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Bioinformation. 2009 Jul 27;3(10):430-4.

High temperature unfolding of Bacillus anthracis amidase-03 by molecular dynamics simulations.

Author information

  • 1Department of Microbiology, C.C.S. University, Meerut, India. ravidattasharma@gmail.com

Abstract

The stability of amidase-03 structure (a cell wall hydrolase protein) from Bacillus anthracis was studied using classical molecular dynamics (MD) simulation. This protein (GenBank accession number: NP_844822) contains an amidase-03 domain which is known to exhibit the catalytic activity of N-acetylmuramoyl-L-alanine amidase (digesting MurNAc-Lalanine linkage of bacterial cell wall). The amidase-03 enzyme has stability at high temperature due to the core formed by the combination of several secondary structure elements made of beta-sheets. We used root-mean-square-displacement (RMSD) of the simulated structure from its initial state to demonstrate the unfolding of the enzyme using its secondary structural elements. Results show that amidase-03 unfolds in transition state ensemble (TSE). The data suggests that alpha-helices unfold before beta-sheets from the core during simulation.

KEYWORDS:

Bacillus anthracis; amidase-03; high temperature unfolding; hydrolase enzyme; molecular dynamics; protein unfolding

PMID:
19759865
[PubMed]
PMCID:
PMC2737499
Free PMC Article
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