Protein structures

Membrane anchored proteins

Soluble globular proteins
Fibrilar proteins

Prepared by Iwona Ktnik-Prastowska

Topic:
General characteristics of
Proteins as polymers of L-amino acids
Diverse molecular weight
Diverse functions
Unique three-dimensial shape
Distribution of proteins in tissues

Proteins are polymers of L-amino acids

Proteins play a vital role in the

organization and function of living
organisms. They
can
Enzymes
and its
inhibitors
play diverse
functions:
1) They shows specific biological
roles:
Peptide hormones
Enzymes, Antibodies,
Adhesion and receptor proteins
Factors controlling of protein
biosynthesis, protein folding, and
metabolism,
2) They can transport other
molecules,
3) They play storage role and
a structural role

A receptor

Distribution of proteins in tissues

1. Soluble globular proteins of biological
fluids
2. Cell-membrane bound
3. Structural fibrilar proteins of
extracellular matrix and connective
tissue
4. Intracellular-proteins

Proteins of biological fluids

blood plasma,
salivia,
amniotic fluid,
synovial fluid, milk,
cerebrospinal fluid
are water soluble.
They shape resemble globule,
They form a class of

globular proteins
which are water and salt
solution soluble.

There are number types of proteins in nature and

each has certain physical and chemical properties
that are uniquely suited to its role in the living
organism:
Proteins are large
polypeptides
with molecular
weights ranging
from a few
thousand into the
millions
Da Dalton
kDa kilo Da
kDa=1 000 Da

Topic:

Globular proteins
as the enormous class of proteins, abundant,
bioactive and essential for most of metabolic
processes.

Globular proteins

form enormous class of proteins.

They are abundant and essential for most of
metabolic processes.
Some examples:

Serum albumin
Myoglobin, hemoglobin,
Immunoglobulins,
Some peptide hormones,
Cellular receptors,
Cytokines,
Transferrin,
Ceruloplasmin,
Glycoproteins, lipoproteins,
phosphoproteins.

Globular
proteins

Globular proteins

are so named,
because
their
polypeptide
chains
are folded into
compact
structures,
very unlike the
extended,
filamentous
forms of the

fibrous
proteins

Fibrilar proteins

All globular proteins have a defined

inside and outside
The amino acid side chains
in globular proteins are spatially distributed
according to their polarities

Interior:
Core
of a protein

Val, Leu, Ileu,

Met, Phe
Water
molecules
are largely
excluded from
the interiors

Surface
of a protein
Arg, His, Lys,
Asp, and Glu

H2O

The surface of globular

H2O proteins of biological
fluids
is in contact with the
aqueous solvent.

Surfaces of globular
proteins are coated
by water molecules

The distribution of hydrophilic and hydrophobic

residues in globular proteins is characteristic:

Red:

Hydrophobic aa

Green:

Hydrophilic aa

Topic: Proteins bound with cellular

membrane: the arrangement of an protein
protein in the lipid bilayer

Membrane
proteins
are classified
according to
how tighly
they are
associated
with
membranes

The ways how protein can be

anchored in the membrane:
GPI-anchored
protein

GPI

Peripheral protein

Integral
proteins

cy t o p l a sm

Peripheral protein

Integral (intrinsic) proteins

are tighly bound to
membrane
by hydrophobic forces
and can only be seperated
from them
by treatment with agents
(such as organic solvent,
detergents, chaotropic agents)
that disrupt membranes
.

Peripheral
protein
is loosely
anchored in
membrane by
hydrophobic,
helical
C-terminal
segment.

GPI-anchor
Some protein are anchored to the membrane
by covalent type linkage named
Glycosyl-Phosphatidyl-Inositol, (GPI) anchor.

GPI- anchor

Protein

Ma
n

Man

Man

GlcN

Cell surface

CYTOPLASM

Introduction to Glycobiology, 2003

Digestion of GPI from cell membrane:

Protein

Enzymatic hydrolysis)
GPI-PLD

Man

Man

Man

GlcN

Cell surface
GPI-PLC
cytoplasm
13

Digestion of GPI from cell membrane:

Protein

Enzymatic hydrolysis)
GPI-PLD

Man

Man

Man

GlcN

Cell surface
GPI-PLC
cytoplasm
13

GPI-anchored protein:

There is enormous number

of possibilities of protein
structures

Primary
level

Secondary

Tertiary

Each protein has

an own three
dimensional structure

Quaternary

Four levels for describing

the protein structure

Primary level: proteins are polymers

of L-amino acids

Peptide consists of defined

sequences of amino acids
written in our genes

Rigid and
planar
peptide
bonds
between aa
create a
backbone of
a polypeptide
chain

The similar primary structure but

different biological activity of hormons
secreted by the pituitary gland:

vasopressin

oxytocin
Both hormones are used as a drugs, vasopressin to
combat loss of blood pressure after surgery, while
oxytocin to induce labor.

The consequences of amino acid substitution:

Blood protein Hb: a change in only one

aa in alpha chain of 146 is enough to
cause a fatal disease
- sickle cell anemia
Normal Hb: Glutaminic acid (Glu)
Sickle cell anemia, HbS- Val

The electrophoretic
pattern of Hb from
normal individuals and
those with sickle cell
anemia:

Normal erythrocytes:

Sickled erythrocytes from

patients with cell anemia.

The secondary protein structures:

The structural pattern of a peptide can fold or align

themselves in such manner that certain patterns
repeat themselves

Secondary structure

Two most common regular secondary

structures of proteins:

Lineus
Pauling
1954
Nobel
Price

The helix

The pleated sheet

Unregular secondary
structure
Non-repetitive
structures
random coil or
loop conformation
i.e. regions
(segments)
disordered,
and bulges

Certain subgrouping of secondary structural

elements,
are named

supersecondary structures
They occur in many globular proteins.

Some supersecondary motifs in proteins.

They can be formed by helices, sheets,
and both types of structures

Helical coils motifs in proteins

2-7 helices are

coiled together
like the strands of
a rope.

Coiled coils can exist in some protein families:

superhelix,
helical wheels,
leucine zipper (pair of parallel helices),
helix bundles (triple-strandled bundle),
barrel (12 helices)

Leucine zipper
Spatial structural protein motif which
contains leucines

Leucines form hydrofobic core linking

two parrarel helical polypeptides
(dimerization)

Wikipedia modified

Superstructures (motifs)
in proteins
build from -pleated sheets:

Beta meander
Twisted sheets
Ribbon sheets
Beta sandwich
Cylinders
Beta barrels

consists of an antiparallel
sheet formed by sequential
segments of polypeptide
chain, that are connected
by relatively tight reserve
turns

Two units
of parallel and antiparallel structures
are joined together by segment of
hairpin:

The pleated
antiparallel sheets

can form U-turn

named a hairpin
structure, or turns.
The chain abruptly
changes a direction
Pro, Gly, Ser, Asp,
Asn, are mainly
present in turns;

 loop is reverse turn,

which involve of 6-16
aa residues;

Omega loop (),

Omega turn:

loop is compact
globular entities, they
side chains tend to fill
in their internal
cavities.
loops are almost
invariably located on
the protein surface,
they may have
an important role in
biological recognition
process
More stick figure that turns

Barrels might be formed by helical and

extended sheet structures:

Tertiary structure of proteins:

that is the folding of its secondary structural

elements, together with spatial dispositions
of its side chains:

It is folding of
polypeptide, that gives
the molecule its overall
three dimensional
shape.
Proteins
are folded into
compact structures

Tertiary

The spatial protein structures are

stabilized by noncovalent interactions
and disulphide bridge between folded
polypeptide chain:
disulfide
bonds

Hydrogen bonding
Ionic
interactions

Hydrophobic
interactions

Disulphide bridges

Intra-S-S

Inter-SS-

A quartenary level of protein

organization
The proteins
quaternary
structure
is the spatial
arrangement of
protein subunits.

A secondary

A tertiary

A quaternary

Proteins with quaternary structure

are multisubunit molecules
The term quaternary
structure refers
to the interaction
of several polypeptide chains
in a noncovalent manner to form
multisubunit protein particles
termed oligomers.
The individual subunit polypeptide
chains are also referred to as
protomers.

Topic
Mosaic proteins and multidomain proteins

A mosaic proteins:

Some proteins can be constructed from

a set of a number of modules,
repeated many times
in this same or even in many different
proteins.
Such a sequence has a similar secondary
and tertiary structure in each case

Mosaic proteins are build from moduls named also

segments which repeat in the protein.
An example fibronectin (FN)

6
1

2
Type I, II, III segments

EDA

EDB
RGD
PHSRN

IIICS

COOH

NH2

FN modules might occur in other proteins

Some sequences/modules
of large polypeptides can form
domains:
Polypeptide chains that consist of more than ~200
aa usually fold into two or more globular clusters
known as

domains,

which give these proteins

multiglobal appearance.

Domains of
proteins
Domain: A large
polypeptide chain
is often locally folded
into globular clusters

The domains
give the protein
multiglobal
appearance

Domain is a portion of polypeptide chain that

folds on itself to form a compact unit that
remains recognizably distinct within the tertiary
structure of the whole protein;

Domains are structurally independent units,

each have the characteristic
of a small globular protein.
Domains often have a specific function such as
the binding of a small and larger molecules.

Some types of domains

in proteins
EGF

FN I

sushi
FN II
FN III

Coagulation
factor V

Immunoglobulin-like

Many
domains
are
present
in
multiple
copies in
their
parent
proteins

The serum albumin family proteins are the most

abudant and important evolutionary, structurally
and functionally related:
Serum albumin
Alpha-fetoprotein
Vit D-binding protein
Afamin- Vit E-binding protein
Each of them have three homologous domains of
~190 residues
They are major transport proteins in plasma and
bind and transport various types of compounds
through vascular system.

Some proteins may exist

in many molecular forms
Conformational
compact, extended, transition states,
monomer, dimer, superfibronectin
Alternatively spliced: EDA, EDB, IIICS
Type and degree of glycosylation

Closed and open conformation

of a protein:

The simple proteins

are built from amino acids only.
An example: serum albumin

The conjugated proteins are described on the

basis of their non-amino acid components:
The conjugated
proteins

The prosthetic group

Lipoproteins

Lipids

Glycoproteins

Sugar/s, glycan/s

Nucleoproteins

Nucleic acid

Heme proteins

Heme

Metalloproteins

Ions of some metals:

Mg++, Co++, Fe++, Ca++

Phosphoproteins

Phosphatic acid.

Topic
THE GLYCOPROTEINS

In contrast to the GLYCATION

- nonenzymatic protein
modification which happend when
glucose concentration in the cell
increases (in pathological states of
organism, such as diabetes,
Alzheimer disease, aging)
the PROTEIN GLYCOSYLATION is
enzymatic posttranslational event
written in our genes

Glycation

Seminar
can mainly undergo hemoglobin,
albumin, some membrane proteins, and nervous
system proteins, some matrix proteins (collagen),
Protein
Protein

Glucose
Protein

Protein

Protein

Glycoproteins

are conjugated proteins,

carry covalently attached
oligosaccharide chains (glycans).
The carbohydrate content vary
from few percent up to 50%
The transfer of glycosyl groups is
the enzymatic process and written in
our genes

Subclasses of glycoproteins:

N-, O- glycoproteins
Mucins
Proteoglycans
Peptydoglycans in bacteria

N- and O- glycoproteins:
Two ways
of bonding
oligosaccharide
chains (glycans) with
proteins to form
glycoprotein:

Asn
Protein
chain
N-glycoproteins:
N-AcGlc and an asparagine
Thr or
Ser

N-glycosidic bond
O-glycosidic bond

Protein
chain

O-glycoproteins:
N-AcGlc/N-AcGal and
serine or threonine

Microheterogenetic forms
of N-glycans attached to
the same protein part
are called glycoforms
In living organism
You can find
TetraDiTridifferent glycoforms
building
this same
glycoprotein.
The distribution of
glycoprotein
glycoforms is stable
Glycoforms1,2,3
in physiological state

Glycoproteins

microheterogeneity
depending on type of
glycans
attached to their
protein part

IMPORTANT:
The distribution
of glycoprotein glycoforms
is stable
in physiological state of human organism

Role of sugar part

in glycoproteins
1. Structural: it protects protein part
against degradation
2. Functional:Glycoforms are known to
participate in reactions of biological
recognition.They serves as specific
receptors for animal and bacterial lectins
3. Hypothesis: specific sugar sequences
create a code in reaction of biological
recognition and transfer signals between
cells

Carbohydrate-binding proteins (blue)

and the selective recognition of various
sugar epitopes of glycoproteins
Adhesion

Signalling

Degradation

Apoptosis

Topic
Other distinct family
of O-linked glycoproteins
are

THE MUCINS

The broad definition of MUCINS

An extremly large oligomers containing,
as greater than 55% of its mass O-linked
oligosaccharides,
The glycans can be diverse with more
than 100-800 different oligosaccharides
present on a single protein
They are extremly heterogenetic, form a
mucin family

The secretory epithelial mucins

constitute the large part of
the protective viscous, hydrated
mucus,
that covers and protects
epithelial tissues of the human:
oral cavity,
the tracheobronchial,
gastrointestinal,
reproductive tracts
against potential hostile environments

The general function

of secretory mucins:
Protection of cellular surface of
ductal epithelia
lubrication,
Possible role in innate immunity
against certain pathogenic bacteria
and viruses

General mucin structure:

Non-PTS region, mainly
globular
Sites of N-glycosylation
Cysteine region
Filamentous part
PTS region
Variable region of
tandem repeats
Places of O-glycosylation

Cysteine region

Non-PTS region, mainly

globular
sites of N-glycosylation

MUC2

MUC1

Mucins show molecular

heterogeneity:
In humans
at least 14 distinct
epithelial mucin
have been identified
and numbered according to
the order of the mucin gene
discovery as:
MUC 1, MUC 2, .MUC-14.

Topic
PROTEOGLYCANS
are essential parts of
tissues of
skin, cartilage,
cornea of the eye
where they provide
strength, flexebility,
and elasticity

are beside collagen one of

ECM components

The proteoglycans
are special class of glycoproteins:
They have
a protein core,
and
a long polysaccharide chains (80%)
made of acidic glucosaminoglycans
(GAG)

Structure of proteoglycans
Glucosoaminoglycans (GAG) chains are
usually bound to the protein core
through either short oligosaccharide linkage
Xyl, Gal, GalNAc, GlcNAc,
Protein part-Ser-O- b1-Xyl-Gal-GalNAc-GlcNAcLinkage
b1-4 repeating units of chondroitin,
dermatan, heparan-sulfates

Proteoglycans of connective tissue

may constitute of silicon:
Some of the carbohydrate chains are
cross linked by bridges of the type with
silicon:

R and R are sugar monomers of adjanted chains.

One silicone for every 100 sugar monomers.

Topic
LIPOPROTEINS

Lipoproteins particles
consits of noncovalently associated
lipids and proteins.
Lipoproteins function in the blood plasma:
transport vehicles for triacylglycerols and
cholesterol.

Plasma lipoproteins
form globular micelle like particles,
that consists of:
triacylglycerols,
cholesteryl esters,
proteins,
phospholipids,
cholesterols.

The protein components of

lipoproteins are known as
apolipoproteins or just apoproteins.
There are at least 9 apolipoproteins that
are distributed in significant amount in
the different human lipoproteins

Plasma lipoproteins

form globular micelle like

particles

cholesterol

protein,
cholesterol

Triacylglycerols,
cholesteryl esters

phospholipid

protein
protein

cholesterol
phospholipid

nonpolar core
surrounded by
an amphiphilic
coating of

Lipoproteins
have been classified into five broad
categories on the basis
of their functional and physical properties:

1. Chylomicrons
2. Very low density lipoproteins:
VLDL
3. Intermediate density
lipoproteins: IDL
4. Low density lipoproteins: LDL
5. High density lipoproteins: HDL

Characteristics of the major classes of

lipoproteins in human plasma:

A scheme of LDL structure:

On the surface of
LDL cluster
are molecules
with polar
groups:
phospholipids,
free cholesterol
as well as
proteins
Cholesteryl
esters
Hydrophobic
part inside

Protei
n

Basic function of
Very low density lipoproteins VLDL,
Intermediate density lipoproteins
IDL,
Low density lipoproteins LDL is:
Transport of endogenous
(internally supplied: the liver synthesizes
triacylglycerols from excess
carbohydrates)
triacylglycerols
and cholesterol
from the liver to the tissue

Basic function of HDL:

Transport of endogenous
cholesterol
from the tissues
to the liver

The HDL:

the smallest lipoproteins,

and the highest density.

(reverse than LDL).

It carry 20-35% of total plasma

cholesterol.
HDL comprise:
3% of triacylglycerides,
20-30% phospholipids,
15-20% cholesteryl esters,
5% free cholesterol,
45-59% apolipoprotein.