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OJBTM
Online
Journal of Bioinformatics ©
Volume 14 (1): 9-14, 2013.
In silico prediction and conservancy analysis of
promiscuous epitopes in a novel adenovirus HAdV-65
Rezaul Islam MD1, Lamia Khan1, Amran
Gazi MD1,
Motaher Hossain1,
Farhana Shafrin2,
Aubhishek Zaman3, Ahsan Habib Polash2
1Department of
Biochemistry and Molecular Biology, 2Molecular
Biology Laboratory, 3Department of Genetic Engineering and
Biotechnology, University of Dhaka, Bangladesh.
Islam R, Khan L, Gazi A, Hossain M, Shafrin F, Zaman A, Polash AH.,
In silico prediction and conservancy analysis of promiscuous epitopes in a
novel adenovirus HAdV-65, Online J Bioinform., 14
(1):9-14, 2013. Human adenovirus-65 has been associated with infantile
gastroenteritis in Bangladesh. In Silico
promiscuous epitopes for antigenic
capsid proteins and core components of HAdV-65 followed by conservancy analysis
in 3 randomly selected genotypes 1, 2 and 3 from NCBI database from different
regions were determined. A total
of 191,056 candidate promiscuous epitopes for MHC-I molecules based on their
binding affinity to different MHC-I alleles were predicted. Epitopes having an
IC50 score ≤ 50 nM were selected from TAP, proteasomal, IC50 scores, and number of interactions with
epitopes interacting with ≥ 3 MHC-I alleles. From this data, a catalogue
of epitopes was created. Hexon protein had most (26.14%), T cell promiscuous
epitopes of all the viral antigenic proteins. A total of 219 T cell epitopes
were predicted to be promiscuous binders against 51 MHC-II alleles and 23
epitopes were predicted to bind with all of the subjected MHC-II alleles. A
considerable number of predicted epitopes having higher affinity for both MHC-I
and MHC-II alleles were found to be conserved in other adenovirus genotypes and
may be potential candidates for design of epitope vaccines. To our knowledge,
this study is the first in silico
method to predict promiscuous epitopes for antigenic proteins in HAdV-65 and
must be validated by In-vitro
tests.
Keywords: Adenovirus; in silico; epitope based vaccine;
promiscuous T cell epitopes
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