BACK TO CONTENTS   |    PDF   |    PREVIOUS   |    NEXT

Title

 

 

 

 

 

A modeled structure for amidase-03 from Bacillus anthracis

 

Authors

 

Ravi Datta Sharma1, Nabajyoti Goswami2, Andrew M. Lynn3, Rajnee4, Pradeep Kumar Sharma1, Safdar Jawaid5

 

Affiliation

1Department of Microbiology, C.C.S. University, Meerut, India; 2Center for Biotechnology, Anna University, Chennai, India; 3School of Information Technology, CCBB, Jawaharlal Nehru University, New Delhi, India; 4Department of Obstetrics and Gynecology, School of Medicine, West Virginia University, WV, USA; 5Department of Chemistry and Biochemistry, George Mason University, Fairfax, VA, USA

 

Email

 

ravidattasharma@gmail.com

Article Type

 

Hypothesis

Date

 

Received May 06, 2009; Revised October 9, 2009; Accepted October 22, 2009; Published December 31, 2009

 

Abstract

Homology models of amidase-03 from Bacillus anthracis were constructed using Modeller (9v2). Modeller constructs protein models using an automated approach for comparative protein structure modeling by the satisfaction of spatial restraints. A template structure of Listeria monocytogenes bacteriophage PSA endolysin PlyPSA (PDB ID: 1XOV) was selected from protein databank (PDB) using BLASTp with BLOSUM62 sequence alignment scoring matrix. We generated five models using the Modeller default routine in which initial coordinates are randomized and evaluated by pseudo-energy parameters. The protein models were validated using PROCHECK and energy minimized using the steepest descent method in GROMACS 3.2 (flexible SPC water model in cubic box of size 1 instead of rigid SPC model). We used G43a1 force field in GROMACS for energy calculations and the generated structure was subsequently analyzed using the VMD software for stereo-chemistry, atomic clash and misfolding. A detailed analysis of the amidase-03 model structure from Bacillus anthracis will provide insight to the molecular design of suitable inhibitors as drug candidates.

 

Keywords

Homology modeling; modeller; amidase-03; hydrolase enzyme; Bacillus anthracis,

 

Citation

 

Sharma et al., Bioinformation 4(6): 242-244 (2009)

Edited by

 

P. Kangueane

 

ISSN

 

0973-2063

 

Publisher

 

Biomedical Informatics

 

License

 

 

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.