High temperature unfolding of Bacillus anthracis amidase-03 by molecular dynamics simulations.
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.
Sharma
Ravi Datta
RD
Department of Microbiology, C.C.S. University, Meerut, India. ravidattasharma@gmail.com
Lynn
Andrew M
AM
Sharma
Pradeep Kumar
PK
Rajnee
Jawaid
Safdar
S