Rajesh guru mits orissa

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InIn--silicosilico study of NP antigenic peptide crossstudy of NP antigenic peptide cross

immunity amongimmunity among Indian 2009Indian 2009 and 1980and 1980 H1N1H1N1viral strains.viral strains.

Authors :-

Raghunath Satpathy ,

Rashmiranjan Behera,

Rajesh Ku. Guru

MIRC LAB,MITS Engineering

college,Rayagada,Orissa


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Introduction

Cross-reactivity is the reaction between an

antigen and an antibody which was generated

against a different but similar antigen.

Immune system is specific to a single antigenwhich creates it.

'antigens' are a mixture ofmacromolecules (e.g.

bacteria, toxins, proteins, pollen, fungi, viruses,

etc) which contain several epitopes.


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Contact with a complex antigen such as a virus

will stimulate multiple immune responses to thedifferent individual macromolecules that make up

the virus as well as the individual epitopes of

each macromolecule.

Medicinal uses for this idea include immunization

to infections. The protein that creates the

immune response will have an epitope on it that

stimulates the response. Denaturing of the

protein may 'disarm' its function but allow the

immune system to have an immune responsethus creating an immunity without harming the

patient.


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OBJECTIVE

Identifying the potential MHC binding antigenic

peptide from 2009 H1N1 and 1980 H1N1 viral

strain .

Docking study of the peptides from selected locus

with Human MHC protein molecule.

Comparative analysis for cross reactivity of theselected antigen peptides of the above two

strains.


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Materials and Methods

Retrieval of NP gene sequence from NCBI for

1980 (gb|ABO38366.1) and 2009

(gb|ACZ97468.1) influenza virus Indian strains.

Prediction of MHC binding peptide for thesequences by Propred1 tool

The selected peptide fragments were energy

minimized by Prodrg server.

Docking analysis with Human MHC 1 (present inPDB ) and the predicted peptides by using HEX

6.1 Tool.


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Results and Discussions


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Basing on the real score the allele HLA-20

cattle was considered and two common

positions 47-56 and 228-237 in each

sequence were considered .


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Energy minimization of peptides by GROMOS 96 A

FORCE FIELDS


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Antigenic Peptides

2 4


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Antigenic Peptides


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Docking study

Then docking analysis of the peptides and

Human MHC 1 protein (obtained from pdb)

was performed by HEX 6.1 tool.


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Docking scores (1980 STRAIN)

SERIAL NO. PEPTIDE POSITION DOCKING SCORE

1 30 -404.04

2 47 -395.10

3 213 -409.48

4 228 -410.42

Docking scores (2009 STRAIN)

SERIAL NO PEPTIDE POSITION DOCKING SCORE

1. 47 -409.98

2. 90 -412.20

3.228

-415.33

4. 349 -415.33


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1980 docking (2)


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1980 docking (4)


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2009 docking (1)


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2009 docking (3)


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Results

The peptide ligands shares a common position in

MHC protein.

The calculated docking energy is obtained as -

395.10 and -409.48 for the position 47-56 and -

410.42 and -415.33 for the position 228-237 in

case of 1980 and 2009 strains respectively.


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Conclusion

These results obtained suggests that, a strong

immune cross reactivity exists among two viral

strains due to previous exposure of different viral

strains. This work having important consequences for

more powerful vaccine development against the

deadliest diseases.


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References StephanieGras et al,Cross-reactiveCD8+T-cellimmunitybetween

the pandemic H1N1-2009 and H1N1-1918 Inuenza A viruses,

PNAS,2010 ,1259912604.

DavidW.Ritchie et al Accelerating and focusing protein protein

docking correlations using multi Dimensional rotational FFT

generating functions .2008,18651873.

Olfa Frikha-Gargouri et al,Evaluation of an in silico predicted

specific and immunogenic antigen from the Omc B protein forthe serodiagnosis of Chlamydia trachomatis infections ,BMC

Microbiol, 2008, 8-217.

Jiezhong Chen, Influenza virus antigenic variation, host antibody

production and new approach to control epidemics. Virology

Journal,2009, 6-30. Michael E. Bose et al, Rapid Semiautomated Subtyping of

Influenza Virus Species during the 2009 Swine Origin Influenza A

H1N1 Virus, J Clin Microbiol. 2009, 27792786.


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Acknowledgement

We are thankful to C.E.O., of MITS group orissa

for providing us MIRC lab for computing facility


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