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

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.

SUBMITTER: Sharma RD

PROVIDER: S-EPMC2737499 | biostudies-literature | 2009 Jul

REPOSITORIES: biostudies-literature

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

Sharma Ravi Datta RD Lynn Andrew M AM Sharma Pradeep Kumar PK Rajnee Jawaid Safdar S

Bioinformation 20090727 10

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 secon ...[more]

PMID: 19759865

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