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Authors :-
Raghunath Satpathy ,
Rashmiranjan Behera,
Rajesh Ku. Guru
MIRC LAB,MITS Engineering
college,Rayagada,Orissa
Introduction

‡ 3MM    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 antigen
which creates it.
‡ 'antigens' are a mixture of macromolecules (e.g.
bacteria, toxins, proteins, pollen, fungi, viruses,
etc) which contain several epitopes.
‡ Contact with a complex antigen such as a virus
will stimulate multiple immune responses to the
different 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 response
thus creating an immunity without harming the
patient.
‡ The above approach is also applicable for
suitable vaccine design for deadliest viral
infections like 2009 H1N1 virus , which is in
pandemic state now.
OBJECTIVE

ΠIdentifying the potential MHC binding antigenic

peptide from 2009 H1N1 and 1980 H1N1 viral
strain .

ΠDocking study of the peptides from selected locus

with Human MHC protein molecule.

ΠComparative analysis for cross reactivity of the

selected antigen peptides of the above two
strains.
Materials and Methods

ΠRetrieval of NP gene sequence from NCBI for

1980 (gb|ABO38366.1) and 2009
(gb|ACZ97468.1) influenza virus Indian strains.
ΠPrediction of MHC binding peptide for the
sequences by Propred1 tool
ΠThe selected peptide fragments were energy
minimized by Prodrg server.
ΠDocking analysis with Human MHC 1 (present in
PDB ) and the predicted peptides by using HEX
6.1 Tool.
Results and Discussions
ΠBasing 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 .
Energy minimization of peptides by GROMOS 96 A
FORCE FIELDS
Antigenic Peptides

2 4
Antigenic Peptides
Docking study

‡ Then docking analysis of the peptides and

Human MHC 1 protein (obtained from pdb)
was performed by HEX 6.1 tool.
0
 M M   !"#
$!"%& $ 0$& & 0&3 '3&!$

1 30 -404.04

2 47 -395.10

3 213 -409.48

4 228 -410.42

0
M M !"#
$!"%& $ 0$& & 0&3 '3&!$

1. () (

2. 90 -412.20
3.  -(*++

4. 349 -415.33
1980 docking (2)
1980 docking (4)
2009 docking (1)
2009 docking (3)
! M
 M

‡ 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.
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.
References
‡ StephanieGras et al,Cross-reactiveCD8+T-cellimmunitybetween
the pandemic H1N1-2009 and H1N1-1918 InÀuenza A viruses,
PNAS,2010 ,12599±12604.
‡ DavidW.Ritchie et al Accelerating and focusing protein protein
docking correlations using multi Dimensional rotational FFT
generating functions .2008,1865±1873.
‡ Olfa Frikha-Gargouri et al,Evaluation of an ë
ëë predicted
specific and immunogenic antigen from the Omc B protein for
the serodiagnosis of 
ë ë
infections ,BMC
Microbiol, 2008, 8-217.
‡ G ,-
 3-
, Influenza virus antigenic variation, host antibody
production and new approach to control epidemics. ^ë
  ,2009, è30.
‡ 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, 2779±2786.
Acknowledgement

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

for providing us MIRC lab for computing facility