Title: Functional and structural analysis of mice TRPC6 with human analogue through homology modelling

Authors: Soumya Chigurupati; Arnima Bhasin; Krishna Kishore Inampudi; Swapna Asuthkar; Bhanupriya Madarampalli; Ramana Kumar Kammili; Kiran Kumar Velpula

Addresses: Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, 4000 Central Florida Blvd, Orlando, FL 32816, USA ' University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA ' Department of Chemistry, University of Hyderabad, Hyderabad 500046, India ' University of Illinois College of Medicine at Peoria, One Illini Drive, Peoria, IL, 61656, USA ' Department of Virology, Sri Venkateswara University, Tirupati 517502, India ' Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, 4000 Central Florida Blvd, Orlando, FL 32816, USA ' University of Illinois College of Medicine at Peoria, One Illini Drive, Peoria, IL, 61656, USA

Abstract: Homology models are increasingly used to determine structural and functional relationships of genes and proteins in biomedical research. In the current study, for the first time, we compared the TRPC6 gene in mouse and human. The protein encoded by this gene forms a receptor activated calcium channel in cell membrane. Defects in this gene have been implicated in a wide range of diseases including glioblastomas. To determine the structural similarities in mouse and human TRPC6, we used standard bioinformatics tools such as fold prediction to identify the protein 3D structure, sequence-structure comparison, and prediction of template and protein structure. We also used glioblastoma cell line U373MG and human glioblastoma tumour tissues to study the expression of TRPC6 in disease conditions to implicate this gene in pathological ailment. Based on the results we conclude that human TRPC6 contains 90% identity and 93% similarity with mouse TRPC6, suggesting that this protein is well conserved in these two species. These isoforms likely demonstrate similar mechanisms in regulating gene expression; thus TRPC6 studies in mice may be extrapolated to humans.

Keywords: glioblastoma; brain tumour; mice; TPRC6 gene; homology modelling; fold prediction; protein 3D structure sequence-structure comparison; protein structure; functional analysis; structural similarities; human analogue; bioinformatics; gene expression.

DOI: 10.1504/IJBRA.2014.059536

International Journal of Bioinformatics Research and Applications, 2014 Vol.10 No.2, pp.206 - 216

Available online: 25 Feb 2014 *

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