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United States Department of Agriculture

Agricultural Research Service

Research Project: INTERVENTION STRATEGIES TO SUPPORT THE GLOBAL CONTROL AND ERADICATION OF FOOT-AND-MOUTH DISEASE VIRUS (FMDV)

Location: Foreign Animal Disease Research

Title: Homology modelling and analysis of structure predictions of the bovine rhinitis B virus RNA-dependent RNA polymerase (RdRp)

Authors
item Rai, Devendra -
item Rieder, Aida

Submitted to: International Journal of Molecular Sciences
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: July 11, 2012
Publication Date: July 19, 2012
Repository URL: http://handle.nal.usda.gov/10113/55239
Citation: Rai, D., Rieder, A.E. 2012. Homology modelling and analysis of structure predictions of the bovine rhinitis B virus RNA-dependent RNA polymerase (RdRp). International Journal of Molecular Sciences. 2012(3):8998-9013.

Interpretive Summary: In this study we have built a homology model for the 3D polymerase, the enzyme responsible for the replication of Bovine rhinitis B virus (BRBV). This is the closest relative to foot-and-mouth disease virus (FMDV), which causes devastating disease in livestock. The aim of this study was to examine relevant functional domains to broaden the understanding of the function of the 3D polymerase. This information will be useful in identifying targets for antiviral drugs and in predicting regions of the 3D polymerase that could be changed in order to attenuate BRBV. This information will ultimately be applied to the development antivirals and also attenuated FMDV strains that could be used as candidate vaccines and against this devastating disease.

Technical Abstract: Bovine Rhinitis B Viruses (BRBV) are picornaviruses responsible for mild respiratory infection of cattle and probably the least characterized member of the Aphthoviruses. BRBV is the closest relative known to Foot and Mouth Disease virus (FMDV) with around a 43 percent identical polyprotein sequence and as much as 67 percent identical sequence for the 3D polymerase. In the present study, we have carried out phylogenetic analysis, structure based sequence alignment and prediction of three dimensional structure of BRBV RNA dependent RNA polymerase (RdRp) using a combination of different computational tools. Modeled structures were verified for the stereo chemical quality and accuracy. The 3D^pol structure predicted by Swiss model had highest scores in terms of accuracy and stereo chemical quality. The active site, template binding site and overall structure were observed to be in agreement with the crystal structure of un-liganded as well as template/primer, nucleotide tri-phosphate (NTP) and pyrophosphate (PPi) bound FMDV 3Dpol (pdb, 1u09 and 2e9z). The scores from the structure of BRBV 3D^pol structure modeled via Swiss model were in the range of very high quality crystal structure (less than or equal to 2 angstroms resolution). The observation of closest proximity of BRBV and FMDV 3D^pol compared to human rhinovirus and rabbit hemorrhagic fever virus polymerases is also supported by phylogeny tree and other calculations such as root-mean square deviation (RMSD) and Ramachandran plot. The information generated in this study could be valuable in the design of structure-function interventions and to identify molecular targets for drug design applicable to Aphthovirus RdRps.

Last Modified: 9/10/2014
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