S.Prasanth Kumar, S.Prasanth Kumar, BioinformaticianBioinformatician

Immunoinformatics

Epitope Prediction and its AlgorithmsEpitope Prediction and its Algorithms

S.Prasanth Kumar, S.Prasanth Kumar, BioinformaticianBioinformatician

S.Prasanth Kumar Dept. of Bioinformatics Applied Botany Centre (ABC) Gujarat University, Ahmedabad, INDIA

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Epitope

Antigenic determinants or Epitopes are the portions of the antigen molecules which are responsible for specificity of the antigens in antigen-antibody (Ag-Ab) reactions and that combine with the antigen binding site of Ab, to which they are complementary.

Antibody Epitope

They occur on the surface of the protein and are more flexible than

the rest of the protein

They have high degree of exposure to the solvent.

The amino acids making the epitope are usually charged and

hydrophilic

Epitope’s Properties and its Types

Sequential / Continuous Epitopes

Antibody Recognized by TH cellsLinear peptide fragmentsAmphipathic helical 9-12 mer

Conformational / Discontinuous Epitopes

Antibody Recognized by both TH & B cellsNon-linear discrete amino acid sequences, come together due to foldingExposed 15-22 mer

Paratope

Paratope

Sites of Antigen binding on Antibody molecule

Immunological Processes

Ag-Ab Complex

MHC molecules function as antigen-recognition molecules

Class I – Presents Ag so that TC

cells recognize & kill. Requires CD8+ on Tc

Class II – Presents Ag so that TH cells recognize & kill. Requires CD4+ on TH

Immunological Processes

Endogenous pathway (class I MHC)

Endogenous antigen Cytosol

Proteasome

Antigenic peptides

peptidases

N-terminally trimmed peptides

TAP (transporter associated with antigen processing)

Immunological Processes

CytosolER

*aminopeptidase associated with antigen processing (ERAAP)

ERAAP

N-terminally trimmed peptides MHC Class I

GC

Exogenous Antigen

Class II

Exogenous pathway (class II MHC) Cell Surface

Immunological Processes

Cytosol

Cell Surface

Where MHC are expressed ? Class-I all nucleated cells e.g. virus infected cells Class-II APCs (macrophages, B lymphocytes, and dendritic cells)

TH cells expresses CD4,CD4 recognizes MHC class II molecules TC cells expresses CD8,CD8 recognizes MHC class I molecules

TH Cell

TCR

CD4

MHC Class II

Antigenic PeptideTC Cell

CD8

MHC Class I

Immuological Responses

B-Cell Epitope Prediction

Hopp & Woods method

……-Ser-Thr-Cys-Asn-Glu-…… ……-Ser-Thr-Val-Asn-Glu-…..

e.g. ser-1, thr-2, cys-3,asn-4,glu-5, etc,…..x-10 alignment score = 22

Based on alignment score predict Antigenicity

1 + 2 + 10 + 4 + 5 = 22

Database of Known Epitopes

% of Epitope aa : % of aa in the avg. composition of a protein

Assigns an antigenicity value for each amino acid from the relative occurrence of the amino acid in epitope

Welling’s method

B-Cell Epitope Prediction

High antigencity value

Extend to 11-13 aa Report Probable

Low antigencity value

Karplus & Schultz

Structural parameters

Parker & Hodges method

B-Cell Epitope Prediction

HPLC from retention co-efficient of model synthetic peptides

Hydrophilicity

Janin’s scale

Summing the ASA parameters for each residue of a seven-residue segment and assigning the sum to the fourth residue

Surface profile Flexibility

Predict Antigenicity

B-Cell Epitope Prediction

Semi-empirical method

Kolaskar & Tongaonkar’s method

Frequencies of occurrence of amino acids in experimentally known epitopes

Physiological properties of amino acid residues

Data of 169 epitopes from 34 different proteins was collected of which 156 which have less than 20 aa per determinant

It is available as Antigen under ExPaSy and in EMBOSS Suite

Predict Validate

T-Cell Epitope Prediction

Margalit, Spouge et al. method

Considers Amphipathic helix segments (tetramer & pentamer motifs)

A polar residueCharged residues &/ Glycine Hydrophobic residues

1st amino acid 2nd amino acid 3rd amino acid&/

4th amino acid

Predict Antigenicity

Rothbard & Taylor method

T-Cell Epitope Prediction

Immunodominant secondary structure capable of binding to MHC with high affinity

Database of Sequence motifs

3D Structures

Sequence based search Predict Antigenicity

Stille et al. method

T-Cell Epitope Prediction

Known MHC polymorphisms from HLA

Identify anchor residues for different polymorphisms

Construct Virtual matrices

…….

……

.

MHC polymorphism

anch

or r

esid

ues

Sequence based search with MHC polymorphism

Predict Antigenicity

T-Cell Epitope Prediction

MHC binding is based on molecular dynamic simulation

Darren R Flower et al. method

Calculate the free energy of binding for a given molecular system

No reliance on known binding data, but based on de novo prediction

Required Experimentally determined structure, or a homology model, of a MHC peptide complex

Databases & Prediction Servers

SYFPEITHIMHCPEPJenPepFIMMMHCBN HLALigand/Motif databaseHIV Molecular Immunology databaseEPIMHC

Prediction of MHC binding

BIMASSYFPEITHI

PREDEPPEpipredict

PredictPropred

MHCPredNetMHC

MHC-binding peptides databases

SYFPEITHI Epitope Prediction Server

SYFPEITHI Epitope Prediction Server

Thank You For Your Attention !!!