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Title
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High temperature unfolding of Bacillus anthracis amidase-03 by molecular dynamics simulations
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Authors
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Ravi Datta Sharma1, Andrew M. Lynn2, P. K. Sharma1, Rajnee3, Safdar Jawaid4 | |
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Affiliation
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1Department of Microbiology, C.C.S. University, Meerut, India; 2School of Information Technology, CCBB, Jawaharlal Nehru University, New Delhi, India; 3Department of Obstetrics and Gynecology, School of Medicine, West Virginia University, WV, USA; 4Department of Chemistry and Biochemistry, George Mason University, Firefax, VA, USA
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Article Type |
Hypothesis | |
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Date
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Received March 21, 2009; revised April 08 2009; accepted May 25, 2009; published July 27, 2009
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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-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 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 structural elements. Results show that amidase-03 unfolds in transition state ensemble (TSE). The data suggests that α-helices unfold before β-sheets from the core during simulation.
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Keywords |
amidase-03; Bacillus anthracis; high temperature unfolding; hydrolase enzyme; molecular dynamics; protein unfolding
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Citation |
Sharma et al, Bioinformation 3(10): 430-434 (2009) | |
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Edited by |
P. Kangueane
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ISSN |
0973-2063
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Publisher |
Biomedical Informatics
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License
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This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.
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