In this ppt one can know the diiferent softwares and several online servers for the epitope mapping.This mapping helpful for production of different vaccines and antibodies.

1. EPITOPE MAPPING THROUGH
BIOINFORMATICAL ANALYSIS
Jajati Keshari Nayak
PhD1st yr
MBGE,GBUA&T
ID-55493

2. Antigen-antibody interaction
• Antigen is recognized by the immune system and stimulates an
antibody response
• Can be a bacteria, virus, a protein…
• Originally the term antigen came from antibody generator
Antigen

3.  An
• Antigen is recognized as foreign by the immune system and
is engulfed by antigen presenting cells, such as macrophages,
monocytes and dendritic cells
Antigen presenting cell
Antigen
Antigen-antibody interaction

4. Antigen-antibody interaction
• The antigen is degrated into smaller fragments and displayed
on the cell surface together with specialized glycoproteins
Antigen presenting cell
Antigen

5. Antigen-antibody interaction
• T-cells recognize the antigen-glycoprotein complex
Antigen presenting cell
T-cell
Antigen

6. Antigen-antibody interaction
• T-cells stimulate B-cells to produce
 antibodies towards the specific antigen
Antigen presenting cell
T-cell
B-cell
Antibodies
Antigen

7. Antigen
Antigen presenting cell
Epitope
T-cell
B-cell
Antibodies
• The antibodies interact with the antigen
• The region of an antigen that interact with the antibody is defined as an
epitope
Antigen
Antigen-antibody interaction

8. Antigen presenting cell
T-cell
B-cell
Antigen
Antibodies
• Finally the antigen is neutralized
Antigen
Antigen-antibody interaction

9. Antigen presenting cell
T-cellSelf protein
(auto-antigen)
B-cell
Auto-antibodies
• Abnormal functioning of the immune system, it fails to recognize
protein/tissue ~ antibody response is produced against these
• A disease that results from such an immune response is termed an
autoimmune disease
Auto-immune disease

10. Epitope mapping
• Epitope mapping is the process of identifying the binding
sites of antibodies on their target antigens
• Several strategies for epitope mapping exist:
 recombinant proteins
 X-ray co-crystallography
 phage-display
 peptide scanning
 truncated resin-bound peptides
 Through Bioinformatical analysis

11. Need
 Used for vaccine development against influenza,small
pox,pertusis
 mAB and Polyclonal antobodies production.
 To know the antigen-antibody interaction.

12. Why epitope mapping ??
 Conventional vaccine production is time consuming.
 Atteneuated or killed pathogen may cause disease in
host genome.
 To know the different consensus and conserved
sequence which forms epitopes.

13. Epitope based vaccine
 Immunoprotective and immuno dominat epitopes are
used.
 rDNA technology is used for multitarget vaccine
production.
 Linear epitope or conformational epitope is used.
 Also used as adjuvents. e.g T cell epitopes.

15. Prediction of potential T- cell
binding-epitopes
 Interaction occures between R groups of epitope and
Grooves/pocket of MHC molecules.
 RANKEP –online server predicts peptides binders to
MHC-I and MHC-II alleles.
 PSSM(position specific scoring matrices) algorithim is
used in RANKEP.

16. Lets take an example
>A56881 PIR2 release 71.00
MWNLLHETDSAVATARRPRWLCAGALVLAGGFFLLGFLFGWFIKSSNEATNITPKH
NMKAFLDELKAENIKKFLYNFTQIPHLAGTEQNFQLAKQIQSQWKEFGLDSVELA
HYDVLLSYPNKTHPNYISIINEDGNEIFNTSLFEPPPPGYENVSDIVPPFSAFSPQGMP
EGDLVYVNYARTEDFFKLERDMKINCSGKIVIARYGKVFRGNKVKNAQLAGAKGVIL
YSDPADYFAPGVKSYPDGWNLPGGGVQRGNILNLNGAGDPLTPGYPANEYAYRRGI
AEAVGLPSIPVHPIGYYDAQKLLEKMGGSAPPDSSWRGSLKVPYNVGPGFTGNFSTQ
KVKMHIHSTNEVTRIYNVIGTLRGAVEPDRYVILGGHRDSWVFGGIDPQSGAAVVH
EIVRSFGTLKKEGWRPRRTILFASWDAEEFGLLGSTEWAEENSRLLQERGVAYINADS
SIEGNYTLRVDCTPLMYSLVHNLTKELKSPDEGFEGKSLYESWTKKSPSPEFSGMPRI
SKLGSGNDFEVFFQRLGIASGRARYTKNWETNKFSGYPLYHSVYETYELVEKFYDPM
FKYHLTVAQVRGGMVFELANSIVLPFDCRDYAVVLRKYADKIYSISMKHPQEMKTYS
VSFDSLFSAVKNFTEIASKFSERLQDFDKSNPIVLRMMNDQLMFLERAFIDPLGLPD
RPFYRHVIYAPSSHNKYAGESFPGIYDALFDIESKVDPSKAWGEVKRQIYVAAFTVQA
AAETLSEVA
Protein blast was done to know the function of this protein

17. That sequence is prostate specific antigen

18. Let’s Predict putative peptide sequences which may form a epitope through
RANKPEP server.

21. Same protein sequence of prostate antigen put in IEDB analysis resources data
base.

24. TAP associated epitope prediction
What is TAP ???
Transporter associated with antigen processing

27. Interface of CTLpred server.

28. PREDICTION OF B-CELL BINDING
EPITOPES
 B cell epitopes are recognized by B cell receptors or
antibodies in their native structure.
 Score is calculated on the bais of AA properties such as
hydrophilicity,charge,exposed surface area and secondary
structures.
 Different online server are present for continuous and
discontinous B-cell epitopes.
 It has been tested on B cell epitope database (BCIPEP),
and will therefore presumbly have better performance for
prediction of B cell epitope of the antigen. Bcepred can
predict continuous B cell epitopes.

30. PEPTIDE BASED VACCINE
AGINST HIV

31. Different HIV virus epitope prediction

32. CONCLUSION
 Epitope mapping gives high throughput analysis of
dfferent candidate sequences for prediction of
potential epitopes.
 Less time consuming and less expensive.