Journal of Proteomics & Bioinformatics- Open Access www.omicsonline.com Research Article JPB/Vol.2/August 2009 In Silico Identification of Putative Proton Binding Sites of a Plasma Membrane H +-ATPase Isoform of Arabidopsis Thaliana, AHA1

Abstract

jpb.1000095 Copyright: © 2009 Kumar S, 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. The plasma membrane potential and secondary transport systems in all eukaryotes are energized by the activity of P-type ATPase membrane proteins: H + ATPase (the proton pump) in plants and fungi and Na +, K +- ATPase (the sodium-potassium pump) in animals. The overall shape of proton pumps has been revealed by electron microscopy. The crystal structure of AHA2, a plasma membrane H +-ATPase isoform of Arabidopsis thaliana, by X-ray crystallography at 3.6 Å was available. The isoform is expressed mainly in root. In the present study homology modeling along with transmembrane topology predictions has been used to build the atomic model of AHA1, another plasma membrane H +-ATPase isoform of Arabidopsis thaliana expressing in both root and shoot. AHA2 was used as the template. The homology modeling was done using the MODELLER9v2 software. The model energy was minimized by applying molecular mechanics method. The root mean square deviation (RMSD) for C