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

Enzymes

and its inhibitors

Proteins play a vital role in the organization and function of living organisms. They can 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

are so named, because

their polypeptide

chains are folded into

compact structures,

very unlike the extended,

filamentous

forms of the fibrous proteins Fibrilar proteins

Globular 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

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

Interior: Core of a protein Val, Leu, Ileu,

Met, Phe Water molecules are largely excluded from the interiors

The surface of globular proteins of biological

fluids is in contact with the

aqueous solvent.

Surfaces of globular proteins are coated by water molecules

H2O H2O

The distribution of hydrophilic and hydrophobic residues in globular proteins is characteristic:

Red: Hydrophobic aa

Green: Hydrophilic aa

Membrane proteins

are classified according to

how tighly they are

associated with membranes

Topic: Proteins bound with cellular membrane: the arrangement of an protein

protein in the lipid bilayer

The ways how protein can be anchored in the membrane:

c y t o p l a s m

GPI

Peripheral protein Peripheral protein

Integral

proteins

GPI-anchored

protein

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 .

Integral (intrinsic) proteins

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

Peripheral protein

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

GPI-anchor

GPI- anchor

5

Cell surface

Ma

n

CYTOPLASM

Man Man GlcN

Protein

Introduction to Glycobiology, 2003

Cell surface

Man Man Man GlcN

Protein

Digestion of GPI from cell membrane:

13

Enzymatic hydrolysis)

GPI-PLD

GPI-PLC

cytoplasm

Cell surface

Man Man Man GlcN

Protein

Digestion of GPI from cell membrane:

13

Enzymatic hydrolysis)

GPI-PLD

GPI-PLC

cytoplasm

29

GPI-anchored protein:

Four levels for describing the protein structure

Primary level

Secondary

Tertiary

Quaternary

There is enormous number of possibilities of protein structures

Each protein has an own three dimensional 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:

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

oxytocin

vasopressin

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

Normal erythrocytes:

Sickled erythrocytes from patients with cell anemia.

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

The pleated sheet The helix

Two most common regular secondary structures of proteins:

Lineus Pauling 1954 Nobel Price

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

Unregular secondary structure

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

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)

2-7 helices are coiled together like the strands of a rope.

Wikipedia modified

Leucine zipper Spatial structural protein motif which contains leucines Leucines form hydrofobic core linking two parrarel helical polypeptides (dimerization)

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; 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

Omega loop (), Omega turn:

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:

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

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-S-

S-

The proteins quaternary structure

is the spatial arrangement of protein subunits.

A quartenary level of protein organization

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

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

A mosaic proteins:

Mosaic proteins are build from moduls named also segments which repeat in the protein. An example fibronectin (FN)

Type I, II, III segments

IIICS

COOH

2 1 4 3

6

5 EDA EDB

NH2

S

S

S

S RGD

PHSRN

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.

Domain: A large polypeptide chain

is often locally folded into globular clusters

The domains give the protein

multiglobal appearance

Domains of proteins

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.

EGF

sushi

FN I

FN II

FN III

Some types of domains in proteins

Coagulation

factor V

Many domains are present in multiple copies in their parent proteins

Immunoglobulin-like

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

Seminar

Glucose

Protein

Protein

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

N-, O- glycoproteins Mucins Proteoglycans Peptydoglycans in bacteria

Subclasses of glycoproteins:

N- and O- glycoproteins:

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

N-glycoproteins: N-AcGlc and an asparagine

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

Thr or Ser Protein chain

Asn Protein chain

Microheterogenetic forms of N-glycans attached to the same protein part are called glycoforms

In living organism You can find different glycoforms building this same glycoprotein. The distribution of glycoprotein glycoforms is stable in physiological state of organism

Tetra- Di- Tri-

Glycoforms1,2,3

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

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

1. Structural: it protects protein part against degradation

Carbohydrate-binding proteins (blue) and the selective recognition of various sugar epitopes of glycoproteins

Adhesion Signalling

Apoptosis Degradation

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

Filamentous part PTS region Variable region of tandem repeats Places of O-glycosylation

Non-PTS region, mainly globular Sites of N-glycosylation

Non-PTS region, mainly globular sites of N-glycosylation

Cysteine region

Cysteine region

General mucin structure:

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.

MUC1 MUC2

Topic PROTEOGLYCANS

are beside collagen one of ECM components

are essential parts of

tissues of skin, cartilage,

cornea of the eye where they provide strength, flexebility,

and elasticity

The proteoglycans are special class of glycoproteins:

They have a protein core, and a long polysaccharide chains (80%) made of acidic glucosaminoglycans (GAG)

Glucosoaminoglycans (GAG) chains are usually bound to the protein core through either short oligosaccharide linkage Xyl, Gal, GalNAc, GlcNAc,

b1-4 repeating units of chondroitin, dermatan, heparan-sulfates

-Xyl-Gal-GalNAc-GlcNAc-Linkage

Protein part-Ser-O- b1-

Structure of proteoglycans

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

nonpolar core surrounded by an amphiphilic coating of

Triacylglycerols, cholesteryl esters

Plasma lipoproteins form globular micelle like particles

protein,

protein phospholipid

phospholipid

cholesterol

cholesterol

protein

cholesterol

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:

On the surface of LDL cluster are molecules with polar groups: phospholipids, free cholesterol as well as proteins

Cholesteryl esters

Hydrophobic part inside

A scheme of LDL structure:

Protein

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 (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.

The HDL: the smallest lipoproteins, and the highest density.