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Atomic-resolution dissection of the energetics and mechanism of isomerization of hydrated ATP- Mg2+ through the SOMA string method.
- Source :
- Journal of Computational Chemistry; Mar2016, Vol. 37 Issue 6, p575-586, 12p
- Publication Year :
- 2016
-
Abstract
- The atomic mechanisms of isomerization of ATP-Mg<superscript>2+</superscript> in solution are characterized using the recently developed String Method with Optimal Molecular Alignment (SOMA) and molecular-dynamics simulations. Bias-Exchange Metadynamics simulations are first performed to identify the primary conformers of the ATP-Mg<superscript>2+</superscript> complex and their connectivity. SOMA is then used to elucidate the minimum free-energy path (MFEP) for each transition, in a 48-dimensional space. Analysis of the per-atom contributions to the global free-energy profiles reveals that the mechanism of these transitions is controlled by the Mg<superscript>2+</superscript> ion and its coordinating oxygen atoms in the triphosphate moiety, as well as by the ion-hydration shell. Metadynamics simulations in path collective variables based on the MFEP demonstrate these isomerizations proceed across a narrow channel of configurational space, thus validating the premise underlying SOMA. This study provides a roadmap for the examination of conformational changes in biomolecules, based on complementary enhanced-sampling techniques with different strengths. © 2015 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]
Details
- Language :
- English
- ISSN :
- 01928651
- Volume :
- 37
- Issue :
- 6
- Database :
- Complementary Index
- Journal :
- Journal of Computational Chemistry
- Publication Type :
- Academic Journal
- Accession number :
- 112861454
- Full Text :
- https://doi.org/10.1002/jcc.23991