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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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