alexa Theoretical Modeling and Docking Studies of Silkworm Serotonin Receptor
ISSN: 0974-276X

Journal of Proteomics & Bioinformatics
Open Access

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Research Article

Theoretical Modeling and Docking Studies of Silkworm Serotonin Receptor

Ramasamy Sumathy1, SK Ashwath1 and VK Gopalakrishnan2*

1Bioinformatics centre, Central Sericultural Research and Training Institute, Mysore, Karnataka, India

2Department of Biochemistry and Bioinformatics, Karpagam University, Coimbatore, Tamilnadu, India

*Corresponding Author:
V.K. Gopalakrishnan
Professor and Head
Department of Biochemistry and Bioinformatics
Karpagam University, Coimbatore-641021 Tamil Nadu, India
E-mail: [email protected]

Received Date: August 14, 2012; Accepted Date: September 11, 2012; Published Date: September 13, 2012

Citation: Sumathy R, Ashwath SK, Gopalakrishnan VK (2012) Theoretical Modeling and Docking Studies of Silkworm Serotonin Receptor. J Proteomics Bioinform 5: 230-234 doi: 10.4172/jpb.1000242

Copyright: © 2012 Sumathy R, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

 

Abstract

The Silkworm serotonin receptor protein is an integral membrane protein which belongs to the largest superfamily of G protein-coupled receptors that communicate signals across the cell membrane through their interaction with heterotrimeric G proteins and regulate many of the physiological processes including the regulation of feeding, aggression, mood, perception, pain, anxiety etc. Despite the importance of serotonin receptor protein its structure have not yet determined experimentally due to difficulty in crystallization. The three-dimensional structure was modelled by the MODELLER program using the template rh1A which has 33% identity. The modelled structure was validated using Procheck and Ramachandran plot. It was found that the percentage of residue lying in the most favoured regions, additionally allowed regions, generously allowed regions, disallowed regions are 93.3%, 6.4%, 0% and 0.3%, respectively and it indicates reasonably good model. The overall Procheck G-factor and overall quality factor of ERRAT graph were 0.04 and 80.759, respectively. The binding site of the serotonin receptor protein was predicted using Q-Sitefinder and the interaction studies carried out with serotonin, agonist and reveals that the seven interaction residues Asp141, Val142, Gln218, Thr227, Ser230, Phe382, Leu405 of serotonin receptor protein interact with the serotonin form three hydrogen bond. This study provides a structural understanding at the atomic level of three-dimensional structure of silkworm serotonin receptor protein and their binding-sites and to elucidate of many promising active lead compounds.

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