQSGY 1-2------1 23
RRSKEITVR 1-3-----1 14 GRWPGSSLYY 4-1------1 23
FRYNGLIHR 3-2-----1 14 GRKTGQAPGY 4-X------1 23
KRFEGLTQR 4-1-----1 14 GRILSGVVTK 4-2------1 23
HRAQVIYTR 3-3-----1 23 RKGGNNKLIK 1-5------1 23
SRYWAIRTR 4-2-----1 14‡ LRDNIQGITK 5-5------1 This study
RRFMPYYVY 1-1-----1 16 KRWIILGLNK 4-1------1 HIV‡¶
SRVKLILEY 4-2-----1 This study RRFVNVVPTF 1-1------4 This study
RRFFPYYVY 1-1-----1 17,35 KRWQAIYKQF 4-1------4 23
RRVLVQVSY 1-2-----1 23 RRIKEIVKKH 1-2------X 16
RRISGVDRY 1-2-----1 14,16§ Undecamers
RRIKEIVKK 1-2-----1 14 RRYLENGKETL 1-2-------1 17
RRVKEVVKK 1-2-----1 14 RRMGPPVGGHR 1-1-------1 16
ARLFGIRAK 3-1-----1 14,16 WRLGSSDILNY 2-1-------1 This study
GRIDKPILK 4-2-----1 14 Dodecamers
GRFEGTSTK 4-1-----1 23 RRFVNVVPTFGK 1-1--------1 23
GRAFVTIGK 4-3-----1 HIV‡
* Except for the peptides of viral or bacterial origin, all other peptides are from endogenous proteins of the cell. Residues that were scored are shown
in boldface type in the sequences. The binding scores are rated 1–5, from high to low, on the basis of the binding efficiency of the corresponding
poly-Ala analogs, as follows: 1 ⫽ EC50 ⱕ10 ␮M; 2 ⫽ EC50 11–20 ␮M; 3 ⫽ EC50 21–40 ␮M; 4 ⫽ EC50 41–80 ␮M; 5 ⫽ EC50 ⬎80 ␮M. X ⫽ score
not determined. The reference numbers for previously reported ligands are given. Human immunodeficiency virus (HIV)–derived peptides were
obtained from the HIV Molecular Immunology Database of Los Angeles National Laboratory (http://hiv-web.lanl.gov/).
† Previously reported as an octamer (ARLQTALL) based on Edman sequencing (see ref. 16). Also found as a nonamer (ARLQTALLV) in B*2709
(see ref. 23).
‡ Peptide of viral or bacterial origin.
§ Reported as a nonamer also in B*2701 (see ref. 20) and as a decamer (RRISGVDRYY) in B*2703 (see ref. 17) and B*2710 (see ref. 19).
¶ A natural variant of this peptide with the L6M change is also known.
P9. Since P9 is usually a basic or nonpolar residue binding of 2 natural ligands of B*2705 and of a series of
among B*2705-bound peptides (Table 1), the analysis of poly-Ala analogs carrying 1 or more of the anchor
the contribution of this position to B*2705 binding was residues of each ligand. We first measured how much
restricted to these residues. Pro was also tested, since it the introduction of these anchor residues increased or
is a C-terminal motif among HLA–B73–bound peptides decreased binding relative to ARA7. We then calculated
which, as in HLA–B27, also have Arg-2 (37). As ex- the ratio between the relative binding of each ligand, or
pected, K, R, aliphatic, and Y residues were strongly analog carrying multiple anchor residues of that ligand,
favored. In contrast, F and, even more, W and Pro were and the additive value of the relative binding of poly-Ala
disfavored (Figure 1). analogs carrying single anchor residues. If the contribu-
Additive contribution of anchor residues to pep- tion of individual residues is additive, this ratio should
tide binding. In the next set of experiments, we analyzed be 1. If interactive effects among anchor residues play a
whether binding of a natural B*2705 ligand could be role, this ratio should deviate significantly from 1. Two
explained by the additive contribution of anchor resi- natural B*2705 ligands and their corresponding analogs
dues or whether this binding was a more complex were tested: RRYQKSTEL and KRYKSIVKY. The
function involving interactive effects. Thus, we tested the first one was used as the reference peptide to calculate
the EC50 for all other peptides. To account for experi-

mental error in the determination of EC50 values, ratios
between 1.5 (1.5:1) and 0.67 (1:1.5) were considered to
reflect the additive contribution of anchor residues. This
range was chosen because it was similar to the differ-
ences observed among EC50 values obtained in individ-
ual experiments when binding of a given peptide to
B*2705 was repeatedly measured.
As shown in Figure 2A, binding of most of the
peptide analogs carrying multiple anchor residues of
RRYQKSTEL (P1, P3, P7, P9) was accounted for, in 4
of 5 cases, by the additive contribution of the corre-
sponding analogs carrying single anchor residues. Simi-
larly (Figure 2B), binding of KRYKSIVKY analogs was
accounted for, in 4 of 5 cases, by the additive contribu-
tion of analogs carrying single or a smaller number of
anchor residues, with 1 case (KRAAAAAAY, ratio 0.6)
showing a small deviation from the 0.67–1.5 range.
These results indicate that, in general, the bind-
ing efficiency of a given peptide is a simple additive
function of the contribution of individual anchor resi-
dues. However, mutual effects among peptide side
chains may occasionally affect binding.
The joint contribution of the P4–P6 and P8
residues was inferred from the ratio between the relative
binding of each peptide and of its corresponding analog
carrying the P1, P2, P3, P7, and P9 residues. Thus, the
ratio between the binding of RRYQKSTEL relative to
ARA7 (10-fold) and that of the RRYAAATAL analog
(15-fold) was 0.67, indicating little contribution of P4–P6 Figure 2. Relationship between binding of peptides carrying anchor
and P8 to binding of the natural ligand (Figure 2A). In residues of A, RRYQKSTEL or B, KRYKSIVKY. Solid bars indicate
the second example (Figure 2B), the ratio between the binding relative to ARAAAAAAA (ARA7), expressed as the molar
ratio between the EC50 of ARA7 and that of each peptide (x-axis). For
binding of KRYKSIVKY relative to ARA7 (7.5-fold) substitutions that were detrimental relative to A (T7, K1), the decrease
and that of the KRYAAAVAY analog (4.3-fold) was on binding was expressed as 1 minus the relative binding. Open bars
1.74, which is slightly outside the 0.67–1.5 range, and indicate the additive value of the relative binding of poly-Ala analogs
therefore compatible with some contribution of P4–P6 carrying single substitutions at P1, P3, P7, or P9. The effect of V7 was
and P8 to binding of this natural ligand. not analyzed separately. Instead, the ARAAAAVAY analog was used.
To account for experimental error in the determination of EC50 values,
Rules determining usage of anchor residues the data indicated by the solid and open bars were considered equal
among natural HLA–B27 ligands. After observing the when their ratio was between 0.67 (1:1.5) and 1.5 (1.5:1). Ratio values
effect of individual residues at P1, P3, and P⍀ on outside this range are marked with an asterisk. Data are the mean of
binding and finding that their contribution was additive, at least 2 independent experiments.
it was possible to address the question of whether
natural B*2705 ligands used only suitable anchor resi-
dues or used detrimental ones at these 3 positions. To
examine this, we started with a database of 54 natural carrying this residue. Scores 1 and 2 were assigned to
B*2705 ligands of known sequence, including 10 re- residues whose corresponding poly-Ala analogs bound
ported for the first time here, consisting of 2 octamers, better than ARA7 (EC50 30 ␮M). Score 1 was an EC50 of
34 nonamers, 14 decamers, 3 undecamers, and 1 dodec- ⱕ10 ␮M, and score 2 was an EC50 of 11–20 ␮M. Score 3
amer (Table 1). The P1, P3, and P⍀ residue of each was assigned to residues whose effect was similar to Ala
ligand was assigned a score ranging 1–5 according to the (EC50 21–40 ␮M). Scores 4 and 5 corresponded to
binding efficiency of the corresponding poly-Ala analog residues that were less suitable than Ala at the corre-
1980 LAMAS ET AL
sponding position (score 4 EC50 41–80 ␮M; score 5 EC50 Table 2. Natural ligands of B*2704 and B*2706 and binding scores
⬎80 ␮M). of their P1, P3, and P⍀ residues*
As shown in Table 1, 44 of the 51 peptides (86%) Ligand Binding score Ref. number
scored at P⍀ had optimal anchor residues (score 1), and B*2704
only 7 (14%) had P⍀ residues similar or worse than Ala RRFFPYYV 1-1----1 36
(scores 3 and 4). Similarly, good anchor residues were RRYQKSTEL 1-1-----1 21
RRIYDLIEL 1-1-----1 44†
largely predominant at P3: 45 of 53 peptides (85%) were RRRWRRLTV 1-2-----1 44†
scored 1 (51%) or 2 (34%) at this position, and 8 GRLTKHTKF 1-1-----4 21
peptides (15%) showed P3 residues with a score equal to QRKKAYADF 3-X-----4 21
GRFNGQFKTY 1-1------3 21
or worse than that of Ala. In contrast, P1 residues with RRYLENGKETL 1-1-------1 47
a score of 1 or 2 occurred in only 24 of 54 peptides B*2706
(44%), and 26 (48%) had residues less suitable than Ala. RRLRNHMAV 1-1-----1 21
IRHNKDRKV 2-1-----1 21
This indicates that P1 is more permissive than P3 or P⍀. RRHWGGNVL 1-1-----1 21
Two additional points are worth noting. First, the RRYQKSTEL 1-1-----1 21
11-mer and 12-mer peptides had good anchors (score 1 QRKKAYADF 1-X-----2 21
RRYLENGKETL 1-1-------1 47
or 2) at the 3 positions. This suggests that the peptide
repertoire that deviates from the canonical size of class * Except for peptides of viral origin, all other peptides are from
endogenous proteins of the cell. Residues that were scored are shown
I ligands (8–10 residues) has a more stringent residue in boldface type in the sequences. Scores were calculated on the basis
specificity at P1, P3, and P⍀. Second, all of the peptides of the binding efficiency of the corresponding poly-Ala analogs as
with P⍀ residues scoring 3 or higher (5 nonamers and 2 described in the text. X ⫽ score not determined. Binding scores for
B*2704 ligands are assigned as for B*2705 (see footnote to Table 1).
decamers) had an optimal (score 1) P3 residue, irrespec- Scores for B*2706 ligands were assigned as follows: 1 ⫽ EC50 ⱕ5 ␮M;
tive of P1. Conversely, P3 anchors scoring 3 or higher, 2 ⫽ EC50 6–10 ␮M; 3 ⫽ EC50 11–20 ␮M; 4 ⫽ EC50 21–40 ␮M; 5 ⫽
which were observed in 5 nonamers and 3 decamers, EC50 ⬎40 ␮M.
† Peptide of viral origin.
always occurred with an optimal (score 1) P⍀ residue,
also irrespective of P1. These results indicate that defi-
cient anchoring at either P3 or P⍀ is always compen-
sated with an optimal anchor at the other position. increasing binding relative to Ala was smaller than the
Finally, of the 30 peptides with P1 residues effect of R1 on B*2705. In addition, G and K were
scoring 3 or higher, 18 (60%) had residues with a score slightly detrimental for binding to B*2705 (Figure 1), but
of 1 or 2 at both P3 and P⍀, and all had this in at least not for B*2704 binding. Otherwise, the pattern of P1
1 of these 2 positions. Seven peptides had detrimental residues that were equivalent to Ala (H, and aromatic
(score 4 or 5) residues at P1 and at either P3 or P⍀, but residues) or detrimental (acidic, polar, and aliphatic)
in all these cases, the other position had an optimal was similar to that for B*2705.
(score 1) residue. Thus, detrimental P1 residues require The effect of P1 substitutions on B*2706 binding
at least an optimal P3 or P⍀ anchor. (Figure 3) was different than that for B*2704, mainly in
These rules derived for B*2705 also applied to that only D was strongly detrimental, whereas E, polar
the few known natural ligands of B*2704 and B*2706 (S, T, N), and aliphatic (V, I, L, M) residues were similar
(Table 2) and are likely to apply generally to other class to Ala, and Q was favored, also in contrast to B*2705.
I proteins. These results indicate that HLA–B27 subtypes
Modulation of P1, P3, and P⍀ specificity by with an identical A pocket have nonidentical residue
B*2704 and B*2706 polymorphism. In these experi- specificities.
ments, we addressed the effect of B*2704 and B*2706 P3. B*2704 was similar to B*2705 in its accep-
polymorphism on residue selection at these 3 peptide tance of H and aliphatic (V, I, L, M) and aromatic (F, Y,
positions. ARA7 bound to B*2704 and B*2706 more W) residues at P3, and in that acidic (D, E), polar (S, T,
efficiently (EC50 10 ␮M and 9 ␮M, respectively) than to N, Q), G, and P residues were disfavored (Figure 4). A
B*2705. This probably reflects a stronger interaction of difference was that, in contrast to B*2705 (Figure 1),
Ala residues at 1 or more anchor positions. Ala-3 was no worse than bulkier nonpolar residues for
P1. The effect of the P1 residue on binding to binding to B*2704. In addition, N was less suitable than
B*2704 (Figure 3) was similar to that for B*2705, but Ala in B*2704 binding, but not in B*2705 binding.
with some differences. For instance, G rather than R was The specificity of B*2706 for P3 residues showed
the most favored residue for B*2704, but its effect on important differences in comparison with B*2704 (Fig-
This subtype was similar to B*2705 in the detrimental

effect of F, W, and P residues.
B*2706 differed from B*2704 in that F was not
detrimental relative to Ala or to other aromatic residues
(Figure 5), and in its much stronger preference for bulky
aliphatic residues than for Ala. As in B*2704, Y, W, P,
and basic residues were detrimental. However, the det-
rimental effect of P was smaller on B*2706, and that of
K was larger, in comparison with B*2704.
DISCUSSION
The strategy used in this study to analyze the
peptide specificity of HLA–B27 was an epitope stabili-
zation assay, which measures peptide binding to “emp-
ty” HLA–B27 molecules expressed on the surface of
TAP-deficient cells. No in vitro binding assay fully
reproduces peptide loading in vivo, since this is a highly
organized and incompletely known process requiring
physical association of the TAP transporter, several
chaperones, and the HLA molecule. However, natural
B*2705 ligands consistently bind with high affinity in our
Figure 3. Relative binding of poly-Ala P1 analogs to B*2704 and

B*2706. Each analog (x-axis) is represented by the 1-letter code of the
amino acid residue introduced at P1 into the ARAAAAAAA (ARA7)
sequence. The RRYQKSTEL peptide is designated by an asterisk.
Binding of each analog was measured as described in Materials and
Methods and its relative binding (y-axis, logarithmic scale) was ex-
pressed as the ratio between the EC50 of ARA7 (10 ␮M for B*2704
and 9 ␮M for B*2706) and that of the analog. Since the maximum
amount of peptide tested was 100 ␮M, relative binding values lower
than 0.1, which indicate lack of binding in this assay (EC50 ⬎100 ␮M),
could not be measured. Data are the mean of at least 2 independent
experiments.
ure 4). For instance, H, R, and polar residues were

significantly favored relative to Ala in B*2706, and G, P,
and acidic residues were less detrimental. In addition,
nonpolar aliphatic and aromatic residues were more
suitable than Ala, but Y was less favored than many
other residues, including other aromatic ones. Ala itself
was among the best residues in B*2704, but worse than
many others in B*2706.
These results indicate that B*2704 and B*2706
polymorphisms affect P3 specificity, so that these 2
subtypes differ from B*2705 and between each other in
their residue preferences at this position. Figure 4. Relative binding of poly-Ala P3 analogs to B*2704 and
P9. B*2704 differed from B*2705 in the detri- B*2706. Each analog (x-axis) is represented by the 1-letter code of the
mental effect of basic and Y residues at P9 (Figure 5). In sequence. The RRYQKSTEL peptide is designated by an asterisk.
addition, although aliphatic residues were favored on Peptide binding is expressed as described in Figure 3. Data are the
B*2704, this was not significantly above the effect of Ala. mean of at least 2 independent experiments.
1982 LAMAS ET AL
residues can substantially reduce peptide affinity (1).

Thus, the unsuitability of Pro-9 for binding to B*2705 is
a critical difference in comparison with HLA–B73,
which is an antigen that has the same B pocket as
HLA–B27 and also binds peptides with Arg-2, but has
Pro as a prominent C-terminal motif (37).
Our study is consistent with a previous one (25)
that also used poly-Ala peptide analogs to test the role
of P3 and P9 on B*2705 binding. In particular, it
confirms the suitability of basic and aliphatic residues at
P9 and of nonpolar aromatic residues at P3. However,
the reported suitability of F9 and relatively low accep-
tance of Y9 is in contrast to our results. This difference
might be related to the fact that, in the previous study, a
refolding assay was used to assess binding and the
poly-Ala analogs used were different, since, besides R2,
they had residues other than Ala at several anchor
positions.
The examination of residues present among nat-
ural HLA–B27 ligands reveals that the most suitable
residues are predominant at P3 and P⍀. However, there
is a significant allowance (⬃15%) for suboptimal resi-
dues at each of these positions, which is always compen-
Figure 5. Relative binding of poly-Ala P9 analogs to B*2704 and sated with the presence of an optimal residue at the
B*2706. Each analog (x-axis) is represented by the 1-letter code of the
other position. Because there are virtually no exceptions
sequence. The RRYQKSTEL peptide is designated by an asterisk. to this pattern among the known B*2705 ligands, this
Peptide binding is expressed as described in Figure 3. Data are the emerges as a significant constraint to the B*2705 peptide
mean of at least 2 independent experiments. repertoire in applying it to the prediction of natural
ligands, in addition to putative additional constraints
imposed by proteasomal cleavage and peptide transport
assay (32), suggesting that the peptide specificity of (38–41). That P1 was significantly more permissive for
HLA–B27 as measured in the present study closely suboptimal residues among B*2705 ligands supports the
reflects its specificity in vivo. Poly-Ala analogs are smaller contribution of this position to peptide binding.
commonly used to compare the contribution of different However, this permissivity was limited by the require-
amino acid residues at single positions, since the poly- ment of a good anchor residue at P3 and/or P9.
Ala backbone provides a uniform background to which That these 3 positions generally contributed in an
binding of peptide analogs can be related. Although the additive way to binding and, together with R2, restored
Ala side chain may have a contribution to binding at much of the affinity of natural ligands, strongly suggests
some peptide positions, its effects are minimized due to that a reliable prediction of HLA–B27 ligands can be
its small size and neutral chemical character. done on the basis of P1, P3, and P⍀ only. In further
The data concerning peptide binding to B*2705 support of this, nonpeptidic ligands with significant
demonstrate that residue variability at P1, P3, or P⍀ can affinity for an HLA class I molecule can be obtained by
significantly affect binding. However, on the basis of our keeping the P1–P3 and P⍀ residues of a given peptide
observations regarding the effect of the best residue at ligand and substituting organic spacers for P4–P8
each of these positions on increasing binding relative to (42,43). Although the limited number of known ligands
ARA7, the importance of these positions can be ranked larger than 10-mers makes it somewhat risky to derive
as P9 ⬎ P3 ⬎ P1. Thus, K9 increased binding by a factor general rules, our data might suggest that peptides that
of 8, W3 by a factor of 6, and R1 by a factor of ⬃3. That are suboptimal in size (11-mers, 12-mers) bind in vivo
multiple residues were detrimental emphasizes that pep- only if they have good anchors at the 3 positions, P1, P3,
tide binding is determined by both positive and negative and P⍀.
effects at individual positions. In particular, detrimental A second issue addressed herein was the compar-
ison of the peptide specificities of B*2705 and B*2704. because both subtypes have an identical A pocket, which
These 2 subtypes are both associated with AS (9) and is the site where P1 binds. This suggests that long-range
differ in only 3 amino acid residues: D77S, V152E, and effects of distant polymorphic residues in HLA–B27
A211G. Aside from rather slight differences in residue modulate its interaction with N-terminal peptide resi-
specificity at P1 and P3, these 2 subtypes differ mainly at dues. Long-range effects on B pocket specificity have
P⍀. The detrimental effect of basic P⍀ residues is been previously observed in B*2701 (20).
consistent with the absence of these motifs among The different residue specificity of B*2704 and
B*2704-bound peptides (21), and is consistent with B*2706 at multiple anchor positions implies that their
findings in previous binding studies (32). In spite of the differential association with AS correlates not only with
detrimental effect of C-terminal Y and F for binding to their differential acceptance of C-terminal Y, but also
B*2704, these residues are C-terminal motifs for with a more complex modulation of their peptide rep-
B*2704-bound peptides (21). However, as in B*2705, a ertoires, affecting at least also P1 and P3 residues.
detrimental C-terminal residue can occur among B*2704 Therefore, B*2704 and B*2706 may differ significantly
ligands if they have optimal P3 residues. On the basis of in their peptide repertoires, although they share com-
our results, it is likely that the B*2705 and B*2704 mon ligands (21). The actual extent of their overlap and
peptide repertoires overlap to a significant extent. The the type of peptides that are bound in vivo to only 1 of
overlapping repertoire probably consists mainly of pep- these subtypes will require a more extensive analysis of
tides with C-terminal aliphatic residues, and peptides their natural ligands.
with C-terminal Y or F plus nonpolar P3 residues. In conclusion, the results in this study revealed
The peptide-binding differences between B*2704 the preferences of B*2705 for P1, P3, and P⍀ residues
and B*2706 are particularly relevant because, in contrast and some major rules governing residue usage in these
to the former subtype, B*2706 is less or not associated positions among natural ligands. This will allow a mean-
with AS in various populations (11–13). B*2706 differs ingful prediction of B*2705 ligands based on P1, P2, P3,
from B*2704 in 2 amino acid residues, H114D and and P⍀. Thus, from any protein putatively involved in
D116Y, both of which are located in the ␤-pleated sheet disease-related T cell responses, it is now possible to
floor of the peptide-binding site and can affect the select a rather limited number of peptides fulfilling these
interaction with at least the P3 and P⍀ residues of bound rules to test their role as HLA–B27–restricted antigens.
peptides. Previous sequencing studies revealed that a In addition, our results show that 2 subtypes differen-
major difference between B*2706 and B*2704 was the tially associated with AS differ in their residue specificity
absence of Y as a C-terminal motif in B*2706 (21). In at multiple anchor positions, suggesting that many pep-
vitro binding studies also have shown that aliphatic tides having R2 and C-terminal motifs common to
C-terminal residues were much better than Y for B*2706 B*2704 and B*2706 may nevertheless bind with different
binding, and that this difference was smaller for B*2704 efficiency or to only 1 subtype. Since this point is crucial
binding (32). In agreement with these previous data, our for assessing the nature of putative arthritogenic pep-
results now confirm the high suitability of nonpolar tides, correlations between the binding score of different
aliphatic residues for B*2706 binding. In addition, the residues at each position and their actual usage among
absence of Y as a C-terminal motif for this subtype is natural ligands should be determined, as was done for
explained because bulky aliphatic and F residues bind B*2705 in this study. However, this requires a more
more strongly, relative to Y, than in B*2704. Therefore, extensive database of natural B*2704 and B*2706 li-
peptides with C-terminal Y will compete less advanta- gands, of which very few are yet known.
geously in vivo for binding to B*2706. This study has defined some major peptide fea-
B*2704 and B*2706 showed additional differ- tures that shape HLA–B27–bound peptide repertoires,
ences in their P1 and P3 residue specificity, which have and has described how these features are modulated by
not been revealed by previous studies. Most noteworthy disease-related subtype polymorphism. The peptide-
were the specificity differences at P3, especially those binding specificity of HLA–B27 is probably a critical
concerning the better acceptance of R and polar resi- feature for its linkage to spondylarthropathy, but the
dues in B*2706, and the worse suitability of A and Y pathogenetic role of this antigen is unlikely to be ex-
relative to many other residues. These differences are plained solely by its peptide-binding properties. The
probably due mainly to the presence of D114 in B*2706, critical question as to which HLA–B27–bound peptides
instead of H114 in B*2704 and other subtypes. P1 may become target antigens of autoimmune T cell
differences between B*2704 and B*2706 were surprising responses in disease pathogenesis remains unanswered.
1984 LAMAS ET AL
ACKNOWLEDGMENTS susceptibility to spondylarthropathies. J Clin Invest 1996;98:

2764–70.
We thank Jesús Vazquez and Anabel Marina (Depart- 18. Griffin TA, Yuan J, Friede T, Stevanovic S, Ariyoshi K, Rowland-
ment of Protein Chemistry, CBMSO) for help in mass spec- Jones SL, et al. Naturally occurring A pocket polymorphism in
trometry, Juan Pablo Albar (Centro Nacional de Biotecnolo- HLA-B*2703 increases the dependence on an accessory anchor
gı́a, Madrid, Spain) and Francisco Gavilanes (Universidad residue at P1 for optimal binding of nonamer peptides. J Immunol
1997;159:4887–97.
Complutense de Madrid) for help in peptide chemistry, and
19. Garcia F, Rognan D, Lamas JR, Marina A, Lopez de Castro JA.
Manuel Ramos (CBMSO) for his contributions to the database An HLA-B27 polymorphism (B*2710) that is critical for T-cell
of HLA–B27 ligands. recognition has limited effects on peptide specificity. Tissue
Antigens 1998;58:1–9.
20. Garcia F, Galocha B, Villadangos JA, Lamas JR, Albar JP, Marina
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HG. Dominant aromatic/aliphatic C-terminal anchor in HLA- ogy of an HLA-B27 allospecific T cell epitope lacking peptide
B*2702 and B*2705 peptide motifs. Immunogenetics 1994;39: specificity. J Immunol 1994;152:2317–23.
74–7. 34. Ellis SA, Taylor C, McMichael A. Recognition of HLA-B27 and
17. Boisgérault F, Tieng V, Stolzenberg MC, Dulphy N, Khalil I, related antigens by a monoclonal antibody. Hum Immunol 1982;
Tamouza R, et al. Differences in endogenous peptides presented 5:49–59.
by HLA-B*2705 and B*2703 allelic variants: implications for 35. Paradela A, Garcia-Peydro M, Vazquez J, Rognan D, Lopez de
Castro JA. The same natural ligand is involved in allorecognition 42. Rognan D, Scapozza L, Folkers G, Daser A. Rational design of
of multiple HLA-B27 subtypes by a single T cell clone: role of nonnatural peptides as high-affinity ligands for the HLA-B*2705
peptide and the MHC molecule in alloreactivity. J Immunol human leukocyte antigen. Proc Natl Acad Sci U S A 1995;92:
1998;161:5481–90. 753–7.
36. Yague J, Vazquez J, Lopez de Castro JA. A single amino acid change 43. Krebs S, Lamas JR, Poenaru S, Folkers G, Lopez de Castro JA,
makes the peptide specificity of B*3910 unrelated to B*3901 and Seebach D, et al. Substituting nonpeptidic spacers for the T cell
closer to a group of HLA-B proteins including the malaria-protecting receptor-binding part of class I major histocompatibility complex-
allotype HLA-B53. Tissue Antigens 1998;52:416–21. binding peptides. J Biol Chem 1998;273:19072–9.
37. Barber LD, Percival L, Parham P. Characterization of the peptide- 44. Brooks JM, Murray RJ, Thomas WA, Kurilla MG, Rickinson AB.
binding specificity of HLA-B*7301. Tissue Antigens 1996;47:472–7.
Different HLA-B27 subtypes present the same immunodominant
38. Van Endert PM, Riganelli D, Greco G, Fleischhauer K, Sidney J,
Epstein-Barr virus peptide. J Exp Med 1993;178:879–87.
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1883–95. ghe HF, Hoogerhout P, Osterhaus AD, et al. Human HLA class I-
39. Uebel S, Kraas W, Kienle S, Wiesmuller KH, Jung G, Tampe R. and HLA class II-restricted cloned cytotoxic T lymphocytes iden-
Recognition principle of the TAP transporter disclosed by combina- tify a cluster of epitopes on the measles virus fusion protein.
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40. Daniel S, Brusic V, Caillat-Zucman S, Petrovsky N, Harrison L, 46. Ugrinovic S, Mertz A, Wu P, Braun J, Sieper J. A single nonamer
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peptide loading. Immunity 1998;8:531–42. Antigens 1997;49:23–8.
ANEXO -6-
THE JOURNAL OF BIOLOGICAL CHEMISTRY Vol. 273, No. 30, Issue of July 24, pp. 19072–19079, 1998
© 1998 by The American Society for Biochemistry and Molecular Biology, Inc. Printed in U.S.A.
Substituting Nonpeptidic Spacers for the T Cell Receptor-binding

Part of Class I Major Histocompatibility Complex-binding Peptides*
(Received for publication, December 23, 1997, and in revised form, April 21, 1998)
Stefan Krebs‡, José, R. Lamas§, Sorana Poenaru¶, Gerd Folkers‡, José A. López de Castro§,
Dieter Seebach¶, and Didier Rognan‡储
From the ‡Department of Pharmacy, Swiss Federal Institute of Technology, Winterthurerstrasse 190, CH-8057 Zürich,
Switzerland, the ¶Laboratory for Organic Chemistry, Swiss Federal Institute of Technology, Universitätstrasse 16, CH-
8092 Zürich, Switzerland, and the §Centro de Biologia Molecular “Severo Ochoa,” Universidad Autonoma de Madrid,
Facultad de Ciencas, E-28049 Madrid, Spain
X-ray diffraction studies as well as structure-activity generally nonamers, tightly bind to conserved MHC residues
relationships indicate that the central part of class I in a sequence-independent manner at their N and C termini
major histocompatibility complex (MHC)-binding non- (3), whereas the central part of the bound peptide bulges out
apeptides represents the main interaction site for a T of the binding groove (4). Peptide specificity is governed by
cell receptor. In order to rationally manipulate T cell the position and chemical nature of some anchoring side
epitopes, three nonpeptidic spacers have been designed chains (often P2, P3, and P9) that bind to MHC polymorphic
from the x-ray structure of a MHC-peptide complex and pockets (5, 6). Complementary to x-ray structure determina-
substituted for the T cell receptor-binding part of sev- tions, sequencing self-peptides naturally bound to MHC pro-
eral antigenic peptides. The binding of the modified teins allows the determination of peptide binding motifs (7, 8)
epitopes to the human leukocyte antigen-B*2705 protein and thus the identification of conserved amino acids respon-
was studied by an in vitro stabilization assay, and the
sible for MHC binding (named dominant anchors, generally
thermal stability of all complexes was examined by cir-
at positions P2 and P9) and more variable residues hypoth-
cular dichroism spectroscopy. Depending on their
esized to account for TcR recognition (usually in the central
chemical nature and length, the introduced spacers may
be classified into two categories. Monofunctional spac- part of the peptide sequence, from P4 to P8). Peptide muta-
ers (11-amino undecanoate, (R)-3-hydroxybutyrate tri- tion (9, 10) as well as recently determined x-ray structures of
mer) simply link two anchoring peptide positions (P3 ␣␤ TcRs in complex with a MHC-peptide (11, 12) unambigu-
and P9) but loosely contact the MHC binding groove and ously support this assumption. Since some class I MHC alle-
thus decrease more or less the affinity of the altered les are associated with either susceptibility or resistance to
epitopes to human leukocyte antigen-B*2705. A bifunc- human diseases (13–15), altering TcR contact residues of T cell
tional spacer ((R)-3-hydroxybutyrate tetramer) not only epitopes has been proposed for designing altered peptide li-
bridges the two distant anchoring amino acids but also gands with TcR antagonist properties (16), leading to in vivo T
strongly interacts with the binding cleft and leads to a cell anergy (17). However, natural peptides cannot be easily
5-fold increase in binding to the MHC protein. To our used as immunosuppressors because of poor enzymatic stabil-
knowledge, this is the first report of a nonpeptidic mod- ity and pharmacokinetic properties (18). Herewith, we describe
ification of T-cell receptor binding residues that signif- the substitution of nonpeptidic moieties for the TcR contact
icantly enhances the binding of altered peptide ligands amino acids of several T cell epitopes naturally presented by
to their host MHC protein. The presented modified li- the class I MHC protein B*2705, which is strongly linked to
gands constitute interesting tools for perturbing the T severe inflammatory diseases like ankylosing spondylitis (13)
cell response to the parent antigenic peptide. or reactive arthritis (19). Some reports in which a similar
strategy has been followed (20 –22) show that the altered pep-
tide ligands still form stable complexes with their host MHC
Class I MHC1 molecules are highly polymorphic proteins
protein but often present a reduced affinity relative to the
that play a key role in immune surveillance by presenting
parent peptide. The present study describes a novel oligomeric
foreign peptides to cytotoxic T lymphocytes (1). The molecu-
spacer able not only to link two MHC anchoring positions (P3
lar mechanisms of peptide selection have been characterized
and P9) but also to significantly improve binding to the restrict-
by x-ray diffraction studies of several MHC proteins in com-
ing class I MHC protein.
plex with either a peptide pool or single ligands (2). Peptides,
EXPERIMENTAL PROCEDURES
* This work was supported by the Schweizerischer Nationalfonds zur Computer-assisted Ligand Design—Molecular mechanics and dy-
Förderung der wissenschaftlichen Forschung (Project 31-45504.95); namics calculations were carried out using the AMBER 4.1 package
Ministry of Education Grant PM95– 002 and Plan Nacional de I ⫹ D (23), using the parm94 parameter set (24) and an all-atom force field
Grant SAF97– 0182 (to J.A.L.C.); and an institutional grant of the representation. Force field parameters for the ester group were taken
Fundacion Ramon Areces to the Centro de Biologia Molecular “Severo
from the literature (25). Atomic charges for the Aua and HB monomers
Ochoa.” The costs of publication of this article were defrayed in part by
were calculated using the GAUSSIAN 94 package (26) and the HF/6 –
the payment of page charges. This article must therefore be hereby
marked “advertisement” in accordance with 18 U.S.C. Section 1734 31G* basis set by fitting atom-centered charges to an ab initio electro-
solely to indicate this fact. static potential, using the RESP method (27) according to a previously
储 To whom correspondence should be addressed. Fax: 41-1-635-68-84; described procedure (28). Atomic charges for both new monomers are
E-mail: didier@pharma.ethz.ch. listed in Table I.
1
The abbreviations used are: MHC, major histocompatibility com- Initial coordinates for the MHC-ligand complexes were obtained from
plex; HLA, human leukocyte antigen; TcR, T cell receptor; Pn, peptide the x-ray structure of HLA-B*2705 (3) as described previously (20, 29).
position n; Fmoc, N-(9-fluorenyl)methoxycarbonyl; Aua, 11-amino un- The spacers were substituted for the natural pentapeptide sequence
decanoate; HB, (R)-3-hydroxybutyrate. using the SYBYL modeling package (TRIPOS Association, Inc., St.
19072 This paper is available on line at http://www.jbc.org

Nonnatural HLA-B27 Ligands 19073
TABLE I
Restrained electrostatic potential-derived point charges, calculated using the RESP method (26) from GAUSSIAN 94 HF/6 –31G* electrostatic
potentials
a
Ab initio derived electrostatic potentials have been calculated for protected monomers (Ac-Aua-NMe, Ac-HB-OMe) and atomic charges of the
isolated monomers (Aua and HB) adjusted to neutrality using Lagrange constraints, as previously described (28). Charges for equivalent hydrogen
atoms are only mentioned once.
b
11-aminoundecanoate.
c
(R)-3-hydroxybutyrate.
Louis, MO). From a starting fully extended conformation, dihedral The synthesis of ligands 9 –12 will be reported elsewhere.2
angles of the main chain between P3 and P9 were modified by hand in Epitope Stabilization Assay—The quantitative assay used was de-
order to reproduce a correct trans geometry for the newly introduced scribed previously (30). Briefly, RMA-S transfectants expressing
amide or ester bonds. The ligand was first relaxed by 500 steps of B*2705 or B*2704 were used. These are murine cells with impaired
conjugate gradient energy minimization while maintaining the protein TAP-mediated peptide transport and low surface expression of (empty)
fixed. It was then submitted to a 100-ps simulated annealing protocol in class I MHC molecules, which can be induced at 26 °C (31) and stabi-
order to sample the broadest conformational space accessible. Starting lized at the cell surface through binding of exogenously added ligands.
with random velocities assigned at a temperature of 1000 K, the ligand These cells were incubated at 26 °C for 24 h. After this, they were
was first coupled for 50 ps to a heat bath at 1000 K using a relatively incubated 1 h at 26 °C with 10⫺4 to 10⫺9 M peptides, transferred to
weak temperature coupling constant ␶ (0.2 ps) and then linearly cooled 37 °C, and collected for flow microcytometry analysis with the ME1
down to 50 K for the next 50 ps while ␶ was strengthened to a value of monoclonal antibody (IgG1, specific for HLA-B27, -B7, and -B22) (32)
0.05 ps. During these 100 ps, no protein atoms were allowed to move. after 4 h for B*2705 or after 2 h for B*2704. The determinant recognized
The last conformer was then solvated in a 10-Å-thick TIP3P water shell. by ME1 is not affected by bound peptides or by polymorphism in these
Energy minimization of the ligand, of the MHC-ligand complex, fol- two subtypes (data not shown). Binding of a given ligand was measured
lowed by 200-ps molecular dynamics simulation of the fully solvated as its C50. This is its molar concentration at 50% of the fluorescence
MHC-ligand pair was performed as previously reported (20). obtained with that ligand at 10⫺4 M. Ligands with C50 ⱕ 5 ␮M were
Synthesis of the Modified Peptides—Ligands 1– 8 (Table II) were considered to bind with high affinity, since these were the values
obtained by automated solid-phase peptide synthesis using a Fmoc/tert- obtained for most of the natural B27-bound peptides. C50 values be-
butyl protecting strategy. Chain elongation was performed by a robot tween 5 and 50 ␮M were considered to reflect intermediate affinity. C50
system (Syro Multi-Syn-Tech, Bochum, Germany) with a subsequent ⱖ 50 ␮M indicated low affinity. Binding of peptide analogs was meas-
manual deprotection and analysis. Fmoc-protected amino acids were ured as the concentration of the peptide analog required to obtain the
coupled to the diisopropylcarbodiimide-activated carboxyl terminus in fluorescence value at the C50 of the unchanged peptide. This was des-
10-fold excess using 1-hydroxybenzotriazole as a coupling reagent. The ignated as EC50. Relative binding was the ratio between the EC50 of the
final peptide was simultaneously cleaved from the resin and depro- peptide analog and the C50 of the corresponding unchanged peptide.
tected by the addition of trifluoroacetic acid with thiocresole and thio- HLA-B*2705 Expression and Purification—A cDNA encoding for hu-
anisole as scavengers. The peptides were precipitated and washed with man ␤2-microglobulin (gift of Dr. C. Vilches, Clinica Puerta de Hierro,
ice-cold ether and further lyophilized from water. Natural as well as Madrid) was cloned into a pGex vector (Amersham Pharmacia Biotech),
nonnatural peptides were analyzed by reverse phase high performance yielding a fusion protein with glutathione S-transferase. Escherichia
liquid chromatography (Merck-Hitachi, Darmstadt, Germany) on a coli cells transformed with this pGex vector were grown under vigorous
nucleosil 5␮, C-18 column (125 ⫻ 3 mm) at a flow rate of 600 ␮l/min. shaking in LB broth for 24 h at 25 °C after induction with isopropyl-1-
Absorbance was measured at 220 nm. The solvent system consisted of thio-␤-D-galactopyranoside. Cells were frozen at ⫺70 °C, thawed, sus-
0.1% trifluoroacetic acid in water (buffer A) and 0.1% trifluoroacetic pended in TBS (20 mM Tris, 150 mM NaCl, pH 8.0), and lysed by the
acid in acetonitrile (buffer B). A linear gradient from 10 to 60% B in 30 addition of lysozyme and brief sonication. The crude extract was passed
min was applied. Furthermore, peptides were analyzed by ion spray over a glutathione-agarose column (Sigma), and after extensive wash-
mass spectrometry on a triple quadrupole mass spectrometer, APII III,
with a mass range of m/z 10 –2400 equipped with an ion spray interface
(Sciex, Thornhill, Canada). The mass spectrometer was operated in
2
positive ion mode under conditions of unit mass resolution for all D. Seebach, S. Poenaru, G. Folkers, and D. Rognan, manuscript in
determinations. preparation.
19074 Nonnatural HLA-B27 Ligands
TABLE II
Binding of natural and altered T cell epitopes
Sequence EC50a
Ligand Tmb
P1 P2 P3 Spacer P9 B*2705 B*2704
␮M °C
1 R R R WRRLT Vc 1.2 0.8 52.8 ⫾ 0.7
2 Auad 4.0 1.0 42.9 ⫾ 0.3
3 S R Y WAIRT Re 3.0 5.4 46.3 ⫾ 0.5
4 Aua 8.6 100.0 39.5 ⫾ 0.2
5 G R A FVTIG Kf 1.8 6.4 61.9 ⫾ 0.3
6 Aua 7.0 ⬎100.0 48.1 ⫾ 0.4
7 Q R L KEAAE Kg 10.0 62.8 ⫾ 0.7
8 Aua 46.5 ⫾ 0.2
9 (HB)3h 40.0
10 (HB)4 2.5
11 A (HB)3 20.0 63.2 ⫾ 0.6
12 (HB)4 1.6 62.1 ⫾ 0.7
a
Concentration of ligand at which HLA-B27 fluorescence (measured by flow microcytometry analysis with an anti-B27 monoclonal antibody) on
RMA-S cells was half the maximum obtained with the wild type peptide (30).
b
Melting temperature: midpoint of the thermal unfolding of the B*2705 heavy chain. Tm values are means of three denaturation experiments
performed on independently reconstituted heavy chain-␤2-microglobulin-ligand heterotrimers. S.D. values have been obtained by fitting the
obtained curves to a two-state model as previously described (35).
c
Epstein-Barr virus latent membrane protein (236 –244) (49).
d
Aua: 11-amino undecanoate.
e
Influenza A nucleoprotein (383–391) (50).
f
Human immunodeficiency virus 1 glycoprotein 120 (314 –322) (39).
g
E. coli DnaK protein (260 –268) (20).
h
HB: (R)-3-hydroxybutyrate.
ing with TBS, the ␤2-microglobulin was eluted by thrombin cleavage as with a reference peptide (GRAFVTIGK; compare Ref. 34 and Table II).
a single band at 11 kDa (SDS-polyacrylamide gel electrophoresis). Three denaturation curves from independent refolding preparations
The HLA-B*2705 heavy chain was affinity-purified under denatur- were averaged, after conversion to molar ellipticity values. The curves
ing conditions as a His6 fusion protein. The expression vector was were reduced to 70 data points by replacing each of the 10 neighboring
obtained by subcloning the cDNA encoding for the first extracellular points with their mean value. By assuming a two-state equilibrium (35),
274 amino acids (gift of Dr. K. C. Parker, National Institutes of Health, data were fitted by a nonlinear least-squares routine with the program
Bethesda) into the polycloning site of the oligohistidine vector pQE30 Origin 2.9 (MicroCal Software, Inc.) to the following equations.
(Quiagen) with the restriction endonucleases BamHI and HindIII. The
heavy chain was expressed in E. coli at 35 °C for 2 h after induction ⌰共T兲 ⫽ ⌰u ⫹ 共⌰f ⫺ ⌰u/1 ⫹ exp共x兲兲 (Eq. 1)
with isopropyl-1-thio-␤-D-galactopyranoside. Longer expression times
led to an increase of immature or degraded heavy chains. Inclusion x ⫽ 共⫺⌬Hm/R兲共1/T ⫺ 1/Tm兲 ⫹ 共⌬Cp/R兲共共Tm/T ⫺ 1兲 ⫹ ln共T/Tm兲兲 (Eq. 2)
bodies were prepared using a standard procedure (33) and solubilized in The measured ellipticity (⌰) is given as a function of the temperature
8 M urea, 20 mM Tris, 150 mM NaCl at pH 8.0. Purification on a (T) with the enthalpy (⌬Hm), heat capacity upon unfolding (⌬Cp), and
nickel-nitriloacetate-agarose column led to the HLA-B*2705 heavy the midpoint temperature of unfolding (Tm) being the fitting parame-
chain with two minor impurities of lower molecular weights consisting ters. Initial estimates for ⌬Hm were obtained by plotting ln K versus 1/T
of truncated heavy chains. (van’t Hoff plot) in the transition region. ⌬Cp was assumed to be tem-
Folding of the MHC Protein upon Ligand Binding—Reconstitution of perature-independent (36), and initial values were estimated from the
the heavy chain-␤2-microglobulin-ligand heterotrimer was achieved by primary sequence (37). The linear base-line functions of the unfolded
dialysis (cellulose ester tubings, 500-Da cut-off) of a solution containing and folded states ⌰u and ⌰f were determined as linear regressions of the
0.15 mg/ml heavy chain, 0.1 mg/ml ␤2-microglobulin, and 0.1 mg/ml pre- and post-transitional regions. The enthalpy change at the midpoint
peptide ligand, using 5 mM glutathione to establish reducing conditions of unfolding (⌬Hm) was determined by the least-squares fit of the
in 6 M urea against TBS. The solution was sparged with nitrogen to unfolding curve to Equation 1. Because ⌬Cp estimates obtained by this
prevent premature formation of disulfide bridges and oxidation of free approach are not very accurate and the ⌬Hm values are largely influ-
Cys67 in the B*2705 heavy chain. After 36 – 48 h at 10 °C, the mixture enced by the observed deviations from a two-state model, a direct
was concentrated to 500 ␮l in a Centripep ultrafiltration unit (Amicon- extrapolation from the midpoint of unfolding to obtain ⌬⌬Gunfolding at
Grace Ltd.). The folded heterotrimer was purified by gel filtration on a 25 °C was not taken into consideration.
superdex 75 column (Amersham Pharmacia Biotech) with UV detection
at 280 nm. The chromatogram showed three major peaks at 9-, 11.5-,
RESULTS
and 14-ml elution volume corresponding to heavy chain aggregates,
refolded complex, and excess ␤2-microglobulin, respectively. The overall Replacing a Pentapeptide with a Polymethylene Spacer in
yield of the fully reconstituted heterotrimer varied around 5%. The Four Unrelated Natural Epitopes—For mimicking the se-
heterotrimer peak was collected, concentrated in a Centricon 30 ultra- quence of the central pentapeptide part (P4 –P8) of MHC-bound
filtration unit (Amicon-Grace), and immediately subjected to thermal
nonapeptides, any nonpeptidic fragment needs first to repro-
denaturation.
Monitoring the Thermal Stability of MHC-Ligand Complexes by CD duce as closely as possible the conformation of this bulging part
Spectroscopy—All CD measurements were done on a Jasco J-720 polar- and second to allow the same intermolecular distance between
imeter with a water-jacketed 1-mm sample cell connected to a comput- the neighboring anchoring positions (P3 and P9) that are
er-interfaced Neslab 111 circulating water bath. Temperature control linked by the new spacer. The key distance between C-␣ atoms
was achieved by measuring the circulating water immediately after the of P3 and P9 positions is 16.6 Å in the x-ray structure of
sample cell. The thermal denaturation profiles were recorded at 218 nm
HLA-B*2705 complexed by a nonapeptide model (3). The same
in 10 mM Tris, 150 mM NaCl (pH 8.0) with the Jasco TEMPSCAN
software using 0.1 °C increments at a heating rate of 30 °C/h. Sample distance can be easily obtained after linking a polymethylene
concentrations were determined photometrically and held at 0.2 mg/ml. chain (Aua, Fig. 1) to P3 and P9 residues by simple amide
Different scan rates did not affect the Tm value of B*2705 in complex bonds. The 11-amino undecanoate fragment was then chosen
ues reported here are fairly similar to those found for B*2705-
binding peptides by other groups (21, 34, 41). The highest
stability against temperature was found for complexes with
peptides 5 and 7, which all present a lysine at P9. Less favored
amino acids at P9 are Val (peptides 1 and 2) and especially Arg
(peptides 3 and 4), which gives by far the least stable complexes
with B*2705 (peptides 1 and 3, respectively).
Binding of peptides 1– 6 to a closely related HLA-B27 sub-
type (B*2704) was also examined by the same in vitro stabili-
zation assay. B*2704 differs from B*2705 by two amino acid
changes in the peptide binding groove (Asp77 to Ser; Val152 to
Glu), which influence its peptide specificity, relative to B*2705
(42). In contrast to B*2705, substitution of Aua spacers for
P4 –P8 dramatically decreases binding to B*2704 in our epitope
stabilization assay (Table II) when the last anchoring position
(P9) is a basic amino acid (Lys, Arg). If P9 is an apolar residue
(Val, peptide 2), no real change in B*2704 binding was noticed.
Substituting 3-Hydroxybutyrate Oligomers for the P4 –P8 Se-
quence of a Natural Peptide—The decreased binding of the Aua
analogues to B*2705 is probably due to the nonfunctionalized
nature of the introduced spacer and the lack of interactions
between the unsubstituted Aua moiety and the central part of
the binding groove. Thus, a rational improvement in terms of
binding affinity would be to ramify the spacing moiety in order
to reach one of the two central pockets (pockets C and E) of the
peptide binding groove that face the spacer fragment. The
(R)-3-hydroxybutyrate (HB) monomer was selected for three
main reasons: (i) polymers of HB are chemically stable (43); (ii)
FIG. 1. Chemical structure of the modified peptide analogues.
they adopt conformations whose folding in the free state resem-
bles that found for peptides (44); and (iii) the methyl substitu-
for its optimal length in an extended conformation and the
ent is large enough to fit into pockets C and E. Thus, a trimer
absence of any substituents, which should allow a conforma-
(three units) and a tetramer (four units) of HB were substituted
tional flexibility sufficient for a proper fit into the binding
for the P4 –P8 sequence of one natural peptide (polyesterpep-
groove. To check the independence of the proposed modification
tides 9 and 10; Table II), since they should optimally span the
on the parent epitope sequence, the Aua spacer was introduced
key distance between the two anchor positions (P3 and P9) to
in four unrelated sequences of natural epitopes, known to bind
bridge (Fig. 1).
to B*2705 (Table II). The question of whether the new ligands
were able to remain tightly bound in the peptide binding cleft In order to circumvent cyclization of the N-terminal gluta-
like the natural nonapeptides was addressed by molecular dy- mine (45) that would prevent binding of the peptidic N termi-
namics simulations of the solvated complexes (Table II). The nus in the A pocket of B*2705, the Ala1 analogue was also
computational protocol used has been previously shown to ex- synthesized in the nonnatural series (polyesterpeptides 11 and
plain the binding potency of several HLA-B27-binding peptides 12; Table II).
(38) and to predict the high affinity of designed peptide ana- The modified ligands 9 –12 have totally different binding
logues (20, 29). Energy-minimized conformations show that the affinities in the in vitro stabilization assay (Table II), the tet-
proposed bridging has modified neither the overall conforma- ramer-containing compounds (ligands 10 and 12) being about
tion of the bound ligands nor the intermolecular distance be- 15 times more potent that the trimeric analogues (ligands 9
tween P3 and P9 C-␣ atoms (Fig. 2). Moreover, the chemical and 11). Furthermore, a HB tetramer segment leads to a sig-
substitutions were compatible with the conservation of the nificant enhancement of the binding to B*2705 relative to the
main interactions between the altered peptides and B*2705, natural pentapeptide sequence. Again, the differences observed
especially the electrostatic interactions provided by the two between natural and polyesterpeptides in the in vitro stabili-
charged termini and the arginine found at position 2 of B*2705- zation assay are not reflected by the thermal denaturation
binding peptides (39, 40). experiments, performed only for ligands 11 and 12. Both com-
In order to experimentally validate the proposed model, the pounds promote a similarly high stability of the resulting
four B*2705-restricted T cell epitopes and their modified ana- MHC-ligand pair with Tm values of 62– 63 °C (Fig. 4, Table II)
logues (Table II) were synthesized and then tested for their analogous to that found for the parent peptide 7, and charac-
binding to B*2705, in an in vitro epitope stabilization assay teristic of high affinity ligands (41).
(30). Replacing the central pentapeptide sequence by the un- Molecular Modeling of the Altered Peptides in Complex with
substituted Aua fragment led in all cases to a slight decrease in B*2705—A rationale for the (de)stabilizing effects of the three
B*2705 stabilization (Table II), which was also reflected by a spacers presently studied is proposed by the molecular dynam-
lesser thermal stability of the resulting complexes monitored ics time-averaged conformations of a reference peptide (QR-
by CD spectroscopy (Fig. 3, A–D). The temperature shift in the LKEAAEK; peptide 7) and its analogues (peptides 8 –10). By
midpoint of unfolding depends on the sequence of the reference looking at all close nonbonded contacts between any peptide
peptide but varies from ⫺7 to ⫺14 °C (Table II). Whereas the residue and its protein neighboring atoms, the three spacers
effect of the Aua spacer is similar in both assays, there seems (Aua, HB trimer, and HB tetramer) can be easily distinguished
to be no clear correlation between the EC50 scores obtained (Fig. 5). The Aua spacer provides fewer contacts to the MHC
from the epitope stabilization assay and the Tm values calcu- binding groove than the pentameric P4 –P8 sequence of the
lated from the thermal denaturation experiments. The Tm val- parent peptide 7. This could explain the decreased binding
FIG. 2. Close-up into the binding groove of HLA-B*2705 (orange surface) in complex with peptides 7–10 (Table II). These structures
represent energy-minimized conformations obtained from the x-ray structure of HLA-B*2705 in complex with a model peptide (Protein Data Bank
entry 1hsa) under a previously described protocol (20, 29). The heavy chain backbone atoms of HLA-B*2705 have first been fitted together in the
four complexes, and the protein atoms are not shown for the sake of clarity. Since protein distortion upon energy minimization of the resulting
complexes is minimal, the MHC protein is here represented by a unique molecular surface independent of the bound ligand. The color coding is
as follows: blue, nitrogen; red, oxygen; white, carbon atoms of ligand 7; cyan, carbon atoms of ligand 8; green, carbon atoms of ligand 9; yellow,
carbon atoms of ligand 10. The arrows indicate two methyl substituents of the HB tetramer interacting with the central pockets C/E of the protein.
The figure has been prepared using the program GRASP (51).
affinity of Aua-containing peptides to B*2705. The detrimental DISCUSSION

effect of the HB trimer can be explained by the weakening of Replacing the central TcR-binding residues of MHC class
the interactions between both terminal residues (PN and PC) I-bound peptides (P4 –P8) by nonpeptidic moieties has been
and their respective pockets (A and F). The better complemen- reported previously (20, 21). Herewith, we propose to rational-
tarity of the HB tetramer to the B*2705 binding cleft is prob- ize the effect of three novel spacers on binding to the HLA-
ably related to the following factors: (i) the additional interac- B*2705 protein. The simplest spacer (Aua) is a single poly-
tions provided by two methyl groups of the tetrameric spacer methylene chain linking the P3 and P9 positions by amide
itself and (ii) a higher number of nonbonded contacts of all bonds. In accordance with a previous report studying the effect
other MHC anchors (PN, P2, P3, and PC). of non-␣ amino acids (20), the Aua spacer does not impair
The total buried surface area of the modified ligands 8 –10 binding to B*2705. Only a moderate decrease in relative bind-
has been maintained when compared with that of the parent ing to B*2705 was observed in an epitope stabilization assay,
peptide 7 (about 650 Å2; data not shown). However, the total performed for four unrelated modified peptides (Table II). How-
accessibility of the ligands in their bound state is different. It is ever, the effect of this modification on the thermal stability of
reduced by 20% for HB analogues with respect to the natural the resulting MHC-ligand pair was more significant (Fig. 3,
epitope 7 (from 500 to 400 Å2). The Aua compound 8, although A–D). Depending on the peptide in which the Aua moiety was
slightly less potent, has a much lower accessible surface area introduced, the midpoint of unfolding of the B*2705 heavy
(250 Å2) due to the lack of substituents in the spacing area. chain (Tm) was lowered by 7–14 °C. The corresponding free
FIG. 3. Thermal denaturation, monitored by CD spectroscopy at 218 nm, of HLA-B*2705 loaded with ligands 1 and 2 (A), ligands
3 and 4 (B), ligands 5 and 6 (C), and ligands 7 and 8 (D). The arrows indicate the midpoint of unfolding (Tm) of the B*2705 heavy chain.
FIG. 4. Thermal denaturation, monitored by CD spectroscopy

at 218 nm, of HLA-B*2705 loaded with ligands 7, 11, and 12.
FIG. 5. Nonbonded interactions between the HLA-B*2705 pro-
tein and ligands 7–10, measured on energy-minimized time-av-
energy change in unfolding ⌬⌬Gunfolding at the midpoint of eraged conformations obtained after 200-ps Molecular Dynam-
unfolding, derived from the CD spectra (22), varies from ⫺0.8 ics simulations of the corresponding solvated complexes.
to ⫺1.3 kcal/mol. Since unfolding of the heavy chain should Protein-ligand contacts are recorded for interaction distances up to 4 Å.
follow release of the ligand, this observation supports a faster
dissociation of the modified peptides with respect to the parent related to melting temperatures calculated by CD spectroscopy.
epitope, as recently illustrated in a homogeneous series of A likely explanation for this is that binding, as measured in
H-2Kd-binding nonapeptides (46). However, the present study epitope stabilization assays, is significantly influenced by the
suggests that extrapolating peptide binding differences from association rate of the peptide, whereas CD measurements
Tm values is not allowed for unrelated sequences. For the set of relate only to the dissociation rates. The highest thermal sta-
4 T cell epitopes presently studied, EC50 values cannot be bilities were obtained for the B*2705 protein in complex with
peptide ligands bearing a Lys at P9. This makes sense, since be easily modified by introducing simple nonpeptidic elements
Lys is the P9 residue most complementary to its binding pocket in their central part without drastic changes in binding to their
F. Its side chain forms a buried salt bridge with Asp116, located restriction MHC proteins. Two conditions seem to be necessary
at the bottom of the pocket. The predominance of the enthalpic for these modifications: (i) the last amino acid (PC) should be a
contribution to peptide dissociation would thus be compatible strong anchor, and (ii) the parent epitope should not contain a
with the lower Tm values observed with peptides having an dominant anchor position between the P4 and P8 positions.
amino acid (Val, Arg) for which the interaction with pocket F is Since this is the case for a majority of class I MHC peptide
weaker. It also corroborates previous computational simula- binding motifs (8), such chemical manipulations should be fea-
tions, suggesting that peptide dissociation first occurs at the C sible for many antigenic peptides binding to class I MHC pro-
terminus (20, 29, 38). teins. Class II MHC-binding peptides that utilize nearly all
Interestingly, the effect of the Aua spacer is subtype-depend- peptidic bonds to interact with their host MHC protein (48)
ent, since differences between the natural and the Aua peptides must be excluded from these epitope modifications.
in binding to B*2704 were much more significant (Table II). The altered ligands reported in this study constitute a fur-
B*2704 basically differs from the B*2705 allele by its weak ther step toward obtaining full nonpeptide ligands for class I
propensity to present peptides with basic P9 amino acids and MHC proteins. They represent interesting tools for altering the
its improved suitability for nonpolar P9 residues (42). Thus, the response of B*2705-restricted T cells to naturally occurring
deleterious effect of the Aua spacer is amplified for peptides antigenic peptides and for designing novel synthetic vaccines.
bearing a weak anchoring amino acid at P9 (peptides 4 and 6; Acknowledgment—We thank the calculation center of the ETH Zür-
Table II) and decreased for peptides with nonpolar P9 residues ich for allocation of computer time on the CRAY J90 and PARAGON
(peptide 2). The Aua group can be considered as a monofunc- supercomputers.
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ANEXO -7-
2318 J. Med. Chem. 1999, 42, 2318-2331
Articles
Nonapeptide Analogues Containing (R)-3-Hydroxybutanoate and β-Homoalanine

Oligomers: Synthesis and Binding Affinity to a Class I Major
Histocompatibility Complex Protein
Sorana Poenaru,‡,§ José R. Lamas,† Gerd Folkers,| José A. López de Castro,† Dieter Seebach,*,‡ and
Didier Rognan*,|
Laboratory for Organic Chemistry, Swiss Federal Institute of Technology, Universitätstrasse 16, CH-8092 Zürich, Switzerland,
Centro de Biologia Molecular ”Severo Ochoa”, Facultad de Ciencias, Universidad Autonoma de Madrid,
E-28049 Madrid, Spain, and Department of Pharmacy, Swiss Federal Institute of Technology, Winterthurerstrasse 190,
CH-8057 Zürich, Switzerland
Received December 4, 1998
Crystal structures of antigenic peptides bound to class I MHC proteins suggest that chemical
modifications of the central part of the bound peptide should not alter binding affinity to the
MHC restriction protein but could perturb the T-cell response to the parent epitope. In our
effort in designing nonpeptidic high-affinity ligands for class I MHC proteins, oligomers of
(R)-3-hydroxybutanoate and(or) β-homoalanine have been substituted for the central part of a
HLA-B27-restricted T-cell epitope of viral origin. The affinity of six modified peptides to the
B*2705 allele was determined by an in vitro stabilization assay. Four out of the six designed
analogues presented an affinity similar to that of the parent peptide. Two compounds, sharing
the same stereochemistry (R,R,S,S) at the four stereogenic centers of the nonpeptidic spacer,
bound to B*2705 with a 5-6-fold decreased affinity. Although the chiral spacers do not strongly
interact with the protein active site, there are configurations which are not accepted by the
MHC binding groove, probably because of improper orientation of some lateral substituents in
the bound state and different conformational behavior in the free state. However we
demonstrate that β-amino acids can be incorporated in the sequence of viral T-cell epitopes
without impairing MHC binding. The presented structure-activity relationships open the door
to the rational design of peptide-based vaccines and of nonnatural T-cell receptor antagonists
aimed at blocking peptide-specific T-cell responses in MHC-associated autoimmune diseases.
Introduction independent recognition in which both terminal ends

of the peptide backbone are tightly bonded to conserved
Class I major histocompatibility complex (MHC)-
residues of the MHC binding groove. Allele specificity
encoded proteins play a key role in the intracellular
is ensured by the interaction of anchoring side chains,3,4
immune surveillance by selectively binding to intracel-
usually at positions P2, P3 (Pn standing for position n),
lular peptide antigens and presenting them at the cell
surface to T-cell receptors (TCRs) of cytotoxic T-lym- and the C-terminus with polymorphic pockets5 of the
phocytes (CTL).1 Due to the genetically encoded dis- host MHC protein. The central part of the bound
crepancy between the limited number of class I alleles peptides (from positions 4 to 8) generally zigzags6 or
(about six) expressed by each individual and the infinite bulges7 out of the binding groove and thus allows
number of potential antigenic peptides (usually non- variation in the length of the bound peptides (from 8 to
amers), class I MHC molecules must bind diverse sets 11 amino acids). Systematic peptide mutation8 and
of foreign peptides with a broad specificity but a high X-ray structure of MHC-peptide-TCR ternary com-
affinity. Numerous structural data on class I MHC- plexes9-12 show that this central part whose conforma-
peptide complexes are nowadays available at the three- tion is not complementary to that of the MHC protein
dimensional level2 and provide an explanation for that is the major contact area for Rβ TCRs that trigger the
paradigm. The 27 reported X-ray structures (for nine T-cell response to the foreign peptide.
different class I MHC molecules) illustrate a peptide- The tight association observed between MHC expres-
sion and susceptibility or resistance to autoimmune
* To whom correspondence should be addressed. D. Seebach: fax, disorders led us to consider class I MHC proteins as
+41.1.632 11 44; e-mail, seebach@org.chem.ethz.ch. D. Rognan: fax, particularly interesting targets for the selective immu-
+41.1.635 68 84; e-mail, didier@pharma.ethz.ch.
‡ Laboratory for Organic Chemistry, SFIT. notherapy of autoimmune diseases. At least two ways
† Universidad Autonoma de Madrid.
| Department of Pharmacy, SFIT.
of shunting the T-cell response to autoantigens using
§ Present address: Department of Chemistry, University of Cali- small-molecular-weight molecules have been proposed.
fornia, Berkeley, CA 94720-1460. The first one involving MHC blockade by a high-affinity
10.1021/jm981123l CCC: $18.00 © 1999 American Chemical Society
Published on Web 06/08/1999
Nonapeptide Analogue Binding Affinity to MHC Protein Journal of Medicinal Chemistry, 1999, Vol. 42, No. 13 2319
competitor13 is unlikely as MHC-bound peptides at the Scheme 1a

cell surface are almost impossible to displace.14 The only
way to overcome this drawback would be to supply the
peptide competitor in liposomes15 or as lipopeptides16
into the endoplasmic reticulum where assembly of the
class I MHC-peptide complexes takes place. The second
inhibiting pathway relying on TCR antagonism17 sug-
gests that the presentation of the epitope to autoreactive
T-cells would be antagonized by a modified peptide
analogue. This approach is much more promising since
only a few TCRs at the surface of CTLs need to be
targeted,18 whereas MHC blockade requires saturation
of all MHC binding sites at the cell surface.19 Two
prerequisites are however necessary for designing TCR
antagonists: (i) a good affinity to the MHC-restriction
protein, (ii) a fast dissociation of the corresponding
MHC-ligand complex to the TCR.20,21 The few TCR
antagonists known to date are all peptide analogues for
which one TCR-anchoring amino acid has been mu-
tated.22 Unfortunately, the poor stability and pharma-
cokinetic properties inherent to their peptidic nature
preclude their general use as immunosuppressors. Thus,
there is a need for designing high-affinity nonpeptide
ligands for class I MHC proteins. Rather few variations
around the canonical nonapeptide structure have been
described up to date.23 Peptides bearing unnatural L-
or D-R-amino acids at MHC-anchoring positions,24-29
reduced peptide bond pseudopeptides,30 retroinverso
analogues,31 poly-N-acylated amines,32 or incorporation
of a β-homoglycine residue at the peptide N-terminus33 a (a) DCC, DMAP, CH Cl ; (b) HCl/ether (satd); (c) H , Pd/C,
2 2 2
have been reported. An alternative strategy we initiated MeOH; (d) Boc-Ala-OH, HOBt, EDC, Et3N, CH2Cl2; (e) H2, Pd/C,
3 years ago is to replace the central TCR-binding amino MeOH; (f) HCl•H-Lys(Z)-OBn, HOBt, EDC, Et3N, CH2Cl2; (g) HCl/
acids by various nonpeptidic spacers: oligomers of dioxane (satd); (h) HOBt, EDC, DIEA, CH2Cl2; (i) TFA/CH2Cl2,
1:1.
aminoalkanoates,24,34 phenanthridine derivatives,35 or
poly(ethylene glycol) loops.36 All these chemical modi- thermore, combining β-HAla and HB oligomers should
fications led to ligands that could associate with class I enhance the solubility of the resulting spacers in
MHC proteins but always with a slight decrease in chlorinated solvents42 and thus facilitate their synthetic
binding affinity when compared to that of the parent access. Most of the designed peptide analogues bind
peptides. indeed with a high affinity to a class I MHC protein
We recently described the replacement of a natural (HLA-B*2705 allele), whose expression is associated
pentameric peptide sequence (from positions P4 to P8) with susceptibility to severe autoimmune diseases.43
by (R)-3-hydroxybutanoate (R-HB) oligomers in HLA-
B27-binding nonapeptides37 while enhancing 5-fold the Results and Discussion
binding affinity for the MHC restriction protein.34 Chemistry. Synthesis of the derivative 11 was
However, the partial hydrolysis of oligo-HB ester bonds, achieved using a fragment-type coupling strategy
observed during the synthesis, suggests that these (Scheme 1). Boc-protected β-homoalanine38,44 and benzyl
analogues should have very poor in vivo pharmacoki- 3-hydroxybutanoate (2)45 were coupled using DCC and
netic properties because of their high sensitivity to DMAP as activating reagents46 to give 3. Deprotection
esterases and peptidases. Recent reports on the remark- of the amino group under acidic conditions gave the
able enzymatic stability of β-peptides38,39 led us to amino ester 4, whereas hydrogenolysis of the benzyl
consider oligomers of β-amino acids as potential sur- ester gave acid 5. Coupling of 4 with the commercially
rogates for the TCR-binding residues of class I MHC- available Boc-protected alanine under traditional HOBt/
binding peptides. Since β-homoalanine (β-HAla) is an EDC peptide conditions47-49 gave the fully protected
isostere of HB, binding to HLA-B27 should thus be derivative 6 whose benzyl ester group was cleaved by
retained in light of our previous results on poly(ester H2 (Pd/C) to yield acid 7. 1H NMR measurements led
peptides) (PEPs).34 However, the low solubility of pro- to assignment of all signals to the corresponding protons
tected β-HAla oligomers in any solvent40 could be a of the R-amino acid, of the HB unit, and of the β-HAla
drawback to the synthesis and biological evaluation of moiety.
these compounds. To increase the solubility in water of To obtain the second fragment 9 with free amino and
compounds containing four β-HAla units,41 a positively protected carboxy group, the acid 5 was coupled with
charged peptide epitope from the HIV-1 gp120 protein H-Lys(Z)-OBn, using the HOBt/EDC strategy to give 8
(G314RAFVTIGK322, one-letter amino acid code), known (80%), treatment of which with a saturated HCl/dioxane
to bind well to HLA-B*2705,34 was chosen as template solution yielded the corresponding HCl salt 9. Com-
for the reported chemical modifications (Table 1). Fur- pound 10, consisting of six building blocks, was then
2320 Journal of Medicinal Chemistry, 1999, Vol. 42, No. 13 Poenaru et al.
Scheme 2a Scheme 4a
a (a) HCl•H-Lys(Z)-OBn, HOBt, EDC, Et N; (b) HCl/dioxane

3
(satd); (c) 1, HOBt, EDC, DIEA, DMF; (d) HCl/dioxane (satd); (e)
Fmoc-Ala-OH, DCC, DMAP, CH2Cl2; (f) TFA/CH2Cl2, 1:1; (g)
HOBt, EDC, DIEA, CH2Cl2/DMF, 1:1; (h) Et2NH/DMF, 1:4.
Scheme 3a
a (a) Boc-Arg(NO )-OH, HOBt, EDC, DIEA, DMF; (b) TFA, 10

2
min; (c) Boc-Gly-OH, HOBt, EDC, DIEA, DMF; (d) H2, Pd/BaSO4,
TFE/AcOH, 4:1; (e) TFA, 10 min.
application of the same fragment coupling strategy. The

fragment 15 was synthesized in a linear fashion,
coupling first Boc-β-HAla-OH (1) with H-Lys(Z)-OBn to
give dipeptide 12 (85%) which was deprotected to give
the HCl salt 13 (HCl in dioxane). The amino functional-
ity of 13, set free in situ by the base present in the
reaction mixture, was coupled with 1 to give the fully
protected compound 14 (74% from 12). The Boc group
of 14 was cleaved to yield 15. The fragment 17 was
obtained by ester formation between the hydroxy dimer
1637,51 and Fmoc-protected alanine (using DCC, DMAP),
and cleavage of the tert-butyl ester group (50% TFA)
gave the desired compound 18. It should be noted that
by using a small amount of DMAP (0.05 equiv), no
racemization was observed upon coupling.37 The amino
functionality, generated by in situ deprotonation of the
HCl salt 15, was coupled with the acid group of 18
a (a) HCl•H-Lys(Z)-OBn, HOBt, EDC, DIEA, DMF; (b) TFA, 10
(HOBt/EDC) to give the fully protected compound 19
min; (c) Boc-Ala-OH, HOBt, EDC, DIEA, DMF; (d) TFA, 10 min.
in 92% yield. The Fmoc protecting group was then
obtained in 90% yield by coupling of 7 with 9.50 cleaved (20% diethylamine in DMF52) to give the amino
Subsequent cleavage of the Boc protecting group led to ester 20. It is noteworthy that the backbone of com-
the amino ester 11 which was used for the next coupling pound 19 varies from that of 10 only by the respective
with arginine, without further purification (Scheme 4). positions of HB and β-HAla in the sequence. However
The derivative 20, with HB and β-HAla incorporated their respective solubilities in organic solvents are very
in different sequence (Scheme 2), was synthesized by different. Compound 10 is highly soluble in chlorinated
Table 1. Binding and Analytical Properties of Ligands 27, 28, and 29a-d
compd sequence C50a (µmol) HPLC (tR, min)b MSc (M + 1)+
HIV gp120d Gly-Arg-Ala-[Phe-Val-Thr-Ile-Gly]-Lys 2.8
A68P1e Glu-Val-Ala-Pro-Pro-Glu-Tyr-His-Arg nbf
27 Gly-Arg-Ala-[(S-β-HAla-R-HB)2]-Lysg 2.8 18.7 773.3
28 Gly-Arg-Ala-[(R-HB)2-(S-β-HAla)2]-Lys 17.0 19.5 774.1
29a Gly-Arg-Ala-[(R-β-HAla)4]-Lys 2.8 16.4 771.9
29b Gly-Arg-Ala-[(S-β-HAla-R-β-HAla)2]-Lys 4.8 15.4 772.6
29c Gly-Arg-Ala-[(S-β-HAla)4]-Lys 6.0 15.3 771.9
29d Gly-Arg-Ala-[(R-β-HAla)2-(S-β-HAla)2]-Lys 30.0 15.4 772.0
a Concentration of ligand at which HLA-B*2705 fluorescence (measured by FMC analysis with an anti-B27 monoclonal antibody) on
RMA-S cells was half the maximum obtained with that compound (see Experimental Section). b HPLC purification using a gradient of A
(0.1% trifluoroacetic acid in water) and B (acetonitrile): 0-100% B, 60 min. c MALDI-TOF spectra, recorded on a Bruker Biflex instrument
(Bruker-Franzen Analytik, Bremen, Germany) in linear mode. d HIV-1 glycoprotein 120 (314-322). e Self-peptide eluted from the HLA-
A68 allotype.8 f No detectable binding at 10-4 M. g β-HAla, β-homoalanine; HB, 3-hydroxybutanoate.
solvents such as CH2Cl2, whereas 19 is poorly soluble

even in DMF.
The configurational isomers (diastereoisomers) 21a-d
containing four β-HAla units (Scheme 3) have been
previously prepared, starting from (S)- and (R)-Boc-Ala-
OH and using a fragment coupling strategy.40 These
oligomers are difficult to handle because of their low
solubility in any solvent tested so far. For example, the
1H NMR spectra of protected β-HAla tetramers can only
be measured using dimethyl-d6 sulfoxide as solvent and

show rather broad signals. During the synthesis, larger
amounts of DMF were necessary to dissolve the β-HAla
oligomers (c ) 0.05 M), as compared to those required
in R-peptide synthesis, and reaction times were conse-
quently longer. Therefore, the yields of the reactions are
not specified, since no purification is possible before the
last deprotection step, due to the poor solubility of this
class of compounds.
The acids 21 were coupled with H-Lys(Z)-OBn using
HOBt/EDC, to provide the fully protected derivatives,
the Boc protecting groups of which were cleaved (con-
centrated TFA) to give the TFA salts 22 which were
precipitated with ether and dried in high vacuum before
the next reaction step: deprotonation and reaction with
Boc-Ala-OH to yield, after another deprotection step, the
corresponding TFA salts 23.
During the cleavage of the Boc group, the Z protecting
group of the lysine side chain was partially cleaved,
giving rise to a byproduct (e5%) which has been
detected by mass spectrometry. Such debenzylations
have been previously reported by Merrifield et al.53 Figure 1. Dynamic properties of complexes of B*2705 with
two modified peptides (29b, 29d) and the reference HIV-1
However, considering the much harsher conditions used gp120 (314-322) peptide. (A) Intermolecular hydrogen-bond
by the Merrifield group, the observed loss of the Z group, frequencies, recorded for the whole 500-ps trajectory of HLA-
in our case, was surprising. Due to solubility problems, B27-ligand complexes over 1000 conformations. Frequencies
it was impossible to purify the intermediates at this between 25% and 50% and higher than 50% are displayed as
stage. Thus, we have carried the byproduct all along white and gray columns, respectively. (B) Buried surface areas
the following synthetic steps, with the consequence that of HLA-B27-bound ligands 29b (white columns) and 29d (gray
columns) calculated on energy-minimized time-averaged con-
some additional impurities were formed. After the last formations. Surface areas were calculated using the MS
deprotection step, preparative HPLC purification still program74 with a 1.4-Å radius probe.
gave the desired pure compounds (27-29). The amino
functionalities of the derivatives 11, 20, and 23a-d BaSO4 as catalyst.56 Subsequent treatment with TFA
(Scheme 4) were allowed to react with Boc-Arg(NO2)- led to cleavage of the Boc groups to give, after HPLC
OH,54 using the same coupling procedure as for the purification, the desired nonapeptide analogues 27, 28,
other coupling steps. Again, the Boc groups of the fully and 29a-d which were used for binding assays.
protected derivatives were cleaved with TFA to yield Binding Affinity to HLA-B*2705. The binding
compounds 24, 25, and 26a-d which, in turn, were affinities of the modified peptides clearly show that the
coupled with Boc-Gly-OH to give the fully protected chirality of the spacer is important for recognition of
nonapeptides analogues. The NO2 and Z protecting the B*2705 protein. Compounds in which the chiral
groups, as well as the benzyl ester group, were then building block linked with the C-terminus (PC) has (R)-
simultaneously removed by hydrogenation, using Pd/ configuration (27, 29a-b) were all potent ligands with
binding affinities similar to that of the parent HIV-1 tween the two nonnatural complexes could be correlated
gp120 peptide (Table 1). This observation is in agree- with the H-bond-donating strength of the N-terminus,
ment with our previous report on PEPs for which a well-known to significantly contribute to the binding
penultimate (R)-HB unit was proposed to interact with free energy of nonapeptides to class I MHC proteins.58
the MHC binding groove.34 Analogues bearing a moiety The buried surface areas of each monomer of the
of (S)-configuration next to PC were less active, espe- protein-bound ligand were also very similar with the
cially compounds 28 and 29d sharing the same sequence exception of two residues P5, and PC (Figure 1B). P5
of (R,R,S,S)-configuration of the spacing oligomers corresponds to the second unit of the spacer (R-βHAla
(Table 1). However, an (S)-chiral spacer attached to PC in both cases). Depending on its environment in the
does not necessarily prevent binding (see compound 29c, sequence of the modified peptide, it is more or less
Table 1). Furthermore, it seems that certain configura- deeply buried in the HLA-B27 binding groove. With
tions of the four spacing monomers are detrimental to compound 29b, the P5 position is significantly deeper
binding. Thus, the two weakest binders (28, 29d) share inside the groove than with compound 29d (compare
the same (R,R,S,S)-configuration at positions 4 to 7. Figure 2A,B). However, this feature is unlikely to induce
Replacing ester by amide groups in the spacer (cf. 27 nearly a 10-fold difference in the binding affinity of the
with 29b and 28 with 29d) did not affect binding for corresponding ligands. The C-terminal amino acid (Lys)
both high-affinity and low-affinity ligands. This result also shows a better fit in the case of the high-affinity
is in agreement with the available X-ray structure56 of ligand (Figure 1B). As the C-terminal residue is an
a B*2705-nonapeptide complex, showing weak contri- important anchor to B*2705,56 this structural difference
butions of peptide bonds, located between the P4 and should also contribute to the improved binding of 29b
P8 positions, to the binding of a nonapeptide to HLA- versus 29d.
B27. However, the computed properties of the two ana-
Apart from binding potencies, it should be noticed logues bound to their target protein can only explain a
that HB-containing compounds 27 and 28 are probably part of the experimentally determined difference of
still sensitive to esterases, although stability studies on binding affinities. The modeling study presented here
these compounds have not been performed yet. We also takes into account only enthalpic contributions to the
expect that the replacement of HB oligomers by β-amino binding of each ligand to HLA-B*2705. As desolvation
acids in analogues 29a-d enhances the resistance of energies and rotational/translational entropy losses
the modified peptides to enzymatic degradation. upon binding (assuming a conserved binding mode of
Molecular Modeling of B*2705-Ligand Com- the two compounds) should be very similar due to the
plexes. To find a rational explanation for the weak structural analogy of all modified peptides listed in
binding of compounds with (R,R,S,S)-configuration of Table 1, the 10-fold decreased binding of two analogues
the chiral spacer, a 500-ps molecular dynamics (MD) (28, 29d), having the same configuration, may be due
study of the binary complexes between B*2705 and to different association rates and different conforma-
three ligands was undertaken. Compound 29b was tional populations in the free state. This feature has
chosen as representative of the high-affinity peptides, already been experimentally described for two related
whereas 29d was selected as representative of weak PEPs,34 for which the length of the polyester spacer
binding ligands. The parent HIV peptide was selected varies. Hydrophobic β-peptides are known to have
as reference. The trajectory of the three solvated com- conformations strongly depending on the chirality of
plexes was stable after 350 ps, with rms deviations of their residues and on the nature of their side chains.38,59
the protein backbone from the starting X-ray coordi- The (R,R,S,S)-configuration of four chiral monomers in
nates of ca. 1.5 Å (data not shown). We previously used low-affinity ligands might lead to a conformational space
atomic fluctuations of the bound ligands, as a criterion, arrangement in the free state that is different from that
for discriminating high-affinity from low-affinity pep- of high-affinity compounds (27, 28, 29a-c). The higher
tides.24,33,57 In the present case, they were very similar “strain energy” necessary to bring ligands 28 and 29d
for ligands 29b and 29d. Thus, subtle differences must from the free to the bound state may partially contribute
cause the very different binding affinities of the two to the weaker binding of these two analogues. Unfor-
modified peptides. In fact, recording the frequency of tunately, simulating the free ligands, although compu-
the MHC-ligand hydrogen bonds allows to distinguish tationally easier, is very risky because they adopt no
the two modified peptides. High-affinity ligands (HIV stable secondary structure, as concluded from their CD
gp120, 29b) present many more hydrogen bonds to the or NMR spectra.
HLA-B27 binding groove than the weak binding com-
pound 29d (Figure 1A). Strong H-bonds with a fre- Conclusion
quency higher than 50% were remarkably identical in Replacing the central amino acids of class I MHC-
both cases, but medium H-bonds (with frequencies binding peptides by (R)-3-hydroxybutanoate and(or)
between 25% and 50%) are significantly in favor of 29b. β-homoalanine oligomers leads to still high-affinity
A very similar pattern has already been observed for a ligands. Up to now, β-amino acids have hardly been used
set of four natural peptides binding to two closely in medicinal chemistry. Some natural β-amino acids
related HLA-B27 alleles.33 The major differences be- (taurine, β-aminobutyric acid, β-aminoisobutyric acid)
Figure 2. Three-dimensional structure of HLA-B*2705 in complex with 29b (A) and 29d (B). Peptide positions are labeled at
the CR atom from 1 (P1) to 8 (P8). The backbone trace of the MHC antigen-binding domain (R1, R2) of the B*2705 protein is
represented as bands (R helices), arrows (β strands), and tubes (coil). Altered peptides are displayed by a ball-and-stick model. A
white arrow indicates the position of the second β-ΗAla unit in both chiral spacers. The figure has been prepared using the
MOLSCRIPT75 and RASTER3D76 programs.
have been reported as agonists of the inhibitory glycine DIEA, 3 equiv). HOBt (1.25 equiv), the acid (1 equiv), and EDC
receptor.60 Substituted β-amino acids have also been (1.25 equiv) were then successively added. The reaction
described as fibrinogen receptor GIIb/IIIa antagonists,61 mixture was allowed to warm to room temperature and then
stirred for 18 h. The mixture was diluted with CH2Cl2 and
β-lactamase inhibitors,62 µ-opioid receptor agonists,63 or washed with 1 N HCl, saturated NaHCO3 solution, and brine.
enkephalin-degrading enzyme inhibitors.64 Further- The organic layer was dried over anhydrous MgSO4, filtrated,
more, various β-amino acids are found in natural and concentrated. The resulting residue was purified on silica
antibiotics, fungicides, and antineoplastic compounds.65 gel to afford the pure product.
However, to the best of our knowledge, this is the very General Procedure B: Amino Acid Coupling. The free
first report of biologically active molecules containing amine or the appropriate salt (1 equiv) was dissolved in DMF
β-amino acid oligomers. The present study demonstrates (0.15 M) under argon and cooled to 0 °C. The reaction mixture
that β-amino acids are valuable tools, indeed, for was treated with DIEA (3 equiv). HOBt (1.25 equiv), the acid
(1 equiv), and EDC (1.25 equiv) were then successively added.
designing peptidomimetics of bioactive peptides. By The product was precipitated by the addition of a saturated
contrast to most R-amino acid surrogates, the H-bonding NaHCO3 solution. The precipitate was washed several times
properties of backbone atoms, the backbone direction, with saturated NaHCO3, 1 M KHSO4 solutions and H2O and
or the side chain directionality might be similar in dried 24 h under high vacuum to give the crude product which
natural and β-peptides, at the condition that the β-pep- was utilized in the next step without further purification.
tide can adopt the biologically active conformation of its General Procedure C: Boc Cleavage Using a HCl
natural R-peptide analogue. Thus, if all side chains are Solution. Under argon and at 0 °C, the Boc-protected com-
not mandatory for biological activity, β-amino acids and, pound was dissolved in a saturated HCl/(EtO2 or dioxane)
solution. The mixture was stirred for 15 min to 1 h and then
more generally, β-peptides undoubtedly represent new
evaporated. The resulting HCl salt was precipitated in ether,
promising tools in medicinal chemistry. In the special dried under high vacuum, and used for the next step without
case of class I MHC ligands, one might imagine to use further purification.
β-amino acids for replacing MHC anchors and(or) TCR General Procedure D: Boc Cleavage Using a TFA
contact residues. Such altered peptides may thus lead Solution. Under argon and at 0 °C, the Boc-protected com-
to peptide-based vaccines and TCR antagonists, which pound was dissolved in a TFA/CH2Cl2 (50-100%) solution. The
would be stable to all common peptidases tested so far, mixture was stirred for 10 min to 1 h and then evaporated.
including pronase, 20S proteasome, and proteinase K. The resulting TFA salt was precipitated in Et2O, dried under
high vacuum, and used for the next step without further
Experimental Section purification.
General Procedure E: Final Deprotection. The fully
Abbreviations: (R)-β-homoalanine (R-β-HAla), (S)-β-ho- protected compound was dissolved in TFE/CH3COOH (3/1),
moalanine (S-β-HAla), dicyclohexylcarbodiimide (DCC), diiso- and a catalytic amount of 10% Pd/BaSO4 was added. The
propylethylamine (DIEA), 4-(dimethylamino)pyridine (DMAP), apparatus was evacuated and flushed three times with H2, and
dimethylformamide (DMF), N-(3-(dimethylamino)propyl)-N′- the mixture was stirred under an atmosphere of H2 for ca. 15
ethylcarbodiimide hydrochloride (EDC), 1-hydroxy-1H-benzo- h. The mixture was then filtrated though Celite, concentrated,
triazole (HOBt), trifluoroacetic acid (TFA), trifluoroethanol and precipitated from Et2O. The resulting yellow-white CH3-
(TFE), (R)-3-hydroxybutanoate (R-HB). COOH salt was then treated with concentrated TFA. After 15
Chemistry. Dichloromethane (CH2Cl2) was dried over 4-Å min, the crude product was precipitated from Et2O and
molecular sieves. Solvents for chromatography and workup purified by HPLC.
procedures were distilled from Sikkon (anhydrous CaSO4,
Boc-S-β-HAla-R-HB-OBn (3). To a solution of the (R)-3-
Fluka). Triethylamine (Et3N) was distilled from CaH2 and
hydroxybutanoic benzyl ester (2)45 (1.90 g, 9.8 mmol) in CH2-
stored over KOH. Amino acid derivatives were purchased from
Cl2 (30 mL) was added a solution of the acid 138 (2.00 g, 9.8
Bachem or Senn. All other reagents were used as received from
mmol) in CH2Cl2 (30 mL) under argon, cooled to -5 °C. DCC
Fluka.
1H (300-MHz) and 13C (75-MHz) NMR spectra were recorded (2.12 g, 10.3 mmol) and DMAP (0.09 g, 0.49 mmol) were added.
The resulting mixture was allowed to warm to room temper-
on a Varian Gemini 300 spectrometer and are reported in ppm
ature and then stirred for 24 h. The mixture was diluted with
on the δ scale from TMS. Coupling constants are reported in
Et2O and washed with 1 N HCl, saturated NaHCO3 solution,
hertz (Hz). FAB-MS spectra were obtained with a Hitachi
and brine. The organic layer was dried over anhydrous MgSO4,
Perkin-Elmer RHU-6M using a 3-nitrobenzyl alcohol (3-
filtrated, and concentrated. The residue was purified on silica
NOBA) matrix. Elemental analyses were performed by the
gel (20% Et2O/pentane) and gave compound 3 (3.25 g, 88%)
Microanalytical Laboratory of the Laboratorium für Orga-
as a colorless oil. 1H NMR (300 MHz, CDCl3): δ 7.37-7.33
nische Chemie, ETH-Zürich (only analyses above 0.4% were
given). (m, 5H ar), 5.36-5.26 (m, 1H, CHO), 5.14 (AB, J ) 12.1, 1H,
OCH2Ph), 5.09 (AB, J ) 12.1, 1H, OCH2Ph), 5.00-4.90 (m,
Chromatography generally refers to flash silica gel 60 (Fluka
1H, NH), 4.10-3.96 (m, 1H, CHN), 2.66 (dd, ABX, J ) 7.5,
40-63 mm) and TLC (Merck Kieselgel 60 F254 plates), detec-
15.6, 1H, CH2CHO), 2.54 (dd, ABX, J ) 5.3, 15.6, 1H, CH2-
tion with UV and ninhydrin. HPLC analyses were carried out
CHO), 2.43 (dd, ABX, J ) 5.3, 14.9, 1H, CH2CHN), 2.37 (dd,
on a C18 analytical column on a Knauer HPLC system (pump
ABX, J ) 5.9, 14.9, 1H, CH2CHN), 1.43 (s, 9H, tBu), 1.29 (d,
type 64, EuroChrom 2000 integration package, degaser, UV
J ) 6.2, 3H, Me of HB), 1.17 (d, J ) 6.5, 3H, Me of β-HAla).
detector (variable-wavelength monitor)) using a linear gradient 13C NMR (75 MHz, CDCl ): δ 171.00, 170.42, 155.36, 135.93,
3
of (A) 0.1% CF3COOH in H2O and (B) MeCN at a flow rate of
1 mL/min with UV detection at 220 nm. HPLC purification 128.84, 128.60, 67.58, 66.65, 43.60, 40.77, 28.46, 20.31, 19.96.
was carried out on a C8 preparative column on a Knauer FAB-MS: m/z 759 {26, (2M + 1)+}, 308 {64, (M + 1)+}, 280
HPLC system (pump type 64, programmer 50, UV detector (100).
(variable-wavelength monitor)) using a gradient of (A) 0.1% HCl•H-S-β-HAla-R-HB-OBn (4). According to general
CF3COOH in H2O and (B) MeCN at a flow rate of 4 mL/min procedure C, compound 3 (227 mg, 0.6 mmol) was treated with
with UV detection at 214 nm. Retention times (tR) are given a saturated HCl/Et2O solution (6 mL). The resulting HCl salt
in min. 4 was obtained as a white precipitate and used in the next
General Procedure A: Amino Acid Coupling. The free coupling step without further purification.
amine or the appropriate salt (1 equiv) was dissolved in CH2- Boc-S-β-HAla-R-HB-OH (5). The benzyl-protected com-
Cl2 or 50% CH2Cl2/DMF (0.1 M) under argon and cooled to 0 pound 3 (900 mg, 2.9 mmol) was dissolved in MeOH (20 mL);
°C. The reaction mixture was treated with a base (Et3N or catalytic amounts of 10% Pd/C (90 mg) and acetic acid (0.1
mL) were added. The apparatus was evacuated and flushed ) 6.2, 3H, Me), 1.17 (d, J ) 6.8, 3H, Me), 1.15 (d, J ) 6.5, 3H,
three times with H2, and the mixture was stirred under an Me). 13C NMR (75 MHz, CDCl3): δ 172.49, 170.79, 170.08,
atmosphere of H2 for ca. 8 h. Subsequent filtration though 169.58, 156.98, 136.84, 135.64, 128.86, 128.78, 128.73, 128.54,
Celite and concentration under reduced pressure yielded the 128.37, 128.29, 68.61, 68.27, 67.19, 66.74, 52.39, 42.47, 42.21,
acid 5 (558 mg, 84%) as a colorless oil which was identified by 41.24, 40.40, 31.42, 29.40, 28.41, 22.36, 20.06, 19.85, 19.71,
NMR and used for the next coupling step without purification. 18.81. FAB-MS: m/z 906 {6, (M + Na)+}, 884 {32, (M + 1)+},
Boc-Ala-S-β-HAla-R-HB-OBn (6). According to general 784 (100). Anal. (C45H65N5O13•H2O) C, H, N.
procedure A, to a solution in CH2Cl2 (26 mL) of HCl salt 4 (1 TFA•H-Ala-(S-β-HAla-R-HB)2-Lys(Z)-OBn (11). Accord-
equiv, 2.61 mmol) was added Et3N (1.45 mL, 10.4 mmol). HOBt ing to general procedure D, compound 10 (654 mg, 0.74 mmol)
(440 mg, 3.3 mmol), Boc-Ala-OH (4.94 mg, 2.61 mmol), and was treated with a CH2Cl2/TFA (1:1) solution (6 mL). After
then EDC (623 mg, 3.3 mmol) were successively added to the 30 min, the reaction was completed and the solvent was
reaction. The residue was purified by recrystallization (Et2O/ evaporated. The TFA resulting salt 11 was obtained in almost
pentane, 2/5) to give compound 6 (994 mg, 85%) as a white quantitative yield as a white precipitate (from Et2O) and used
solid. 1H NMR (300 MHz, CDCl3): δ 7.35-7.326 (m, 5H ar), in the next coupling step without further purification.
6.70 (br d, J ) 6.8, 1H, NH), 5.33-5.27 (m, 1H, CHO), 5.12 9 Boc-S-β-HAla-Lys(Z)-OBn (12). According to general pro-
(s, 2H, OCH2Ph), 5.12-5.06 (m, 1H, NH), 4.36-4.22 (m, 1H, cedure A, to a solution in DMF (50 mL) of the HCl salt of Lys-
CHN), 4.18-4.06 (m, 1H, CHN), 2.74-2.66 (m, 1H, CH2CHO), (Z)-OBn (2.00 g, 4.9 mmol) was added Et3N (2.04 mL, 14.7
2.58 (dd, ABX, J ) 5.0, 15.57, 1H, CH2CHO), 2.42 (d, J ) 5.3, mmol). HOBt (0.83 g, 6.1 mmol), the acid Boc-β-HAla-OH (1)
2H, CH2CHN), 1.44 (s, 9H, tBu), 1.34-1.29 (m, 6H, 2 Me), 1.17 (1.00 g, 4.9 mmol), and then EDC (1.17 g, 6.1 mmol) were
(d, J ) 6.8, 3H, Me). 13C NMR (75 MHz, CDCl3): δ 172.12, successively added to the reaction. The residue was purified
170.87, 135.80, 128.86, 128.67, 128.62, 67.87, 66.78, 42.02, by recrystallization (ethyl acetate/hexane, 20/1) to give com-
40.69, 40.33, 28.38, 19.98, 19.66, 18.64. FAB-MS: m/z 901 {11, pound 12 (2.30 g, 85%) as a white solid. 1H NMR (300 MHz,
(2M + 1)+}, 451 {100, (M + 1)+9}, 351 (48). CDCl3): δ 7.37-7.26 (m, 10H ar), 6.48-6.36 (m, 1H, NH),
Boc-Ala-S-β-HAla-R-HB-OH (7). The benzyl-protected 5.22-5.10 (m, 3H, OCH2Ph, NH), 5.09 (s, 2H, OCH2Ph), 4.95-
compound 6 (675 mg, 1.5 mmol) was dissolved in MeOH (10 4.87 (m, 1H, NH), 4.62-4.56 (m, 1H, CHN), 4.00-3.90 (m, 1H,
mL); catalytic amounts of 10% Pd/C (70 mg) and acetic acid CHN), 3.17-3.10 (m, 2H, CH2NHZ), 2.46-2.32 (m, 2H, CH2-
(0.1 mL) were added. The apparatus was evacuated and CHN), 1.90-1.60 (m, 2H, CH2), 1.50-1.25 (m, 4H, CH2), 1.42
flushed three times with H2, and the mixture was stirred under (s, 9H, tBu), 1.16 (d, J ) 6.8, 3H, Me). 13C NMR (75 MHz,
an atmosphere of H2 for ca. 8 h. Subsequent filtration though CDCl3): δ 172.44, 156.90, 136.85, 135.56, 128.89, 128.78,
Celite and concentration under reduced pressure yielded the 128.65, 128.37, 67.29, 66.74, 52.01, 44.18, 42.52, 40.41, 31.61,
acid 7 in almost quantitative yield as a colorless oil which was 29.30, 28.46, 22.15, 20.60. FAB-MS: m/z 556 {28, (M + 1)+},
used for the next coupling step without purification. 456 (100).
Boc-S-β-HAla-R-HB-Lys(Z)-OBn (8). According to general HCl•H-S-β-HAla-Lys(Z)-OBn (13). According to general
procedure A, to a solution in CH2Cl2 (15 mL) of HCl‚H-Lys- procedure C, compound 12 (1.00 g, 1.8 mmol) was treated with
(Z)-OBn (784 mg, 1.9 mmol) was added Et3N (1.08 mL, 7.7 a saturated HCl/dioxane solution (20 mL). After 30 min, the
mmol). HOBt (326 mg, 2.4 mmol), compound 5 (558 mg, 1.9 reaction was completed and the solvent was evaporated. The
mmol), and then EDC (460 mg, 2.4 mmol) were successively resulting HCl salt 13 was obtained in almost quantitative yield
added to the reaction. The residue was purified on silica gel as a white precipitate (from Et2O) and used in the next
(50% Et2O/pentane) to give compound 8 (964 mg, 78%) as a coupling step without further purification.
white solid. 1H NMR (300 MHz, CDCl3): δ 7.38-7.29 (m, 10H Boc-(S-β-HAla)2-Lys(Z)-OBn (14). According to general
ar), 6.96-6.90 (m, 1H, NH), 5.27-5.17 (m, 1H, CHO), 5.22- procedure A, to a solution in DMF (5 mL) of the HCl salt 13
5.09 (m, 2H, OCH2Ph), 5.08 (s, 2H, OCH2Ph), 4.97-4.94 (m, (1 equiv, 1.8 mmol) was added DIEA (0.92 mL, 5.4 mmol).
1H, NH), 4.90-4.86 (m, 1H, NH), 4.66-4.58 (m, 1H, CHN), HOBt (304 mg, 2.2 mmol), the acid Boc-β-HAla-OH (1) (365
4.16-4.05 (m, 1H, CHN), 3.16-3.09 (m, 2H, CH2NHZ), 2.54- mg, 1.8 mmol), and then EDC (430 mg, 2.2 mmol) were
2.27 (m, 4H, CH2CHN, CH2CHO), 1.90-1.60 (m, 4H, 2 CH2), successively added to the reaction. The residue was purified
1.50-1.28 (m, 2H, CH2), 1.40 (s, 9H, tBu), 1.30 (d, J ) 6.2, by recrystallization (CH3Cl/hexane, 20/1) to give compound 14
3H, Me), 1.13 (d, J ) 6.8, 3H, Me). 13C NMR (75 MHz, (850 mg, 74%) as a white solid. 1H NMR (300 MHz, CDCl3):
CDCl3): δ 172.57, 170.84, 169.74, 156.83,155.65, 136.87, δ 7.38-7.26 (m, 10H ar), 6.68-6.65 (m, 2H, NH), 5.23-5.09
135.69, 128.86, 128.76, 128.71, 128.55, 111.19, 79.61, 68.19, (m, 4H, OCH2Ph, NH), 5.09 (s, 2H, OCH2Ph), 4.58-4.50 (m,
67.16, 66.74, 52.19, 43.84, 42.30, 41.96, 40.61, 31.71, 29.46, 1H, CHN), 4.30-4.20 (m, 1H, CHN), 4.00-3.90 (m, 1H, CHN),
28.43, 22.42, 20.90, 19.46. FAB-MS: m/z 642 {12, (M + 1)+}, 3.18-3.10 (m, 2H, CH2NHZ), 2.42-2.22 (m, 4H, CH2CHN),
542 (100). 1.90-1.62 (m, 2H, CH2), 1.52-1.25 (m, 4H, CH2), 1.42 (s, 9H,
HCl•H-S-β-HAla-R-HB-Lys(Z)-OBn (9). According to gen- tBu), 1.19 (d, J ) 6.5, 3H, Me), 1.15 (d, J ) 6.8, 3H, Me). 13C
eral procedure C, compound 8 (712 mg, 1.1 mmol) was treated NMR (75 MHz, CDCl3): δ 172.44, 155.78, 128.88, 128.78,
with a saturated HCl/dioxane solution (10 mL). After 15 min, 128.62, 128.37, 67.30, 66.74, 52.27, 43.10, 40.29, 31.29, 28.56,
the reaction was completed and the solvent was evaporated. 28.48, 22.21, 20.24. FAB-MS: m/z 663 {22, (M + Na)+}, 641
The resulting HCl salt 9 was obtained in almost quantitative {38, (M + 1)+}, 541 (100).
yield as a white precipitate and used in the next coupling step HCl•H-(S-β-HAla)2-Lys(Z)-OBn (15). According to general
without further purification. procedure C, compound 15 (712 mg, 1.1 mmol) was treated
Boc-Ala-(S-β-HAla-R-HB)2-Lys(Z)-OBn (10). According to with a saturated HCl/dioxane solution (10 mL). After 30 min,
general procedure A, to a solution in CH2Cl2 (15 mL) of the the reaction was completed and the solvent was evaporated.
HCl salt 9 (1 equiv, 1.5 mmol) was added DIEA (1.0 mL, 6.0 The HCl resulting salt 15 was obtained in almost quantitative
mmol). HOBt (253 mg, 1.8 mmol), compound 7 (1 equiv, 1.5 yield as a white precipitate (from Et2O) and used in the next
mmol), and then EDC (358 mg, 1.8 mmol) were successively coupling step without further purification.
added to the reaction. The residue was purified on silica gel Fmoc-Ala-(R-HB)2-OtBu (17). To a solution of the hydroxy
(ethyl acetate/hexane, 9/1) to give compound 10 (884 mg, 90%) derivative 1651 (1 equiv, 4.4 mmol) in CH2Cl2 (40 mL) was
as a white solid foam. 1H NMR (300 MHz, CDCl3): δ 7.36- added Fmoc-Ala-OH (1.45 g, 4.4 mmol) under argon, and the
7.30 (m, 10H ar), 7.10-7.00 (m, 3H, NH), 5.34 (d, J ) 7.5, 1H, mixture was cooled to - 5 °C. DCC (0.95 g, 4.62 mmol) and
NH), 5.30-5.10 (m, 3H, CHO, NH), 5.21-5.09 (m, 2H, OCH2- DMAP (0.04 g, 0.22 mmol) were added, and the resulting
Ph), 5.07 (s, 2H, OCH2Ph), 4.60-4.53 (m, 1H, CHN), 4.44- mixture was allow to warm to room temperature and then
4.31 (m, 2H, CHN), 4.17-4.08 (m, 1H, CHN), 3.16-3.08 (m, stirred for 24 h. The mixture was diluted with Et2O and
2H, CH2NHZ), 2.55-2.29 (m, 8H, CH2CHN, CH2CHO), 1.88- washed with 1 N HCl, saturated NaHCO3 solution, and brine.
1.60 (m, 2H, CH2), 1.58-1.22 (m, 4H, CH2), 1.42 (s, 9H, tBu), The organic layer was dried over anhydrous MgSO4, filtrated,
1.31 (d, J ) 6.8, 3H, Me), 1.29 (d, J ) 6.2, 3H, Me), 1.25 (d, J and concentrated. The residue was purified on silica gel (Et2O/
pentane, 2/3) to give compound 17 (700 mg, 30%) as a white soluble in any flash chromatography or HPLC solvent. The
foam. 1H NMR (300 MHz, CDCl3): δ 7.77-7.75 (m, 2H ar), presence of the desired Boc-(S-β-HAla-R-β-HAla)2-Lys(Z)-OBn
7.61-7.59 (m, 2H ar), 7.42-7.37 (m, 2H ar), 7.34-7.26 (m, (11 mg, 90% crude) was confirmed by 1H and 13C NMR and
2H ar), 6.49 (d, J ) 7.2, NH), 5.38-5.22 (m, 2H, CHO), 4.44- MS spectra. Further treatment with TFA (0.55 mL), according
4.32 (m, 3H, CHN, CH2 of Fmoc), 4.25-4.20 (m, 1H, CH of to the general procedure D, gave the TFA salt 22b, which was
Fmoc), 2.69-2.37 (m, 4H, CH2CHO), 1.43 (s, 9H, tBu), 1.30 used without further purification.
(d, J ) 6.2, 3H, Me), 1.29 (d, J ) 6.2, 3H, Me), 1.26 (d, J ) TFA•H-(S-β-HAla)4-Lys(Z)-OBn (22c). According to gen-
6.5, 3H, Me). 13C NMR (75 MHz, CDCl3): δ 172.44, 169.69, eral procedure B, to a solution in DMF (15 mL) of HCl•H-Lys-
169.37, 155.91, 144.23, 144.12, 141.58, 127.94, 125.33, 120.20, (Z)-OBn (515 mg, 1.27 mmol) was added DIEA (0.65 mL, 3.81
81.10, 68.68, 68.21, 67.09, 49.83, 47.27, 40.05, 40.88, 28.09, mmol). HOBt (214 mg, 1.59 mmol), the acid Boc-(S-β-HAla)4-
19.80, 19.67, 18.67. FAB-MS: m/z 540 {6, (M + 1)+}, 484 (100). OH (21c)40 (1 equiv, 1.27 mmol), and then EDC (304 mg, 1.59
Fmoc-Ala-(R-HB)2-OH (18). According to general proce- mmol) were successively added to the reaction. The resulting
dure C, compound 17 (600 mg, 1.1 mmol) was treated with a precipitate was dried under high vacuum and used without
TFA/CH2Cl2 (1:1) solution (6 mL). After 30 min, the reaction further purification as it is not soluble in any flash chroma-
was completed and the solvent was evaporated. The acid 18 tography or HPLC solvent. The presence of the desired Boc-
was obtained in almost quantitative yield as a yellow oil and (S-β-HAla)4-Lys(Z)-OBn (819.1 mg, 79% crude) was confirmed
used in the next coupling step without further purification. by 1H and 13C NMR and MS spectra. Further treatment with
Fmoc-Ala-(R-HB)2-(S-β-HAla)2-Lys(Z)-OBn (19). Accord- TFA (4 mL), according to the general procedure D, gave the
ing to general procedure A, to a solution in CH2Cl2/DMF (1:1, TFA salt 22c, which was used without further purification.
12 mL) of the HCl salt 15 (1 equiv, 1.10 mmol) was added TFA•H-(R-β-HAla)2-(S-β-HAla)2-Lys(Z)-OBn (22d). Ac-
DIEA (0.75 mL, 4.40 mmol). HOBt (185 mg, 1.37 mmol), the cording to general procedure B, to a solution in DMF (11 mL)
acid 18 (1 equiv, 1.10 mmol), and then EDC (262 mg, 1.37 of HCl•H-Lys(Z)-OBn (442 mg, 1.09 mmol) was added DIEA
mmol) were successively added to the reaction. After 15 h (0.56 mL, 3.27 mmol). HOBt (184 mg, 1.36 mmol), the acid
reaction, some of the product precipitated in the reaction Boc-(R-β-HAla)2-(S-β-HAla)2-Lys(Z)-OH (21d)40 (1 equiv, 1.09
mixture. The CH2Cl2 was then evaporated, and the resulting mmol), and then EDC (260 mg, 1.36 mmol) were successively
oil was precipitated in a saturated NaHCO3 solution. The added to the reaction. The resulting precipitate was dried
precipitate was washed several times with saturated NaHCO3, under high vacuum and used without further purification as
KHSO4 (1 N) solutions and finally with H2O and dried 15 h it is not soluble in any flash chromatography or HPLC solvent.
under high vacuum. The presence of compound 19 was The presence of the desired Boc-(R-β-HAla)2-(S-β-HAla)2-Lys-
confirmed by 1H and 13C NMR and MS spectra. Compound 19 (Z)-OBn (796 mg, 90% crude) was confirmed by 1H and 13C
was used without further purification. 1H NMR (300 MHz, NMR and MS spectra. Further treatment with TFA (3.9 mL),
DMSO-d6): δ 8.28-8.22 (m, 1H, NH), 7.30-7.94 (m, 1H, NH), according to the general procedure D, gave the TFA salt 22d,
7.80-7.74 (m, 1H, NH), 7.75-7.65 (m, 2H ar), 7.42-7.24 (m, which was used without further purification.
16H ar), 7.22-7.16 (m, 1H, NH), 5.23-5.02 (m, 3H, CHO, NH), TFA•H-Ala-(R-β-HAla)4-Lys(Z)-OBn (23a). According to
5.208 (s, 2H, OCH2Ph), 5.96 (s, 2H, OCH2Ph), 4.32-4.14 (m, general procedure B, to a solution in DMF (7 mL) of the TFA
2H, CHN), 4.10-4.22 (m, 2H, CHN), 2.96-2.87 (m, 2H, CH2- salt 22a (1 equiv, 0.89 mmol) was added DIEA (0.61 mL, 3.56
NHZ), 2.40-2.00 (m, 8H, CH2CHN, CH2CHO), 1.70-1.51 (m, mmol). HOBt (150 mg, 1.11 mmol), Boc-Ala-OH (202 mg, 1.06
2H, CH32), 1.40-1.10 (m, 4H, 2 CH2), 1.23 (d, J ) 6.8, 3H, mmol), and then EDC (212 mg, 1.1 mmol) were successively
Me), 1.13 (d, J ) 5.0, 3H, Me), 1.04 (d, J ) 5.9, 3H, Me), 1.03- added to the reaction. The resulting precipitate was dried
0.98 (m, 2 Me). 13C NMR (75 MHz, DMSO-d6): δ 172.28, under high vacuum and used without further purification as
170.52, 169.11, 168.09, 167.99, 156.26, 155.99, 144.02, 140.90, it is not soluble in any flash chromatography or HPLC solvent.
137.43, 136.14, 128.55, 128.47, 128.15, 127.94, 127.84, 127.77, The presence of the desired Boc-Ala-(R-β-HAla)4-Lys(Z)-OBn
127.21, 125.38, 120.25, 68.34, 67.77, 65.83, 65.64, 65.12, 63.44, (680 mg, 87% crude) was confirmed by 1H and 13C NMR and
51.88, 49.42, 46.58, 44.25, 42.18, 42.05, 41.82, 41.64, 30.38, MS spectra. Further treatment with TFA (3.1 mL), according
28.86, 23.18, 22.55, 19.82, 19.75, 19.51, 19.38, 19.15. FAB- to the general procedure D, gave the TFA salt 23a, which was
MS: m/z 1028 {23, (M + Na)+}, 1006 {41, (M + 1)+}, 809 (84), used without further purification.
713 (100). TFA•H-Ala-(S-β-HAla-R-β-HAla)2-Lys(Z)-OBn (23b). Ac-
H-Ala-(R-HB)2-(S-β-HAla)2-Lys(Z)-OBn (20). The Fmoc- cording to general procedure B, to a solution in DMF (2 mL)
protected compound 19 (520 mg, 0.52 mmol) was dissolved in of the TFA salt 22b (1 equiv, 0.135 mmol) was added DIEA
DMF/Et2NH (9:1, 4 mL) under argon and cooled to 0 °C. The (0.092 mL, 0.540 mmol). HOBt (23 mg, 0.169 mmol), Boc-Ala-
mixture was stirred for 1-2 h, and concentration under OH (31 mg, 0.162 mmol), and then EDC (32 mg, 0.169 mmol)
reduced pressure yielded the crude amine 20 which was were successively added to the reaction. The resulting pre-
identified by NMR and used without further purification. cipitate was dried under high vacuum and used without
TFA•H-(R-β-HAla)4-Lys(Z)-OBn (22a). According to gen- further purification as it is not soluble in any flash chroma-
eral procedure B, to a solution in DMF (11 mL) of HCl•H-Lys- tography or HPLC solvent. The presence of the desired Boc-
(Z)-OBn (442 mg, 1.09 mmol) was added DIEA (0.56 mL, 3.27 Ala-(S-β-HAla-R-β-HAla)2-Lys(Z)-OBn (73 mg, 61% crude) was
mmol). HOBt (184 mg, 1.36 mmol), the acid Boc-(β-HAla)4- confirmed by 1H and 13C NMR and MS spectra. Further
OH (21a)40 (1 equiv, 1.09 mmol), and then EDC (260 mg, 1.36 treatment with TFA (0.33 mL), according to the general
mmol) were successively added to the reaction. The residue procedure D, gave the TFA salt 23b, which was used without
was dried under high vacuum and used without further further purification.
purification as it is not soluble in any flash chromatography TFA•H-Ala-(S-β-HAla)4-Lys(Z)-OBn (23c). According to
or HPLC solvent. The presence of the desired Boc-(R-β-HAla)4- general procedure B, to a solution in DMF (10 mL) of the TFA
Lys(Z)-OBn (723 mg, 82% crude) was confirmed by 1H and 13C salt 22c (1 equiv, 1.00 mmol) was added DIEA (0.68 mL, 4.00
NMR and MS spectra. Further treatment with TFA (3.6 mL), mmol). HOBt (169 mg, 1.25 mmol), Boc-Ala-OH (227 mg, 1.20
according to the general procedure D, gave the TFA salt 22a, mmol), and then EDC (239 mg, 1.25 mmol) were successively
which was used without further purification. added to the reaction. The resulting precipitate was dried
TFA•H-(S-β-HAla-R-β-HAla)2-Lys(Z)-OBn (22b). Accord- under high vacuum and used without further purification as
ing to general procedure B, to a solution in DMF (2 mL) of it is not soluble in any flash chromatography or HPLC solvent.
HCl•H-Lys(Z)-OBn (62 mg, 0.15 mmol) was added DIEA (0.08 The presence of the desired Boc-Ala-(S-β-HAla)4-Lys(Z)-OBn
mL, 0.45 mmol). HOBt (26 mg, 0.19 mmol), the acid Boc-(S- (762 mg, 86% crude) was confirmed by 1H and 13C NMR and
β-HAla-R-β-HAla)2-OH (21b)40 (1 equiv, 0.15 mmol), and then MS spectra. Further treatment with TFA (3.5 mL), according
EDC (36 mg, 0.19 mmol) were successively added to the to the general procedure D, gave the TFA salt 23c, which was
reaction. The resulting precipitate was dried under high used without further purification.
vacuum and used without further purification as it is not TFA•H-Ala-(R-β-HAla)2-(S-β-HAla)2-Lys(Z)-OBn (23d).
According to general procedure B, to a solution in DMF (10 tography or HPLC solvent. The presence of the desired Boc-
mL) of the TFA salt 22d (770 mg, 0.93 mmol) was added DIEA Arg(NO2)-(S-β-HAla-R-β-HAla)2-Lys(Z)-OBn (74 mg) was con-
(0.64 mL, 3.72 mmol). HOBt (157 mg, 1.16 mmol), Boc-Ala- firmed by FAB-MS. Further treatment with TFA (0.5 mL),
OH (211 mg, 1.12 mmol), and then EDC (215 mg, 1.16 mmol) according to the general procedure D, gave the TFA salt 26b,
were successively added to the reaction. The resulting pre- which was used without further purification.
cipitate was dried under high vacuum and used without TFA•H-Arg(NO2)-Ala-(S-β-HAla)4-Lys(Z)-OBn (26c). Ac-
further purification as it is not soluble in any flash chroma- cording to general procedure B, to a solution in DMF (9 mL)
tography or HPLC solvent. The presence of the desired Boc- of the TFA salt 23c (1 equiv, 0.86 mmol) was added DIEA (0.59
Ala-(R-β-HAla)2-(S-β-HAla)2-Lys(Z)-OBn (490 mg, 60% crude) mL, 3.44 mmol). HOBt (145 mg, 1.07 mmol), Boc-Arg(NO2)-
was confirmed by 1H and 13C NMR and MS spectra. Further OH (329 mg, 1.03 mmol), and then EDC (205 mg, 1.07 mmol)
treatment with TFA (2.2 mL), according to the general were successively added to the reaction. The resulting pre-
procedure D, gave the TFA salt 23d, which was used without cipitate was dried under high vacuum and used without
further purification. further purification as it is not soluble in any flash chroma-
TFA•H-Arg(NO2)-Ala-(S-β-HAla-R-HB)2-Lys(Z)-OBn (24). tography or HPLC solvent. The presence of the desired Boc-
According to general procedure A, to a solution in CH2Cl2/DMF Arg(NO2)-Ala-(S-β-HAla)4-Lys(Z)-OBn (860 mg, 82% crude)
(4:3, 8 mL) of the TFA salt 11 (1 equiv, 0.74 mmol) was added was confirmed by 1H and 13C NMR and MS spectra. Further
DIEA (0.38 mL, 2.22 mmol). HOBt (125 mg, 0.92 mmol), Boc- treatment with TFA (3.1 mL), according to the general
Arg(NO2)-OH (259 mg, 0.81 mmol), and then EDC (176 mg, procedure D, gave the TFA salt 26c, which was used without
0.92 mmol) were successively added to the reaction. The further purification.
resulting residue was purified on silica gel (CH2Cl2/MeOH, 9/1) TFA•H-Arg(NO2)-Ala-(R-β-HAla)2-(S-β-HAla)2-Lys(Z)-
to give compound Boc-Arg(NO2)-Ala-(S-β-HAla-R-HB)2-Lys(Z)- OBn (26d). According to general procedure B, to a solution
OBn (650 mg, 82%) as a fine white powder. 1H NMR (300 MHz, in DMF (9 mL) of the TFA salt 23d (1 equiv, 0.45 mmol) was
CDCl3): δ 8.45-8.30 (m, 1H, NH), 7.80-7.60 (m, 3H, NH), added DIEA (0.31 mL, 1.81 mmol). HOBt (76 mg, 0.56 mmol),
7.8-7.28 (m, 10H ar), 7.20-7.12 (m, 3H, NH), 5.70-5.60 (m, Boc-Arg(NO2)-OH (172 mg, 0.54 mmol), and then EDC (107
1H, NH), 5.34-5.26 (m, 1H, NH), 5.26-5.06 (m, 4H, CHO, mg, 0.56 mmol) were successively added to the reaction. The
OCH2Ph), 5.07 (s, 2H, OCH2Ph), 4.60-4.50 (m, 1H, CHN), resulting precipitate was dried under high vacuum and used
4.46-4.2 (m, 4H, CHN), 3.36-3.24 (m, 2H, CH2NHC), 3.16- without further purification as it is not soluble in any flash
3.07 (m, 2H, CH2NHZ), 2.53-2.33 (m, 8H, CH2CHN, CH2- chromatography or HPLC solvent. The presence of the desired
CHO), 1.90-1.60 (m, 6H, CH2), 1.54-1.10 (m, 4H, CH2) 1.41 Boc-Arg(NO2)-Ala-(R-β-HAla)2-(S-β-HAla)2-Lys(Z)-OBn (460 mg,
(s, 9H, tBu), 1.34 (d, J ) 6.8, 3H, Me), 1.28 (d, J ) 6.2, 3H, 84% crude) was confirmed by 1H and 13C NMR and MS spectra.
Me), 1.24 (d, J ) 6.5, 3H, Me), 1.20-1.16 (m, 6H, Me). 13C Further treatment with TFA (2.2 mL), according to the general
NMR (75 MHz, CDCl3): δ 172.61, 170.35, 170.27, 169.77, procedure D, gave the TFA salt 26d, which was used without
157.09, 136.82, 135.61, 128.87, 128.80, 128.54, 128.37, 128.23, further purification.
80.46, 68.68, 68.40, 67.22, 65.96, 52.48, 49.54, 42.48, 42.16, H-Gly-Arg-Ala-(S-β-HAla-R-HB)2-Lys-OH (27). According
40.46, 31.36, 29.41, 28.39, 24.85, 22.41, 20.02, 19.88, 19.74, to general procedure B, to a solution in DMF (6 mL) of the
19.66, 18.19. FAB-MS: m/z 1107 {60, (M + Na)+}, 1085 {100, TFA salt 24 (1 equiv, 0.50 mmol) was added DIEA (0.26 mL,
(M + 1)+}, 985 (22), 713 (7). Further treatment with TFA (5 1.51 mmol). HOBt (85 mg, 0.63 mmol), Boc-Gly-OH (97 mg,
mL), according to the general procedure D, gave the TFA salt 0.55 mmol), and then EDC (124 mg, 0.63 mmol) were succes-
24, which was used without further purification. sively added to the reaction. The resulting precipitate was
TFA•H-Arg(NO2)-Ala-(R-HB)2-(S-β-HAla)2-Lys(Z)-OBn dried under high vacuum and used without further purification
(25). According to general procedure B, to a solution in DMF as it is not soluble in any solvent to be purified. The presence
(6 mL) of the TFA salt 20 (1 equiv, 0.52 mmol) was added of the desired Boc-Gly-Arg(NO2)-Ala-(S-β-HAla-R-HB)2-Lys-
DIEA (0.26 mL, 1.55 mmol). HOBt (87 mg, 0.65 mmol), Boc- (Z)-OBn (447 mg, 68% crude) as a fine yellow-white powder
Arg(NO2)-OH (198 mg, 0.62 mmol), and then EDC (123 mg, was confirmed by 1H and 13C NMR and MS spectra.
0.65 mmol) were successively added to the reaction. The According to general procedure E, Boc-Gly-Arg(NO2)-Ala-
resulting precipitate was dried under high vacuum and used (S-β-HAla-R-HB)2-Lys(Z)-OBn (300 mg, 0.26 mmol) was dis-
without further purification as it is not soluble in any flash solved in TFE/CH3COOH (3:1, 4 mL) and hydrogenated in the
chromatography or HPLC solvent. The presence of the desired presence of Pd/BaSO4 (10%, 60 mg). The resulting precipitate
Boc-Arg(NO2)-Ala-(R-HB)2-(S-β-HAla)2-Lys(Z)-OBn (409 mg, was purified by HPLC C8 (5-40% B, 30 min), tR 12.5 min, to
77% crude) was confirmed by 1H and 13C NMR and MS spectra. give after lyophilization the pure compound 27 in about 40%
Further treatment with TFA (1.4 mL), according to the general yield. 1H NMR (300 MHz, D2O): δ 5.24-5.10 (m, 2H, CHO),
procedure D, gave the TFA salt 25, which was used without 4.34-4.28 (m, 2H, CHN), 4.22-4.15 (m, 3H, CHN), 3.84 (s,
further purification. 2H, CH2N), 3.19 (t, J ) 6.8, 2H, CH2NHC), 3.00-2.95 (m, 2H,
TFA•H-Arg(NO2)-Ala-(R-β-HAla)4-Lys(Z)-OBn (26a). Ac- CH2NH2), 2.58-2.42 (m, 8H, CH2CHO, CH2CHN), 1.92-1.58
cording to general procedure B, to a solution in DMF (9 mL) (m, 8H, CH2), 1.50-1.40 (m, 2H, CH2), 1.32 (d, J ) 7.5, 3H,
of the TFA salt 23a (1 equiv, 0.77 mmol) was added DIEA (0.53 Me), 1.26 (d, J ) 6.2, 3H, Me), 1.25 (d, J ) 6.2, 3H, Me), 1.18-
mL, 3.08 mmol). HOBt (130 mg, 0.96 mmol), Boc-Arg(NO2)- 1.13 (m, 6H, Me). FAB-MS: m/z 811 {10, (M + K)+}, 795 {32,
OH (295 mg, 0.92 mmol) and then EDC (183 mg, 0.96 mmol) (M + Na)+}, 773 {100, (M + 1)+}. Purity by analytical HPLC
were successively added to the reaction. The resulting pre- (0-100% B, 60 min, tR 18.7 min) >99%.
cipitate was dried under high vacuum and used without H-Gly-Arg-Ala-(R-HB)2-(S-β-HAla)2-Lys-OH (28). Accord-
further purification as it is not soluble in any solvent to be ing to general procedure D, to a solution in DMF (5 mL) of
purified. The presence of the desired Boc-Arg(NO2)-Ala-(R-β- the TFA salt 25 (1 equiv, 0.37 mmol) was added DIEA (0.19
HAla)4-Lys(Z)-OBn (757 mg, 81% crude) was confirmed by 1H mL, 1.11 mmol). HOBt (62 mg, 0.46 mmol), Boc-Gly-OH (77
and 13C NMR and MS spectra. Further treatment with TFA mg, 0.44 mmol), and then EDC (88 mg, 0.46 mmol) were
(2.7 mL), according to the general procedure D, gave the TFA successively added to the reaction. The resulting precipitate
salt 26a, which was used without further purification. was dried under high vacuum and used without further
TFA•H-Arg(NO2)-(S-β-HAla-R-β-HAla)2-Lys(Z)-OBn (26b). purification as it is not soluble in any flash chromatography
According to general procedure B, to a solution in DMF (9 mL) or HPLC solvent. The presence of the desired Boc-Gly-Arg-
of the TFA salt 23b (1 equiv, 0.83 mmol) was added DIEA (NO2)-Ala-(R-HB)2-(S-β-HAla)2-Lys(Z)-OBn (252 mg, 60% crude)
(0.057 mL, 0.33 mmol). HOBt (14 mg, 0.104 mmol), Boc-Arg- was confirmed by 1H and 13C NMR and MS spectra.
(NO2)-OH (32 mg, 0.099 mmol), and then EDC (20 mg, 0.104 According to general procedure E, Boc-Gly-Arg(NO2)-Ala-
mmol) were successively added to the reaction. The resulting (R-HB)2-(S-β-HAla)2-Lys(Z)-OBn (200 mg, 0.17 mmol) was
precipitate was dried under high vacuum and used without dissolved in TFE/CH3COOH (3:1, 3.5 mL) and hydrogenated
further purification as it is not soluble in any flash chroma- in the presence of Pd/BaSO4 (10%, 40 mg). The resulting
precipitate was purified by HPLC (10-40% B, 30 min), tR 6.2 According to general procedure E, Boc-Gly-Arg(NO2)-Ala-
min, to give after lyophilization the pure compound 28 in about (S-β-HAla)4-Lys(Z)-OBn (340 mg, 0.30 mmol) was dissolved in
25% yield. 1H NMR (300 MHz, D2O): δ 5.22-5.06 (m, 2H, TFE/CH3COOH (3:1, 4 mL) and hydrogenated in the presence
CHO), 4.28-4.20 (m, 3H, CHN), 4.16-4.04 (m, 2H, CHN), 3.76 of Pd/BaSO4 (10%, 60 mg). The resulting precipitate was
(s, 2H, CH2N), 3.16-3.10 (m, 2H, CH2NHC), 2.93-2.86 (m, purified by HPLC (10-40% B, 30 min), tR 6.8 min, to give after
2H, CH2NH2), 2.65-2.49 (m, 2H, CH2CHO), 2.43-2.32 (m, 2H, lyophilization the pure compound 29c in about 30% yield. 1H
CH2CHO), 2.36 (d, J ) 7.2, 2H, CH2CHN), 2.26 (d, J ) 7.2, NMR (300 MHz, D2O): δ 4.34-4.27 (m, 2H, CHN), 4.24-4.09
2H, CH2CHN), 1.85-1.53 (m, 8H, CH2), 1.41-1.28 (m, 2H, (m, 5H, CHN), 3.84-3.81 (m, 2H, CH2N), 3.21-3.15 (m, 2H,
CH2), 1.35 (d, J ) 7.2, 3H, Me), 1.20-1.14 (m, 6H, Me), 1.08- CH2NHC), 2.99-2.93 (m, 2H, CH2NH2), 2.45-2.41 (m, 2H,
1.03 (m, 6H, Me). FAB-MS: m/z 811 {12, (M + K)+}, 795 {23, CH2C9HN), 2.40-2.26 (m, 6H, CH2CHN), 1.92-1.57 (m, 8H,
(M + Na)+}, 773 {100, (M + 1)+}. Purity by analytical HPLC CH2), 1.47-1.35 (m, 2H, CH2), 1.31 (d, J ) 7.2, 3H, Me), 1.15-
(0-100% B, 60 min, tR 19.5 min) >99%. 1.09 (m, 12H, Me). 13C NMR (75 MHz, D2O): δ 178.59, 176.58,
H-Gly-Arg-Ala-(R-β-HAla)4-Lys-OH (29a). According to 176.50, 176.08, 175.30, 170.09, 159.82, 56.22, 55.30, 52.71,
general procedure B, to a solution in DMF (7 mL) of the TFA 46.25, 45.22, 44.78, 43.37, 43.13, 42.00, 32.78, 31.13, 28.99,
salt 26a (1 equiv, 0.68 mmol) was added DIEA (0.47 mL, 2.71 27.02, 24.85, 22.16, 21.97, 19.50. FAB-MS: m/z 1542 {17, (2M
mmol). HOBt (115 mg, 0.85 mmol), Boc-Gly-OH (143 mg, 0.82 + 2)+}, 771 {100, (M + 1)+}. Purity by analytical HPLC (0-
mmol), and then EDC (163 mg, 0.85 mmol) were successively 100% B, 60 min, tR 15.3 min) >99%.
added to the reaction. The precipitate was dried under high H-Gly-Arg-Ala-(R-β-HAla)2-(S-β-HAla)2-Lys-OH (29d).
vacuum and used without further purification as it is not According to general procedure B, to a solution in DMF (5 mL)
soluble in any flash chromatography or HPLC solvent. The of the TFA salt 26d (1 equiv, 0.42 mmol) was added DIEA
presence of the desired Boc-Gly-Arg(NO2)-Ala-(R-β-HAla)4-Lys- (0.29 mL, 1.68 mmol. HOBt (71 mg, 0.52 mmol), Boc-Gly-OH
(Z)-OBn (622 mg, 80% crude) was confirmed by 1H and 13C (88 mg, 0.50 mmol), and then EDC (100 mg, 0.52 mmol) were
NMR and MS spectra. successively added to the reaction. The resulting precipitate
According to general procedure E, Boc-Gly-Arg(NO2)-Ala- was dried under high vacuum and used without further
(R-β-HAla)4-Lys(Z)-OBn (200 mg, 0.18 mmol) was dissolved purification as it is not soluble in any flash chromatography
in TFE/CH3COOH (3:1, 3.5 mL) and hydrogenated in the or HPLC solvent. The presence of the desired Boc-Gly-Arg-
presence of Pd/BaSO4 (10%, 40 mg). The resulting precipitate (NO2)-Ala-(R-β-HAla)2-(S-β-HAla)2-Lys(Z)-OBn (333 mg, 70%
was purified by HPLC (5-40% B, 30 min), tR 17.20 min, to crude) was confirmed by 1H and 13C NMR and MS spectra.
give after lyophilization the pure compound 29a in about 25% According to general procedure E, Boc-Gly-Arg(NO2)-Ala-
yield. 1H NMR (300 MHz, D2O): δ 4.32-4.24 (m, 2H, CHN), (R-β-HAla)2-(S-β-HAla)2-Lys(Z)-OBn (150 mg, 0.13 mmol) was
4.21-4.07 (m, 5H, CHN), 3.85-3.80 (m, 2H, CH2N), 3.20-3.14 dissolved in TFE/CH3COOH (3:1, 3 mL) and hydrogenated in
(m, 2H, CH2NHC), 2.98-2.92 (m, 2H, CH2NH2), 2.50-2.25 (m, the presence of Pd/BaSO4 (10%, 25 mg). The resulting pre-
8H, CH2CHN), 1.90-1.58 (m, 8H, CH2), 1.47-1.36 (m, 2H, cipitate was purified by HPLC (2-40% B, 30 min), tR 20.5 min,
CH2), 1.32 (d, J ) 7.2, 3H, Me), 1.14-1.09 (m, 12H, Me). 13C to give after lyophilization the pure compound 29d in about
NMR (75 MHz, D2O): δ 178.57, 176.08, 175.29, 56.37, 55.39, 20% yield. 1H NMR (300 MHz, D2O): δ 4.36-4.28 (m, 2H,
52.77, 46.22, 46.11, 45.20, 43.36, 43.15, 41.95, 32.66, 31.13, CHN), 4.27-4.12 (m, 5H, CHN), 3.87-3.83 (m, 2H, CH2N),
28.98, 27.05, 24.86, 22.00, 19.43. FAB-MS: m/z 1542 {9, (2M 3.23-3.18 (m, 2H, CH2NHC), 3.01-2.96 (m, 2H, CH2NH2),
+2)+}, 771 {100, (M + 1)+}. Purity by analytical HPLC (0- 2.346-2.43 (m, 2H, CH2CHN), 2.41-2.31 (m, 6H, CH2CHN),
100% B, 60 min, tR 16.4 min) >99%. 1.92-1.60 (m, 8H, CH2), 1.50-1.40 (m, 2H, CH2), 1.35 (d, J )
H-Gly-Arg-Ala-(S-β-HAla-R-β-HAla)2-Lys-OH (29b). Ac- 7.5, 3H, Me), 1.17-1.11 (m, 12H, Me). FAB-MS: m/z 793 {15,
cording to general procedure B, to a solution in DMF (2 mL) (M + Na)+}, 771 {100, (M + 1)+}. Purity by analytical HPLC
of the TFA salt 26b (1 equiv, 0.068 mmol) was added DIEA (0-100% B, 60 min, tR 15.4 min) >80%.
(0.046 mL, 0.28 mmol). HOBt (12 mg, 0.085 mmol), Boc-Gly- Molecular Dynamics Simulations. Molecular mechanics
OH (14 mg, 0.082 mmol), and then EDC (16 mg, 0.085 mmol) and dynamics calculations were realized using the AMBER
were successively added to the reaction. The resulting pre- 5.0 package66 using the parm96 parameter set and an all-atom
cipitate was dried under high vacuum and used without force-field representation.67 Force-field parameters for the ester
further purification as it is not soluble in any flash chroma- bonds were taken from the literature.68 Atomic charges for the
tography or HPLC solvent. The presence of the desired Boc- new monomers (R-HB, S-β-HAla, R-β-HAla) were calculated
Gly-Arg(NO2)-(S-β-HAla-R-β-HAla)2-Lys(Z)-OBn (70 mg) was using the GAUSSIAN94 package69 and the HF/6-31G* basis
confirmed by FAB-MS. set, by fitting atom-centered charges to an ab initio electro-
According to general procedure E, Boc-Gly-Arg(NO2)-(S-β- static potential, using the RESP method.70 Initial coordinates
HAla-R-β-HAla)2-Lys(Z)-OBn (70 mg, 0.06 mmol) was dis- for the MHC-ligand complexes were obtained from the X-ray
solved in TFE/CH3COOH (3:1, 1 mL) and hydrogenated in the structure of HLA-B*270556 (Protein Data Bank code 1hsa) as
presence of Pd/BaSO4 (10%, 10 mg). The resulting precipitate previously described.33,34 The spacers were substituted for the
was purified by HPLC (5-40% A, 30 min), tR 8.6 min, to give natural pentapeptide sequence using the SYBYL 6.3 modeling
after lyophilization the pure compound 29b in about 25% yield. package (TRIPOS Assoc., Inc., St. Louis, MO). From a starting
1H NMR (300 MHz, D O): δ 4.26-4.18 (m, 2H, CHN), 4.18-
2 fully extended conformation, dihedral angles of the main chain
4.04 (m, 5H, CHN), 3.76-3.73 (m, 2H, CH2N), 3.12-3.07 (m, between P3 and P9 were modified in order to reproduce a
2H, CH2NHC), 2.91-2.85 (m, 2H, CH2NH2), 2.40-2.32 (m, 2H, correct trans geometry for the newly introduced amide or ester
CH2CHN), 2.30-2.22 (m, 6H, CH2CHN), 1.85-1.50 (m, 8H, bonds. The ligand was first relaxed by 1000 steps of conjugate
CH2), 1.40-1.30 (m, 2H, CH2), 1.26-1.22 (m, 3H, Me), 1.09- gradient energy minimization while maintaining the protein
1.02 (m, 12H, Me). FAB-MS: m/z 771 (86, [M + 1]+). Purity fixed. It was then submitted to a 100-ps Simulated annealing
by analytical HPLC (0-100% B, 60 min, tR 15.4 min) >99%. (SA) protocol in order to sample the broadest possible confor-
H-Gly-Arg-Ala-(S-β-HAla)4-Lys-OH (29c). According to mational space. Starting with random velocities assigned at
general procedure B, to a solution in DMF (8 mL) of the TFA a temperature of 1000 K, the peptide was first coupled to a
salt 26c (1 equiv, 0.77 mmol) was added DIEA (0.53 mL, 3.1 heat bath at 1000 K using a temperature coupling constant
mmol). HOBt (131 mg, 0.97 mmol), Boc-Gly-OH (163 mg, 0.93 Tτ of 0.2 ps and then linearly cooled to 50 K for the next 50 ps
mmol), and then EDC (185 mg, 0.97 mmol) were successively while strengthening Tτ to a value of 0.05 ps. During these 100
added to the reaction. The resulting precipitate was dried ps, no protein atom was allowed to move. As the simulated
under high vacuum and used without further purification as annealing was performed in vacuo, a distance-dependent
it is not soluble in any flash chromatography or HPLC solvent. dielectric function ( ) 4r) was used. A twin cutoff (10.0, 15.0
The presence of the desired Boc-Gly-Arg(NO2)-Ala-(S-β-HAla)4- Å) was used to calculate nonbonded electrostatic interactions
Lys(Z)-OBn (719 mg, 82% crude) was confirmed by 1H and 13C at every minimization step and every nonbonded pair list
NMR and MS spectra. update (10 steps), respectively.
From the last SA conformer, 13 counterions (9 Na+ and 4 (6) Madden, D. R.; Garboczi, D. N.; Wiley, D. C. The antigenic
Cl- ions) were then placed at electrostatic minima to neutralize identity of peptide/MHC complexes: a comparison of the con-
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75, 693-708.
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Universidad Autónoma de Madrid

JOSÉ RAMÓN LAMAS LÓPEZ

Base molecular de la especificidad

Memoria para optar al grado de Doctor en Ciencias

presentada por: José Ramón Lamas López

Director: Dr. José Antonio López de Castro Álvarez

Madrid, Junio de 1999.

APC Células presentadoras de antígeno.

TREONINA SERINA TIROSINA FENILALANINA TRIPTÓFANO

ALANINA VALINA LEUCINA ISOLEUCINA PROLINA

Aminoácidos apolares alifáticos

Ác. ASPÁRTICO Ác. GLUTÁMICO LISINA HISTIDINA ARGININA

I.2. Organización genómica y estructural del MHC humano. ...................................................................................... 4

I.3. Estructura de las proteínas de clase I. ............................................................................................................................. 6

I.3.1. La cadena pesada y la Beta-2 microglobulina (β2m). . .............................................................................. 6

I.4.3. Biosíntesis, Ensamblaje y expresión en membrana de las moléculas de clase I. ........................... 11

I.5. TCR y reconocimiento de los complejos MHC-péptido. ........................................................................................... 11

I.6. HLA-B27. ...................................................................................................................................................................................... 13

I.6.1. Subcavidad A. ............................................................................................................................................................. 13

I.6.4. Subcavidades D y E. ................................................................................................................................................ 15

I.7. HLA-B27 y espondiloartropatías. ....................................................................................................................................... 15

I.7.1. Posible papel patogénico de la presentación de péptidos por HLA-B27. ......................................... 16

I.7.2. Distribución étnica y asociación a enfermedad de los subtipos de HLA-B27. ................................ 17

II. OBJETIVOS. ............................................................................................................................................................................................... 21

III. MATERIALES Y MÉTODOS. .......................................................................................................................................................... 25

III.1. Líneas celulares. ..................................................................................................................................................................................27

III.3. Síntesis, purificación y cuantificación de péptidos. ..........................................................................................................27

III.4.1. Análisis por citometría de flujo. ................................................................................................................................29

III.4.2. Cálculo de la unión de péptidos. ...............................................................................................................................29

IV.1.1.1. Efectos de la pérdidas y ganancias de residuos cargados en las

IV.1.2. Unión de péptidos a B*2701 y B*2702. Efecto del polimorfismo sobre la

IV.1.3.2. Fluctuaciones atómicas, áreas accesibles y no accesibles. ............................................... 41

IV.1.3.3. Analisis cualitativo y cuantitativo de los puentes de hidrógeno. ..................................... 42

IV.2.1. Unión de péptidos virales a diferentes subtipos deHLA-B27, y su relación

IV.2.3. El motivo Arg2, anclaje principal de los péptidos unidos a HLA-B27, no es

IV.4.1. Reemplazamiento de la parte central de epítopos naturales con un

V.1.1. Influencia del polimorfismo de la cavidad C/F sobre la especificidad por el

Resumen y discusión general. ...................................................................................................................................................... 73

VI. CONCLUSIONES. .................................................................................................................................................................................. 75

VII. REFERENCIAS. .................................................................................................................................................................................... 79

VIII. ANEXOS. ................................................................................................................................................................................................. 91

I.1. CARACTERÍSTICAS GENERALES DEL SISTEMA INMUNITARIO.

l sistema inmunitario es el encargado de proteger a un organismo discriminando entre

E lo que le pertenece y lo extraño a él. Cuando esta función falla y lo propio no es

Los linfocitos T se distribuyen en dos subpoblaciones dependiendo del tipo de proteína

I.2. ORGANIZACIÓN GENÓMICA Y ESTRUCTURAL DEL MHC HUMANO.

I.2.1. Organización de los genes del MHC de clase I y clase II.

La región de clase I abarca una extensión de 1600 Kb orientada hacia el extremo

Clase II Clase III Clase I

β α β α β α β β α MIC B MIC A MIC C MIC D MIC E

Figura 1: Mapa genético del complejo principal de histocompatibilidad humano, ubicado en el

I.3. ESTRUCTURA DE LAS PROTEÍNAS DE CLASE I.

Las moléculas HLA de clase I, son glicoproteínas de membrana formadas por la

I.3.1. La cadena pesada y la Beta-2 microglobulina (β2m).

hélice coronan una base constituida por ocho

I.3.2. Los péptidos.

I.4. PROCESAMIENTO DE ANTÍGENO. FORMACIÓN, TRANSPORTE Y PRESENTACIÓN DE

I.4.1. Origen y procesamiento de los péptidos antigénicos.

I.4.2. Translocación al Retículo Endoplásmico.

I.4.3. Biosíntesis, Ensamblaje y expresión en membrana de las moléculas de clase I.

Tras la biosíntesis de las proteínas de clase I, en el correcto plegamiento y ensamblaje de

I.5. TCR Y RECONOCIMIENTO DE LOS COMPLEJOS MHC-PÉPTIDO.

I.5.1. Características estructurales del TCR y reconocimiento de los complejos MHC-péptido.

El receptor de antígeno de los linfocitos T maduros, está compuesto por heterodímeros

IV.1.2. Unión de péptidos a B2701 y B2702. Efecto del polimorfismo sobre la

IV.1.1. Unión de péptidos a HLA-B2705, B2704 y B*2706. Modulación de la especificidad

PÉPTIDO SECUENCIA B2705 B2704 B*2706 S77 Y116 E152 D114 DY

Tabla 2: Unión de ligandos naturales de B2705 y B2702, a subtipos y mutantes de HLA-B27.

Péptido Secuencia B2705 B2704 B*2706 S77 Y116 E152 D114 DY

Péptido Secuencia B2705 B2704 B*2706 Y116 D114

Péptido Secuencia B2705 B2702 B*2701 Y74 A81

Tabla 4: Unión de ligandos naturales de B2705 y B2702 a subtipos y mutantes

Tabla 5: Péptido Secuencia B2705 B2702 B*2701 Y74 A81

Péptido Secuencia B2705 B2702 B*2701 Y74 A81

B2705 y B2703 se diferencian exclusivamente en el cambio Y59H, localizado en la

Los valores entre Péptido Restricción Secuencia B2705 B2702 B*2704