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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