MAIN


©1996-2019.  All Rights Reserved. Online Journal of Bioinformatics . You may not store these pages in any form except for your own personal use. All other usage or distribution is illegal under international copyright treaties. Permission to use any of these pages in any other way besides the  before mentioned must be gained in writing from the publisher. This article is exclusively copyrighted in its entirety to OJB publications. This article may be copied once but may not be, reproduced or  re-transmitted without the express permission of the editors. This journal satisfies the refereeing requirements (DEST) for the Higher Education Research Data Collection (Australia). Linking: To link to this page or any pages linking to this page you must link directly to this page only here rather than put up your own page.


OJBTM

 Online Journal of Bioinformatics © 

  Volume 16 (1): 61-87, 2015.


Molecular modeling and in-silico characterization of alkaline protease from bacillus circulans MTCC 7906

 

Arun Dev Sharma* Gobind Ram  Inderjeet Kaur, Gurvinder Singh Kocher1,

 

PG Department of Biotechnology, Lyallpur Khalsa College, G T Road, Jallandhar-144001, Punjab, India, 1 Dept of Microbiology, Punjab Agricultural University (PAU), Ludhiana, Punjab, India

 

ABSTRACT

 

Sharma AD, Kaur GRI, Kocher S1, Molecular modeling and in-silico characterization of Alkaline Protease from Bacillus circulans MTCC 7906, Onl J Bioinform., 16 (1): 61-87, 2015. We describe in-silico characterization and molecular modeling of bacillus circulans MTCC 7906 (BcAP) through homology search, motif and conserved domain (CD) analysis, secondary structure prediction and 3D structure analysis. Motif scan analysis and CD analysis revealed signature sequences of a catalytic triad. Signature amino acid sequences of Peptidase S8/S53 domain were found in BcAP protein sequence possibly associated to structure and enzymatic function. 3D structure  was predicted using swiss-model server and homology modeling. Structure was refined by energy minimization and stereo-chemical qualities validated with PROCHECK, VADAR, WHAT-IF, Pro-Q, Verify3D and QMEAN servers. Five active sites were predicted for target protein structure. NEST analysis revealed 3 structural motifs in functionally important regions of protein structures. Based on gene ontology (GO) terms in ProFunc server, putative functions of modeled BcAP protein were predicted. 

 

Keywords: Alkaline protease, Bacillus circulans, Bioinformatics, Motif scan, Secondary structure, 3D structure, Ramachandran plot.


MAIN

 

FULL-TEXT(SUBSCRIPTION) OR PURCHASE ARTICLE $25USD