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Three hydrolases and a transferase: comparative analysis of active-site dynamics via the BioSimGrid database

Tai, Kaihsu, Baaden, Marc, Murdock, Stuart, Wu, Bing, Ng, Muan Hong, Johnston, Steven, Boardman, Richard, Fangohr, Hans, Cox, Katherine, Essex, Jonathan W. and Sansom, Mark S.P. (2007) Three hydrolases and a transferase: comparative analysis of active-site dynamics via the BioSimGrid database Journal of Molecular Graphics and Modelling, 25, (6), pp. 896-902. (doi:10.1016/j.jmgm.2006.08.010).

Record type: Article


Comparative molecular dynamics (MD) simulations enable us to explore the conformational dynamics of the active sites of distantly related enzymes. We have used the BioSimGrid ( database to facilitate such a comparison. Simulations of four enzymes were analyzed. These included three hydrolases and a transferase, namely acetylcholinesterase, outer-membrane phospholipase A, outer-membrane protease T, and PagP (an outer-membrane enzyme which transfers a palmitate chain from a phospholipid to lipid A). A set of 17 simulations were analyzed corresponding to a total of ~0.1 µs simulation time. A simple metric for active-site integrity was used to demonstrate the existence of clusters of dynamic conformational behaviour of the active sites. Small (i.e. within a cluster) fluctuations appear to be related to the function of an enzymatically active site. Larger fluctuations (i.e. between clusters) correlate with transitions between catalytically active and inactive states. Overall, these results demonstrate the potential of a comparative MD approach to analysis of enzyme function. This approach could be extended to a wider range of enzymes using current high throughput MD simulation and database methods.

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Published date: 2007
Keywords: biomolecular simulation, database, data mining, molecular dynamics, catalytic triad, conformational change


Local EPrints ID: 44165
ISSN: 1093-3263
PURE UUID: 4175cc94-65ce-4a7a-b515-b18210955c75
ORCID for Steven Johnston: ORCID iD
ORCID for Jonathan W. Essex: ORCID iD

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Date deposited: 19 Feb 2007
Last modified: 17 Jul 2017 15:15

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Author: Kaihsu Tai
Author: Marc Baaden
Author: Stuart Murdock
Author: Bing Wu
Author: Muan Hong Ng
Author: Steven Johnston ORCID iD
Author: Hans Fangohr
Author: Katherine Cox
Author: Mark S.P. Sansom

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