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Evolutionary Analysis and Prediction of Peptide Vaccine Candidates for Foot-and-Mouth-Disease Virus Types A and O in Bangladesh.

Momtaz S, Rahman A, Sultana M, Hossain MA - Evol. Bioinform. Online (2014)

Bottom Line: Peptide vaccine is a safer alternative.The scores of predicted epitopes of one method were cross-checked with other one for potential epitope mining.Within the VP1 antigenic sites, significant evidence of positive selection was present indicating evolution of VP1 under high immune surveillance.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology, University of Dhaka, Dhaka, Bangladesh.

ABSTRACT
Foot-and-mouth disease (FMD), an endemic disease of cloven-hoofed animals, causes an annual economic loss of US$60-150 million in Bangladesh. There is no cross-protection among the foot-and-mouth disease virus (FMDV) serotypes and vaccination escape mutation may happen. Peptide vaccine is a safer alternative. The aim of this study is to predict and map the B and T cell epitopes of VP1 proteins of FMDV serotypes O and A that were circulating in Bangladesh from 2011 to 2013. Using evolutionary and computational approach (BCPred, BepiPred, DiscoTope, ElliPro, and ProPred-I, IEDB analysis for MHC-I prediction), a total of 11 B and T cell epitopes were predicted. Also, the three-dimensional (3D) structure of VP1 protein showed that the predicted five epitopes residing on N- and C-termini can be considered as good vaccine candidates, and epitopes on the G-H loop can serve as receptor recognition sites for vaccine design. The scores of predicted epitopes of one method were cross-checked with other one for potential epitope mining. Within the VP1 antigenic sites, significant evidence of positive selection was present indicating evolution of VP1 under high immune surveillance.

No MeSH data available.


Related in: MedlinePlus

Protein 3D model of VP1 protein of FMDV serotype; type O (A) and type A (B) show different loops with presumptive positions.
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Related In: Results  -  Collection


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f4-ebo-10-2014-187: Protein 3D model of VP1 protein of FMDV serotype; type O (A) and type A (B) show different loops with presumptive positions.

Mentions: Using PyMol visualization tool, target models were superimposed on template models. Several loops (N-termini, BC, EF, FG, GH, C-termini) were labeled (Fig. 4). RMSD (Root-Mean-Square Deviation) for the whole model and loops were calculated using SuperPose version 1.018 to find the deviation among templates and target models (Table 2). Molecular dynamics simulations were done with YASARA force field minimization server for refining target models.28 For type O, the force field energy before minimization was −64360.1 kJ/mol and after minimization was −95945.5 kJ/mol. For type A, energy was −65015.2 kJ/mol, which became −89721.2 kJ/mol after minimization.


Evolutionary Analysis and Prediction of Peptide Vaccine Candidates for Foot-and-Mouth-Disease Virus Types A and O in Bangladesh.

Momtaz S, Rahman A, Sultana M, Hossain MA - Evol. Bioinform. Online (2014)

Protein 3D model of VP1 protein of FMDV serotype; type O (A) and type A (B) show different loops with presumptive positions.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4219755&req=5

f4-ebo-10-2014-187: Protein 3D model of VP1 protein of FMDV serotype; type O (A) and type A (B) show different loops with presumptive positions.
Mentions: Using PyMol visualization tool, target models were superimposed on template models. Several loops (N-termini, BC, EF, FG, GH, C-termini) were labeled (Fig. 4). RMSD (Root-Mean-Square Deviation) for the whole model and loops were calculated using SuperPose version 1.018 to find the deviation among templates and target models (Table 2). Molecular dynamics simulations were done with YASARA force field minimization server for refining target models.28 For type O, the force field energy before minimization was −64360.1 kJ/mol and after minimization was −95945.5 kJ/mol. For type A, energy was −65015.2 kJ/mol, which became −89721.2 kJ/mol after minimization.

Bottom Line: Peptide vaccine is a safer alternative.The scores of predicted epitopes of one method were cross-checked with other one for potential epitope mining.Within the VP1 antigenic sites, significant evidence of positive selection was present indicating evolution of VP1 under high immune surveillance.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology, University of Dhaka, Dhaka, Bangladesh.

ABSTRACT
Foot-and-mouth disease (FMD), an endemic disease of cloven-hoofed animals, causes an annual economic loss of US$60-150 million in Bangladesh. There is no cross-protection among the foot-and-mouth disease virus (FMDV) serotypes and vaccination escape mutation may happen. Peptide vaccine is a safer alternative. The aim of this study is to predict and map the B and T cell epitopes of VP1 proteins of FMDV serotypes O and A that were circulating in Bangladesh from 2011 to 2013. Using evolutionary and computational approach (BCPred, BepiPred, DiscoTope, ElliPro, and ProPred-I, IEDB analysis for MHC-I prediction), a total of 11 B and T cell epitopes were predicted. Also, the three-dimensional (3D) structure of VP1 protein showed that the predicted five epitopes residing on N- and C-termini can be considered as good vaccine candidates, and epitopes on the G-H loop can serve as receptor recognition sites for vaccine design. The scores of predicted epitopes of one method were cross-checked with other one for potential epitope mining. Within the VP1 antigenic sites, significant evidence of positive selection was present indicating evolution of VP1 under high immune surveillance.

No MeSH data available.


Related in: MedlinePlus