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High temperature unfolding of Bacillus anthracis amidase-03 by molecular dynamics simulations |
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| Authors: | Ravi Datta Sharma Andrew M Lynn Pradeep Kumar Sharma Rajnee Safdar Jawaid |
| Affiliation: | 1.Department of Microbiology, C.C.S. University, Meerut, India;2.School of Information Technology, CCBB, Jawaharlal Nehru University, New Delhi, India;3.Department of Obstetrics and Gynecology, School of Medicine, West Virginia University, WV, USA;4.Department of Chemistry and Biochemistry, George Mason University, Fairfax, VA, USA |
| Abstract: | The stability of amidase-03 structure (a cell wall hydrolase protein) from Bacillus anthracis was studied using classicalmolecular dynamics (MD) simulation. This protein (GenBank accession number: NP_844822) contains an amidase-03domain which is known to exhibit the catalytic activity of N-acetylmuramoyl-L-alanine amidase (digesting MurNAc-Lalaninelinkage of bacterial cell wall). The amidase-03 enzyme has stability at high temperature due to the core formed bythe combination of several secondary structure elements made of β-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 structuralelements. Results show that amidase-03 unfolds in transition state ensemble (TSE). The data suggests that α-helices unfoldbefore β-sheets from the core during simulation. |
| Keywords: | amidase-03 Bacillus anthracis high temperature unfolding hydrolase enzyme molecular dynamics protein unfolding |