Gomase V.S.1*, Chitlange N.R.2
1School of Technology, S.R.T.M. University, Sub-Centre, Latur, 413531, MS, India
2School of Technology, S.R.T.M. University, Sub-Centre, Latur, 413531, MS, India
* Corresponding Author : gomase.viren@gmail.com
Received : - Accepted : - Published : 15-06-2009
Volume : 1 Issue : 1 Pages : 7 - 12
Int J Immunol Res 1.1 (2009):7-12
Keywords : Mycobacterium tuberculosis, antigen n, epitope, PSSM, SVM, MHC, peptide
vaccine
Abbreviations: Goldman, Engelberg and Steitz, (GES); major histocompatibility complex,
(MHC); Position Specific Scoring Matrices, (PSSMs); Support Vector Machine, (SVM)
Conflict of Interest : None declared
Mycobacterium tuberculosis causes tuberculosis leading to be an obligatory step in infection. Peptide fragments of antigen can be used to select nonamers for use in rational vaccine design and to increase the understanding of roles of the immune system in bacterial diseases. Analysis shows MHC class II binding peptides of antigen from Mycobacterium tuberculosis are important determinant for protection of host form tuberculosis infection. In this assay, we used PSSM and SVM algorithms for antigen design and predicted the binding affinity of antigen protein having 338 amino acids, which shows 330 nonamers. Binding ability prediction of antigen peptides to major histocompatibility complex (MHC) class I & II molecules is important in vaccine development from Mycobacterium tuberculosis antigen.
[1] K.J.Ryan, C.G. Ray (editors) (2004). Sherris Medical Microbiology (4th ed.).
McGraw Hill. ISBN 0-8385-8529-9
» CrossRef » Google Scholar » PubMed » DOAJ » CAS » Scopus
[2] S.T.Cole, R. Brosch, J. Parkhill, et al., "Deciphering the biology of Mycobacterium
tuberculosis from the complete genome sequence". Nature 393 (6685): 537–44,
1998
» CrossRef » Google Scholar » PubMed » DOAJ » CAS » Scopus
[3] A. Joshi, J. Tang, M. Kuzma, J. Wagner, B. Mookerjee, J. Filicko, M. Carabasi, N.
Flomenberg, P. Flomenberg, "Adenovirus DNA polymerase is recognized by
human CD8+ T cells". J. Gen Virol., 90(Pt 1), 84-94, 2009
» CrossRef » Google Scholar » PubMed » DOAJ » CAS » Scopus
[4] D. McDonald, L. Stockwin, T. Matzow, M.E. Blair Zajdel, G.E.Blair, "Coxsackie and
adenovirus receptor (CAR)-dependent and major histocompatibility complex
(MHC) class I-independent uptake of recombinant adenoviruses into human
tumour cells". Gene Ther., 6(9),1512-9, 1999.
» CrossRef » Google Scholar » PubMed » DOAJ » CAS » Scopus
[5] V.S.Gomase, K.V. Kale and K. Shyamkumar, "Prediction of MHC Binding Peptides
and Epitopes from Groundnut Bud Necrosis Virus (GBNV)". J. of Proteomics &
Bioinformatics, 1 (4), 188- 205, 2008
» CrossRef » Google Scholar » PubMed » DOAJ » CAS » Scopus
[6] V.S.Gomase, K.V. Kale, N.J.Chikhale, S.S. Changbhale, "Prediction of MHC
Binding Peptides and Epitopes from Alfalfa mosaic virus". Curr. Drug Discov.
Technol., 4(2),117-1215, 2007.
» CrossRef » Google Scholar » PubMed » DOAJ » CAS » Scopus
[7] V.S.Gomase and K.V.Kale,"In silico prediction of epitopes: a new approach for
fragment based viral peptide vaccines". Int. J. of Applied Computing, 1(1), 39-46,
2008
» CrossRef » Google Scholar » PubMed » DOAJ » CAS » Scopus
[8] V.S.Gomase and K.V.Kale, "Approach of proteomics system architecture in plant
virus’s database". Int. J. of Applied Computing, 1(1), 33-38, 2008
» CrossRef » Google Scholar » PubMed » DOAJ » CAS » Scopus
[9] V.S.Gomase and K.V.Kale, "Bioinformatics based sequence analysis of
Nucleoplasmin like viral coat protein". Int. J. of Information Retrieval, 1(1), 11-15,
2008
» CrossRef » Google Scholar » PubMed » DOAJ » CAS » Scopus
[10] V.S.Gomase, K.V. Kale, K. Shyamkumar and S. Shankar, "Computer Aided Multi
Parameter Antigen Design: Impact of Synthetic Peptide Vaccines from Soybean
Mosaic Virus". ICETET 2008, IEEE Computer Society in IEEE Xplore, Los
Alamitos, California, 629-634, 2008.
» CrossRef » Google Scholar » PubMed » DOAJ » CAS » Scopus
[11] V.S.Gomase, J.P.Tandale, S.A.Patil, K.V.Kale, “Automatic modeling of protein 3D
structure Nucleoplasmin-like viral coat protein from Cucumber mosaic virus”.
14th International Conference on Advance Computing & Communication,
Published by IEEE Computer Society in IEEE Xplore USA 614-615, 2006
» CrossRef » Google Scholar » PubMed » DOAJ » CAS » Scopus
[12] P.A. Reche, J.P. Glutting, E.L. Reinherz, “Prediction of MHC Class I Binding
Peptides Using Profile Motifs”. Hum Immun., 63, 701-709, 2002
» CrossRef » Google Scholar » PubMed » DOAJ » CAS » Scopus
[13] S. Buus, et al., “Sensitive quantitative predictions of peptide-MHC binding by a
'Query by Committee' artificial neural network approach”. Tissue Antigens, 62,
378-384, 2003.
» CrossRef » Google Scholar » PubMed » DOAJ » CAS » Scopus
[14] M. Nielsen, et al., “Reliable prediction of T-cell epitopes using neural networks with
novel sequence representations”. Protein Sci., 12, 1007-1017, 2003
» CrossRef » Google Scholar » PubMed » DOAJ » CAS » Scopus
[15] M. Bhasin and G.P. Raghava, “Pcleavage: an SVM based method for prediction of
constitutive proteasome and immunoproteasome cleavage sites in antigenic
sequences”. Nucleic Acids Research, 33, W202-207, 2005
» CrossRef » Google Scholar » PubMed » DOAJ » CAS » Scopus