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American Journal of Biochemistry and Molecular Biology
  Year: 2011 | Volume: 1 | Issue: 3 | Page No.: 265-274
DOI: 10.3923/ajbmb.2011.265.274
 
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Phylogenetics and in silico Docking Studies Between Coat Protein of Mimosa Yellow Vein Virus and Whey α-lactalbumin

Rajneesh Prajapat, Avinash Marwal, Anurag Sahu and Rajarshi Kumar Gaur

Abstract:
Begomovirus associated symptoms were observed in several Mimosa pudica plants growing in crop fields of Lakshmangarh, Rajasthan (India). Amplification of a PCR product was found up to the expected size (~570 bp) during agarose gel electrophoresis only in infected samples not in healthy samples. The PCR product was cloned and partially sequenced (GenBank accession HQ876467) and sequence analysis of HQ876467 by using BLASTn revealed the highest 98% nucleotide sequence identities with Ageratum yellow vein china virus (AJ558120). GeneBank-NCBI generated CDC for HQ876467 from 1 to 774 (ADW83735) and it was utilized for in silico analysis. In Neighbor-Joining tree, the coat protein of mimosa yellow vein virus (ADW83735) place in monophyletic clusters of 74 bootstrap values with AV1 protein of Ageratum yellow vein China virus (CAD90081). The closest homologue of coat protein was 2B7R|A, with highest sequence identity only 37% that was selected as representative model using homology modeling softwares. Homology modeling study of coat protein (ADW83735) and docking between α-lactalbumin and coat protein was carried out by using modeling and docking software (Hex 6.3). The ADW83735 model was validated by using Procheck server for reliability that results shown only 49.2% of residues present in core region. On the basis of RMS and energy values, the best docking orientation -1.00 was selected. This study will be used for the screening of inhibitors against mimosa yellow vein virus proteins and can be further applied in future antiviral agent designing.
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How to cite this article:

Rajneesh Prajapat, Avinash Marwal, Anurag Sahu and Rajarshi Kumar Gaur, 2011. Phylogenetics and in silico Docking Studies Between Coat Protein of Mimosa Yellow Vein Virus and Whey α-lactalbumin. American Journal of Biochemistry and Molecular Biology, 1: 265-274.

DOI: 10.3923/ajbmb.2011.265.274

URL: https://scialert.net/abstract/?doi=ajbmb.2011.265.274

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