期刊
BIOINFORMATION
卷 3, 期 10, 页码 430-434出版社
BIOMEDICAL INFORMATICS
DOI: 10.6026/97320630003430
关键词
amidase-03; Bacillus anthracis; high temperature unfolding; hydrolase enzyme; molecular dynamics; protein unfolding
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-L-alanine 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.
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