Conserved and surface inaccessible regions of rotaviral VP7 protein.

<p>Five conserved and surface inaccessible regions are shown in five different colors and they are represented in green colored monomer of trimeric VP7 protein.</p

Position of peptide-c in a 3D space filling model of rotaviral trimeric VP7.

<p>Peptide-c (273 aa to 286 aa) is shown in cyan color and it is positioned in the green colored monomer.</p

<em>In Silico</em> Study of Rotavirus VP7 Surface Accessible Conserved Regions for Antiviral Drug/Vaccine Design

<div><h3>Background</h3><p>Rotaviral diarrhoea kills about half a million children annually in developing countries and accounts for one third of diarrhea related hospitalizations. Drugs and vaccines against the rotavirus are handicapped, as in all viral diseases, by the rapid mutational changes that take place in the DNA and protein sequences rendering most of these ineffective. As of now only two vaccines are licensed and approved by the WHO (World Health Organization), but display reduced efficiencies in the underdeveloped countries where the disease is more prevalent. We approached this issue by trying to identify regions of surface exposed conserved segments on the surface glycoproteins of the virion, which may then be targeted by specific peptide vaccines. We had developed a bioinformatics protocol for these kinds of problems with reference to the influenza neuraminidase protein, which we have refined and expanded to analyze the rotavirus issue.</p> <h3>Results</h3><p>Our analysis of 433 VP7 (Viral Protein 7 from rotavirus) surface protein sequences across 17 subtypes encompassing mammalian hosts using a 20D Graphical Representation and Numerical Characterization method, identified four possible highly conserved peptide segments. Solvent accessibility prediction servers were used to identify that these are predominantly surface situated. These regions analyzed through selected epitope prediction servers for their epitopic properties towards possible T-cell and B-cell activation showed good results as epitopic candidates (only dry lab confirmation).</p> <h3>Conclusions</h3><p>The main reasons for the development of alternative vaccine strategies for the rotavirus are the failure of current vaccines and high production costs that inhibit their application in developing countries. We expect that it would be possible to use the protein surface exposed regions identified in our study as targets for peptide vaccines and drug designs for stable immunity against divergent strains of the rotavirus. Though this study is fully dependent on computational prediction algorithms, it provides a platform for wet lab experiments.</p> </div

Comparison of solvent accessibility and stretch variability in rotaviral VP7 sequence database.

<p>Comparative diagram between solvent accessibility and stretch variability shows the regions of lowest variability and greatest environmentally accessed. All nine variable regions documented from previous research are found clearly distinguishable through our graph. Those regions are marked in green line. Peptide regions (peptide-a, b, c & d) indentified by our method are marked by blue lines.</p

Tabulated from of results derived from ABCpred server.

<p>The bold rows show that the conserved surface exposed regions identified in our method are also covered in five of the ABCpred server predicted regions.</p

Comparative representation of conserved, variable and antigenic regions from rotaviral VP7 protein database.

<p>Comparative schematic diagram for conserved surface accessible region (blue), previously recorded antigenic regions from IEDB server (red) and variable regions of rotavirus (green). Here length of protein VP7 is 326 amino acids.</p

MHC-II binding results for the identified four peptide segments.

<p>Results of the peptide-a, b, c and d submitted to the IEDB T-cell MHC-II binding prediction server are tabulated here. For each peptide the server generates two overlapping peptides; the peptides for the four groups are shown in different colors.</p

Position of Peptide-b is shown from outer surface of the virion in 3D-space filling model of rotaviral trimeric VP7.

<p>Peptide-b (aa 242 to aa 255) is shown in blue color and clearly highlights its discontinuous characteristic.</p

Position of Peptide-b is shown from inner surface of the virion in 3D-space filling model of rotaviral trimeric VP7.

<p>Lower part of Peptide-b (aa 242 to aa 255) is shown in blue color. It’s the same blue peptide as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0040749#pone-0040749-g005" target="_blank">Figure 5</a>.</p

Assignment of axis to individual amino acids.

<p>Assignment of axis to individual amino acids.</p