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 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.

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