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Title

Conformational dynamics of ATP/Mg:ATP in motor proteins via data mining and molecular simulation

Author(s)

Bojovschi, A.;  Liu, Ming S.;  Sadus, Richard J.

Abstract

The conformational diversity of ATP/Mg:ATP in motor proteins was investigated using molecular dynamics and data mining. Adenosine triphosphate (ATP) conformations were found to be constrained mostly by inter cavity motifs in the motor proteins. It is demonstrated that ATP favors extended conformations in the tight pockets of motor proteins such as F1-ATPase and actin whereas compact structures are favored in motor proteins such as RNA polymerase and DNA helicase. The incorporation of Mg2+ leads to increased flexibility of ATP molecules. The differences in the conformational dynamics of ATP/Mg:ATP in various motor proteins was quantified by the radius of gyration. The relationship between the simulation results and those obtained by data mining of motor proteins available in the protein data bank is analyzed. The data mining analysis of motor proteins supports the conformational diversity of the phosphate group of ATP obtained computationally.

Publication type

Journal article

Research centre

Swinburne University of Technology. Faculty of Information and Communication Technologies

Source

Journal of Chemical Physics, Vol. 137, no. 7 (Aug 2012), article no. 075101

Publication year

2012

FOR Code(s)

02 Physical Sciences;  03 Chemical Sciences;  09 Engineering

Keyword(s)

Adenosine triphosphate;  ATP;  Conformational dynamics;  Data mining;  Magnesium;  Mg;  Molecular simulation

Publisher

American Institute of Physics

ISSN

0021-9606

Publisher URL

http://dx.doi.org/10.1063/1.4739308

Copyright

Copyright © 2012 American Institute of Physics. The published version is reproduced with the kind permission of the publisher.

Full text

Peer reviewed