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 Å 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.