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Characterisation of B cell epitopes of dengue virus NS1 protein using bioinformatics approach

Authors:

PD Pushpakumara,

LK
About PD
Institute for Combinatorial Advanced Research and Education, General Sir John Kotelawala Defence University, Ratmalana.
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PH Premarathne,

LK
About PH
Institute for Combinatorial Advanced Research and Education, General Sir John Kotelawala Defence University, Ratmalana.
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CL Goonasekara

LK
About CL
Institute for Combinatorial Advanced Research and Education, General Sir John Kotelawala Defence University, Ratmalana.
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Abstract

Linear B cell epitopes of the dengue virus nonstructural protein 1 (NS1) were predicted using three B cell epitope prediction tools, Ellipro, Bepipred and SVMTrip. Fifty sequences from each dengue serotype, representing a wide geographic area and a time span, were aligned using MEGA 6 software. The predictions were evaluated by comparing the results among the three tools and with currently available data on assay positive immunogenic epitopes of dengue NS1. A total of 22 regions on the NS1 protein ranging 6 to 21 amino acids in size were predicted as epitopes with a high probability score by the three prediction tools. Many were found to be predicted as epitopes by more than one tool, showing a good agreement in the predictions by the three tools. Further, many of the epitopes overlapped with, or partially constituted regions on the NS1 protein, which have been previously identified to be immunogenic as measured by various biochemical assays. Each of the 22 epitopes and the whole NS1 protein were then characterised for their percentages of conservation and phylogenetic relationship among and within each dengue serotypes, using IEDB and MEGA 6 analysis tools. Three epitopes were found to be highly conserved within the serotype but highly variable among the 04 dengue serotypes, suggesting that they could be used as possible serotype specific diagnostic markers. Three other epitopes were specific for the dengue group and more than 85 % conserved among the four dengue serotypes, showing a potential use as dengue group specific diagnostic markers. The bioinformatics approach appears a promising method in the identification of B cell epitopes of dengue NS1 with therapeutic potential. 

How to Cite: Pushpakumara, P., Premarathne, P. & Goonasekara, C., (2016). Characterisation of B cell epitopes of dengue virus NS1 protein using bioinformatics approach. Journal of the National Science Foundation of Sri Lanka. 44(4), pp.417–425. DOI: http://doi.org/10.4038/jnsfsr.v44i4.8024
Published on 27 Dec 2016.
Peer Reviewed

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