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Functional analysis of lassa virus glycoprotein from a newly
identified lassa virus strain for possible use as vaccine
using computational methods
L. E. Okoror1*, H. A. T. Alaiya2 and
I. B. A. Momodu3
1Department
of Microbiology, Faculty of Natural Sciences, Ambrose Alli
University, P. M. B. 14 Ekpoma, Nigeria.
2Department
of Biochemistry, Faculty of Natural Sciences, Ambrose Alli
University, P. M. B. 14. Ekpoma, Nigeria.
3Department
of Computer Sciences, Faculty of Natural Sciences, Ambrose
Alli University, P. M. B. 14, Ekpoma, Nigeria.
*Corresponding author.
E-mail:
LEOkoror@gmail.com.
Accepted 17 July, 2009. |
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Lassa virus is the cause of morbidity and mortality in Ekpoma
Nigeria. Recently, two new strains of the virus were
identified. The genes were sequenced and deposited in the
GenBank. We presume that genes of similar sequence will code
for protein of similar function. Hence any vaccine produced
using this protein could protect against any other similar
virus due to conservation of active and functional regions.
The gene codes for a glycoprotein which could be antigenic
and stimulate the production of antibody. This is however if
the protein could be made non virulence. It then becomes
important to have a proper molecular knowledge and function
of the protein. Determination of the function of the protein
was first by global sequence alignment using blastp with
different parameters. However, not all the parameters used
produced hits even when e- values were adjusted. Pairwise
alignment and multiple sequence alignment (MSA) of the two
newly identified proteins were carried out but full analysis
of only one of the protein (strain) was done. Other tools
used in determining the function of the protein included
hydrophobicity, leader sequence, transmembrane helices, Pfam
using different tools from expasy and PHD tools. Prints and
blocks databases were also searched, but the block database
gave no hit. The hidden Markov’s model structure was also
done before searching for the 3D structure at PDB using
phyre at expasy. The pairwise alignment and MSA were done
with clustal W. This study gives a clear function of the
lassa virus glycoprotein, and also confirms the stability
and antigenicity of the protein so long as multiple domain
repeats are carried out before synthesis which will help
increase the molecular weight while preserving protein
function.
Key words: Lassa virus, multiple sequence alignment, glycoprotein,
protein structure, vaccine. |
