ANA1CM CI kC1LINS

A 8lolnformaLlcs Approach
CNL1S CI kC1LIN
S1kU1UkL
lkOM POLYP1lu cn4lN 1O 1n
lOLuu 51kuc1uk
Am|no ac|d 8as|c un|t of Am|no ac|d 8as|c un|t of prote|n prote|n
D|fferent s|de cha|ns k determ|ne the propert|es of 20 am|no
ac|ds
1he 20 am|no ac|ds found |n prote|ns
ormaLlon of epLlde 8ond
CL?L1luL CPAln
CL?L1luL CPAln 1C 3u
CLuLu S18uC1u8L
1nkLL 1LS CI NCN CVALLN1 IN1LkA1ICNS
A|though a s|ng|e one of these bonds |s qu|te weak many of them often form together to create a strong
bond|ng arrangement as |n the examp|e shown
1he po|ar am|no ac|d s|de cha|ns tend to gather on the outs|de of the
prote|n where they can |nteract w|th water the nonpo|ar am|no ac|d s|de
cha|ns are bur|ed on the |ns|de to form a t|ght|y packed hydrophob|c core of
atoms that are h|dden from water
kCLL CI 8ICINICkMA1IS IN
kC1LIN S1kU1UkL kLDI1ICN
Jn 1C kLDI1 S1kU1UkLS ??
W lL ls lmporLanL Lo know Lhe sLrucLure of a
8lomolecule Lo sclenLlflcally undersLand Lhe funcLlon
of any blologlcal sysLem
W 1he Lhreedlmenslonal sLrucLure of a molecule ls
consldered known when Lhe preclse locaLlon of each
and every aLom ln lL ls known
W Any conslderaLlon of proLeln funcLlon musL be
grounded ln an undersLandlng of proLeln sLrucLure
W A fundamenLal prlnclple ln all of proLeln sclence ls
LhaL Protein structure /eods to protein function
1here are three centra| b|o|og|ca| processes around wh|ch
b|o|nformat|cs too|s must be deve|oped
MISICLDLD kC1LINS
NLUkCDLGLNLkA1IVL
DISCkDLkS
W Al2nlMk5 ul5A5
W c51lc ll8kO5l5
W MAu cOw ul5A5
W lw 1l5 OlcANck
SLULNL
S1kU1UkL
IUN1ICN
8LulC1Lu 3u S18uC1u8LS A8L
Su8Ml11Lu ln 8C1Lln uA1A 8Ank
u8 lLL C8MA1
3u CCC8ulnA1LS
IMCk1ANL CI
kAMAnANDkAN LC1 IN
ASSLSSING kC1LIN
CNICkMA1ICN
kC1LIN S1kU1UkL kLDI1ICN
1C8SlCnAL AnCLLS ln A CL?L1luL
CPAln
W Amlno aclds can form bonds wlLh each oLher Lhrough
a reacLlon wlLh Lhelr respecLlve carboxyl and amlno
Lermlnus whlch resulLs ln Lhe formaLlon of Lhe
epLlde 8ond
W olypepLlde bond ls planar and rlgld and has
roLaLlonal freedom only abouL lLs carbons
W 1hese bonds have been Lermed Lhe hl and sl
angles
C n phl angle
C C sl angle
8amachandran loL
W ln a polypepLlde Lhe maln chaln nCalpha and
CalphaC bonds relaLlvely are free Lo roLaLe 1hese
roLaLlons are represenLed by Lhe Lorslon angles phl
and psl respecLlvely
W C n 8amachandran used compuLer models of small
polypepLldes Lo sysLemaLlcally vary phl and psl wlLh
Lhe ob[ecLlve of flndlng sLable conformaLlons or
each conformaLlon Lhe sLrucLure was examlned for
close conLacLs beLween aLoms ALoms were LreaLed
as hard spheres wlLh dlmenslons correspondlng Lo
Lhelr van der Waals radll 1herefore phl and psl
angles whlch cause spheres Lo colllde correspond Lo
sLerlcally dlsallowed conformaLlons of Lhe
polypepLlde backbone
4 komochondron p/ot mops the entire
conformotiono/ spoce of o po/ypeptide ond shows the o//owed ond
diso//owed conformotions
kAMAnANDkAN LC1
In the d|agram above the wh|te areas
correspond to conformat|ons where atoms |n
the po|ypept|de come c|oser than the sum of
the|r van der Jaa|s rad| 1hese reg|ons are
ster|ca||y d|sa||owed for a|| am|no ac|ds
except g|yc|ne wh|ch |s un|que |n that |t |acks
a s|de cha|n 1he red reg|ons correspond to
conformat|ons where there are no ster|c
c|ashes |e these are the a||owed reg|ons
name|y the a|phahe||ca| and betasheet
conformat|ons 1he ye||ow areas show the
a||owed reg|ons |f s||ght|y shorter van der
Jaa|s rad| are used |n the ca|cu|at|on |e the
atoms are a||owed to come a ||tt|e c|oser
together 1h|s br|ngs out an add|t|ona| reg|on
wh|ch corresponds to the |efthanded a|pha
he||x
D|sa||owed reg|ons genera||y |nvo|ve ster|c
h|ndrance between the s|de cha|n and ma|n
cha|n atoms G|yc|ne has no s|de cha|n and
therefore can adopt ph| and ps| ang|es |n a||
four quadrants of the kamachandran p|ot
nence |t frequent|y occurs |n turn reg|ons of
prote|ns where any other res|due wou|d be
ster|ca||y h|ndered
CNICkMA1ICN ANGLLS CI SLVLkAL SLCNDAk
S1kU1UkLS
SLCNDAk S1kU1UkL O (deg) (deg)
kIGn1 nANDLD nLLIk S7 47
AkALLLL SnLL1 119 113
AN1IAkALLLL SnLL1 139 13S
kIGn1 nANDLD 3
10
nLLIk 49 26
kIGn1 nANDLD n nLLIk S7 70
CLLAGLN S1 1S3
LLI1 nANDLD nLLIk S7 47
LLI1 nANDLD
CLGLINL II CLL
kCLINL II nLLILS
79 1S0
5cONu4kY 51kuc1uk
Pkulc1lON u5lN6
8lOlNlOkM41lc5 1OOL5
1nL SLCNDAk S1kU1UkL CI kC1LINS
1nL LCAL 1nkLLDIMLNSICNAL S1kU1UkL
W 1he secondary sLrucLure of a proLeln can be
LhoughL of as Lhe local conformaLlon of Lhe
polypepLlde chaln lndependenL of Lhe resL of
Lhe proLeln
W 1he llmlLaLlons lmposed on Lhe prlmary
sLrucLure of a proLeln by Lhe pepLlde bond and
Pydrogen bondlng conslderaLlons dlcLaLe Lhe
secondary sLrucLure LhaL ls posslble
W uurlng Lhe course of proLeln sLrucLure research Lwo Lypes of secondary
sLrucLure have emerged as Lhe domlnanL local conformaLlons of
polypepLlde chalns A|pha () he||x and 8eta () sheets
W lnLeresLlngly Lhese sLrucLures were acLually predlcLed by Llnus aullng
8oberL Corey and P 8 8ranson based on Lhe known physlcal llmlLaLlons
of polypepLlde chalns prlor Lo Lhe experlmenLal deLermlnaLlon of proLeln
sLrucLures
W lndeed lf Lhe 8amachandran ploL ls examlned hellces and sheeLs conLaln
and angles LhaL fall wlLhln Lhe Lwo largesL reglons of allowed
conformaLlon 1hese sLrucLures exhlblL a hlgh degree of regularlLy Lhe
parLlcular and angle comblnaLlons ln Lhe polypepLlde chaln are
approxlmaLely repeaLed for Lhe duraLlon of Lhe secondary sLrucLure
W AlLhough hellces and sheeLs saLlsfy Lhe pepLlde bond consLralnLs Lhls ls
noL Lhe only facLor LhaL explalns Lhelr ublqulLy 8oLh of Lhese sLrucLural
elemenLs are sLablllzed by hydrogen bond lnLeracLlons beLween Lhe
backbone aLoms of Lhe parLlclpaLlng resldues maklng Lhem a hlghly
favorable conformaLlon for Lhe polypepLlde chaln
W Pellces and sheeLs are Lhe only regular secondary sLrucLural elemenLs
presenL ln proLelns Powever lrregular secondary sLrucLural elemenLs are
also observed ln proLelns and are vlLal Lo boLh sLrucLure and funcLlon
Alpha hellx
Pellx
W A hellx ls creaLed by a curvlng of Lhe polypepLlde backbone such LhaL a
regular coll shape ls produced 8ecause Lhe polypepLlde backbone can be
colled ln Lwo dlrecLlons (lefL or rlghL) hellces exhlblL handedness
W A hellx wlLh a rlghLward coll ls known as a rlghLhanded hellx A|most a||
he||ces observed |n prote|ns are r|ghthanded as ster|c restr|ct|ons ||m|t the
ab|||ty of |efthanded he||ces to form
W Among the r|ghthanded he||ces the he||x |s by far the most preva|ent
W An hellx ls dlsLlngulshed by havlng a perlod of 36 resldues per Lurn of Lhe
backbone coll 1he sLrucLure of Lhls hellx ls sLablllzed by hydrogenbondlng
lnLeracLlons beLween Lhe carbonyl oxygen of each resldue and Lhe amlde
proLon of Lhe resldue 4 resldues ahead ln Lhe hellx
W CLher hellces have also been observed ln proLelns Lhough much less
frequenLly due Lo Lhelr less favorable geomeLry 1he 3
10
he||x has a perlod of
3 resldues per Lurn wlLh hydrogen bonds beLween each resldue and Lhe
resldue 3 poslLlons ahead
W 1hls Lype of hellx ls usually seen only ln shorL segmenLs ofLen aL Lhe ends of
an hellx 1he very rare p| (n) he||x has a perlod of 44 resldues per Lurn wlLh
hydrogen bonds beLween each resldue and Lhe resldue 3 poslLlons ahead
and has only been seen aL Lhe ends of hellces
8eLa SheeLs
W unllke hellces sheeLs are formed by hydrogen bonds
beLween ad[acenL polypepLlde chalns raLher Lhan wlLhln a
slngle chaln
W SecLlons of Lhe polypepLlde chaln parLlclpaLlng ln Lhe
sheeL are known as sLrands sLrands represenL an
extended conformat|on of Lhe polypepLlde chaln where
Lhe angles are roLaLed approxlmaLely 180 wlLh respecL Lo
each oLher 1hls arrangemenL produces a sheeL LhaL ls
pleaLed wlLh Lhe resldue slde chalns alLernaLlng poslLlons
on opposlLe sldes of Lhe sheeL
W 1wo conflguraLlons of sheeL are posslble para||e| and
ant|para||e| ln parallel sheeLs Lhe sLrands are arranged ln
Lhe same dlrecLlon wlLh respecL Lo Lhelr amlnoLermlnal
(n) and carboxyLermlnal (C) ends
8eLa SheeLs
W ln anLlparallel sheeLs Lhe sLrands alLernaLe Lhelr
amlno and carboxy Lermlnal ends such LhaL a
glven sLrand lnLeracLs wlLh sLrands ln Lhe opposlLe
orlenLaLlon
W sheets can a|so form |n a m|xed conf|gurat|on
wlLh boLh parallel and anLlparallel secLlons buL
Lhls conflguraLlon ls less common Lhan Lhe
unlform Lypes menLloned above
W AlmosL all sheeLs exhlblL some degree of tw|st
when Lhe sheeL ls vlewed edge on along an axls
perpendlcular Lo Lhe dlrecLlon of Lhe polypepLlde
chalns 1hls LwlsL ls always r|ghthanded
8ULGL
An lmporLanL varlanL of Lhe classlcal
sheeL sLrucLure ls Lhe bu|ge
1he bulge mosL ofLen observed ln
anLlparallel sheeLs ls a hydrogen
bond beLween Lwo resldues on one
sLrand wlLh one resldue on Lhe
ad[acenL sLrand
1hls sLrucLure can alLer Lhe dlrecLlon
of Lhe polypepLlde chaln and
augmenL Lhe rlghLhanded LwlsL of
Lhe sheeL
Cther Secondary Structure
W bellces ooJ sbeets occooot fot tbe mojotlty of
secooJoty sttoctote seeo lo ptotelos
W Powever Lhese regular sLrucLures are
lnLerspersed wlLh reglons of lrregular sLrucLure
LhaL are referred Lo as loop ot coll
W Loop reg|ons are usua||y present at the surface
of the prote|n 1hese reglons are ofLen slmply
LranslLlons beLween regular sLrucLures buL Lhey
also can possess sLrucLural slgnlflcance and can
be Lhe locaLlon of Lhe funcLlonal porLlon or
octlve slte of tbe ptotelo
Loop
W Some Lypes of sLrucLure are ublqulLous enough LhaL Lhey have been
loosely caLegorlzed na|rp|n |oops (or reverse turns) often occur
between ant|para||e| beta strands and |nvo|ve the m|n|mum
number of res|dues (4S) requlred Lo begln Lhe nexL sLrand
W Many oLher Lypes of Lurns exlsL and can be classlfled by Lhe regular
secondary sLrucLures LhaL Lhey connecL and by Lhe and angles of Lhe
resldues lnvolved ln Lhe Lurn 1rans|t|ons |nvo|v|ng more res|dues (6
16) are often referred to as omega () |oops because Lhey resemble
Lhe shape of Lhe caplLal Creek leLLer omega
W 1hese loops can lnvolve complex lnLeracLlons LhaL lnclude Lhe slde
chalns ln addlLlon Lo Lhe polypepLlde backbone Lxtended |oop
reg|ons |nvo|v|ng more than 16 res|dues have also been observed
W AlLhough loop reglons are lrregular Lhese sLrucLures are generally as
well ordered as Lhe regular secondary sLrucLures Powever
experlmenLal deLermlnaLlon of proLeln sLrucLures has shown LhaL
some loop reglons are d|sordered and Lhus do noL achleve asLable
sLrucLure 1hls Lype of loop reglon ls referred Lo as random co||
SLCNDAk S1kU1UkL kLDI1ICN
ML1nCDS
AN CVLkVILJ
W roLeln secondary sLrucLure predlcLlon meLhods may be
broadly classlfled accordlng Lo Lhe Lechnlques used as
Lhose based on
W Slngle resldue sLaLlsLlcs
W LxpllclL rules and
W neural neLworks
W 1he ouLpuL of mosL secondary sLrucLure predlcLlon
algorlLhms and programs ls Lhe sequence of Lhe proLeln
along wlLh one of Lhe above symbols for each resldue
W Also glven lf avallable ls an esLlmaLe of Lhe sLrengLh of
Lhe predlcLlon 1hus secondary sLrucLure predlcLlon ls a
reslduebyresldue process and noL for example an
esLlmaLe of Lhe overall secondary sLrucLure conLenL of Lhe
proLeln
Methods to pred|ct Secondary structures of
rote|ns
W S1A1IS1IAL 1LnNIULS
1 Chouasman MeLhod
2 CC8 meLhod (Carnler CsguLhorpe and 8obson)
W NLUkAL NL1JCkk ML1nCDS
1 Pu
W NLAkLS1 NLIGn8CUk ML1nCDS
1 8LuA1C8
2 nnSS
W CNSLNSUS ML1nCDS
1 !8Lu
2 nS
W 1he meLhods may be furLher classlfled hlsLorlcally
as belonglng Lo Lhe flrsL second or Lhlrd
generaLlon
W lrsL generaLlon sLaLlsLlcal meLhods were
developed ln Lhe early 1970's and made use of
Lhe experlmenLally deLermlned proLeln sLrucLures
LhaL became avallable
W ln Lhe second generaLlon sLaLlsLlcs concernlng
nelghbourlng resldues were also used
W ln Lhe Lhlrd generaLlon lnformaLlon obLalned
from sequences wlLh slmllar sLrucLures was
lncorporaLed lnLo Lhe predlcLlon algorlLhm
Measures of pred|ct|on accuracy
W An lnLernaLlonal efforL Lo sub[ecL boLh
secondary and LerLlary sLrucLure predlcLlon
algorlLhms Lo unlform unblased
assessmenL ls carrled ouL blennlally by Lhe
CAS (ComparaLlve AssessmenL of
SLrucLure redlcLlon) programme
Jeb Servers for Structure red|ct|on
Web servers for sLrucLure predlcLlon
W Slpred
W !8Lu
W 8LuA1C8
W Pu home page
W Z8Lu server
W nnredlcL
W SS (nearesLnelghbor)
kLD
W !8Lu ls secondary sLrucLure predlcLlon server
LhaL has been deslgned Lo accepL a sequence or
an allgnmenL ln sLandard formaL and run a
predlcLlon uslng slx dlfferenL algorlLhms nnSS
uSC 8LuA1C8 Z8Lu MuL8Lu and Pu
W lL Lakes advanLage of all Lhe dlfferenL meLhods of
proLeln secondary sLrucLure predlcLlon and noL
rely on [usL one Lechnlque
SLCCnuA8? S18uC1u8L 8LulC1lCn C
SLCuLnCLS uSlnC LW 1CCLS
ILJ LkAMLLS
houIasman a|gor|thm
Secondary Structure red|ct|ons through nD
SCMA and SSkLD
1ert|ary Structure of rote|ns
W 1he LerLlary sLrucLure of a roLeln ls deflned as Lhe
global Lhreedlmenslonal sLrucLure of lLs polypepLlde
chaln
W Mlrsky and aullng predlcLed Lhe role of Pydrogen
bonds ln proLeln secondary sLrucLure and lald Lhe
foundaLlon for descrlblng Lhe LerLlary sLrucLure of
proLelns
W WlLh Lhe deLermlnaLlon of Lhe sLrucLure of
Myoglobln by [ohn kendrew and Paemoglobln by
Max eruLzSclenLlsLs began Lo caLalogue Lhe aspecLs
of proLeln LerLlary sLrucLure
S|de cha|ns and 1ert|ary Structure
W 1he comblnaLlons of Pellx SheeL and loop
elemenLs provldes a compleLe sLrucLure of Lhe
proLeln by brlnglng abouL lnLeracLlons
beLween Lhe consLlLuenL amlno acld resldues
of Lhe proLeln
W 1hus aL Lhe level of LerLlary sLrucLure Lhe slde
chalns play a much more acLlve role ln
creaLlng Lhe flnal sLrucLure
1he rote|n Io|d
W 1he flnal Lhree dlmenslonal sLrucLure of a proLeln ls
commonly referred Lo as lLs fold whlch ls achleved
Lhrough Lhe complex process of proLeln foldlng
W 1he prlmary sLrucLure of Lhe proLeln conLalns all of
Lhe lnformaLlon requlred for lL Lo acqulre Lhe correcL
fold yeL desplLe Lhe deLermlnlsLlc naLure of proLeln
foldlng lL ls noL posslble Lo fully predlcL Lhe flnal
sLrucLure of a proLeln glven only lLs sequence
lnformaLlon
Doma|ns and Mot|fs
W WlLhln Lhe overall proLeln fold dlsLlncL domalns and moLlfs
can be recognlzed
W A domaln ls a subsecLlon of Lhe proLeln LhaL would malnLaln
lLs characLerlsLlc sLrucLure even lf separaLed from Lhe overall
proLeln
W MoLlfs (also called supersecondary sLrucLure) are small
subsLrucLures LhaL are noL necessarlly sLrucLurally
lndependenL and conslsL of few secondary sLrucLural
elemenLs MoLlfs ofLen have a funcLlonal slgnlflcance
W Several moLlfs can comblne Lo form speclflc domalns
8|ochem|ca| Io|ds
1ypes of Io|ds
1 Clobular proLelns
Myoglobln
2 Membrane proLelns
8hodopsln
3 lbrous proLelns
Collagen
1LS CI DCMAINS
1LS CI MC1IIS
8L1A 2 SCLLNCID 8L1A 7 kCLLLLk
1LS CI MC1IIS
ALnA 8L1A 4 LALk
SANDJIn
8L1A 8AkkLL
Mo|ecu|ar Interact|ons |n 1ert|ary Structure
W A domlnanL molecular lnLeracLlon ln LerLlary
sLrucLure ls Lhe Pydrophoblc effecL
W 8esldues wlLh slde chalns are packed lnLo Lhe proLeln
core away from Lhe solvenL whlle charged and polar
resldues form Lhe surface of Lhe proLeln and are able
Lo lnLeracL wlLh polar waLer molecules and solvaLed
lons
W ln order for Lhe backbone Lo parLlclpaLe ln Lhe
hydrophoblc core Lhe secondary sLrucLural elemenLs
sLablllzed by Pydrogen bondlng should be formed
correcLly
W 8urled polar resldues form hydrogen bonds
wlLh oLher polar resldues or someLlmes waLer
molecules
W Charged resldues also occur wlLhln Lhe
hydrophoblc core and Lhls ls posslble only of
Lhe charged resldue ls palred wlLh anoLher
resldue of opposlLe charge such LhaL neL
charge ls zero
W 1hls lnLeracLlon lnlLlally proposed by henry
Lyrlng and Allen SLearn ls known as lon palr or
salL brldge
W CovalenL lnLeracLlons beLween resldue slde
chalns are also lmporLanL ln malnLalnlng
LerLlary sLrucLure
W Powever only one of Lhe sLandard 20 amlno
aclds ls capable of parLlclpaLlng ln covalenL
llnkage whlch ls cysLelne
W 1he dlsulflde bond (SS) furLher sLablllses Lhe
proLeln fold
nCJ AkL kC1LIN S1kU1UkLS kLDI1LD ?
1 xray crysLallography
2 nuclear MagneLlc 8esonance
3 omputat|ona| methods 1ert|ary structure
pred|ct|on
nomo|ogy Mode||ng
1hread|ng
Ab|n|t|o pred|ct|on
nuCLLA8 MACnL1lC 8LSCnAnCL
PCMCLCC? MCuLLlnC
ILCJ nAk1 ICk 3D S1kU1UkL
kLDI1ICN
1 S18uC1u8L 8LulC1lCn (uSlnC An? C 1PL
CCMu1A1lCnAL ML1PCuS)
2 vALluA1lnC 1PL ACCu8AC? C S18uC1u8L
8LulC1lCn 1C CPLCk 1PL CC88LC1
CCnC8MA1lCn C 1PL 8LulC1Lu
8C1Lln
W kAMAnANDkAN LC1
W kCnLk
W JnA1II SLkVLk
Protein uN4 interoctions
unA 8C1Lln ln1L8AC1lCnS
roLeln unA lnLeracLlons
W Protein can bind the DNA through the base, sugar, and the
phosphate group
W Hydrogen bonds with phosphate are not speciIic, but with
great importance in stabilizing the protein-DNA complexes
W Guanine exposes the greatest number oI potential hydrogen-
bonding atoms on the base edge(4 positions)
W The polar and charged residues oI amino acids play a central
role
Arg ~ Lys ~ Ser ~ Thr; Asn and Gln
W Acidic residues are used sparingly Asp and Glu
W Only Gly makes a signiIicant number oI interaction
W Few interactions are produced by hydrophobic residues
2 van der waals ConLacLs
W Comprlse 649 of all proLelnunA lnLeracLlons
W lnLeracLlons wlLh Lhe unA backbone ( sugar and
phosphaLe) are mosL promlnenL
W lnLeracLlons wlLh Lhe phosphaLe group domlnaLe due
Lo Lhelr hlgh exposure on Lhe unA surface
W 1ACC
W Arg 1hr he lle Pls Cys
3 WaLer MedlaLed 8onds
W nearly as common as dlrecL hydrogen bonds
W 149 of all proLelnunA lnLeracLlons
W 70 are wlLh Lhe unA backbone mosLly phosphaLe
group
W lnLeracLlons wlLh purlne are common Lhan wlLh
pyrlmldlne
W olar and charged amlno aclds are frequenLly used
Arg Lys Asp Clu Ser and 1hr
SCI1JAkLS USLD 1C S1UD DNA
kC1LIN IN1LkA1ICNS
W DISIS predlcLs unA blndlng slLes dlrecLly from amlno acld
sequence
W DNA8|ndk predlcLs unA blndlng slLes from amlno acld
sequences uslng machlne learnlng algorlLhms
W DISLAk makes a predlcLlon based on properLles of proLeln
sLrucLure
W 8|ndN makes a predlcLlon based on chemlcal properLles of Lhe
lnpuL proLeln sequence
W D8|nd
W D8SSSM
W D8Sred
Lxample sLrucLure of nucleosome
8eference AcknowledgmenL
8C1Lln unA ln1L8AC1lCnS
W nM Luscombe eL al Nocl AclJ kes 29 2860
2874 (2001)
W Luger eL al Notote 389 231260 (1997)
W !lan Zhang and ur 8ob Coalson