NDLI: Addressing open questions about phosphate hydrolysis pathways by careful free energy mapping.

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Addressing open questions about phosphate hydrolysis pathways by careful free energy mapping.

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Addressing open questions about phosphate hydrolysis pathways by careful free energy mapping.

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Plotnikov, Nikolay V. Prasad, B. Ram Warshel, Arieh
Description	Author Affiliation: Prasad BR ( Department of Chemistry, University of Southern California, SGM 418, 3620 McClintock Avenue, Los Angeles, California 90089, United States.)
Abstract	The nature and mechanism of phosphate hydrolysis reactions are of great interest in view of the crucial role of these reactions in key biological processes. Although it is becoming clearer that the ultimate way of resolving mechanistic controversies must involve reliable theoretical studies, it is not widely realized that such studies cannot be performed at present by using most existing automated ways and that only careful systematic studies can lead to meaningful conclusions. The present work clarifies the above point by considering the hydrolysis of phosphate monoesters. The clarification starts by defining the actual issues that should be addressed in careful studies and by highlighting the problems with studies that ignore the need for unique mechanistic definitions (e.g., works that confuse associative and dissociative pathways). We then focus on the analysis of the proton transfer (PT) pathways in phosphate hydrolysis and on recent suggestions that PT involves more than one water molecule. Here we point out that most of the studies that found a proton transfer through several water molecules have not involved a sufficient systematic search of the relevant reaction coordinates. This includes both energy minimization approaches as well as a recent metadynamics (MTD) simulation study. To illustrate the crucial need of exploring the potential surfaces reliably, rather than relying on automated approaches, we present here a very careful study of the free energy landscape along a 3D reaction coordinate (RC) exploring both the standard 2D RC, comprised of the attacking and leaving group reaction coordinates, as well as of the proton transfer (PT) coordinate. Our study points out that QM/MM minimization or MTD studies that concluded that the hydrolysis of phosphate monoesters involves a PT through several water molecules, have not explored carefully the single water (1W) path (that involves a direct PT form the attacking water molecule to the phosphate oxygen). Furthermore, we identified the most likely reason for the difficulty in finding the 1W path by QM/MM minimization methods, as well as by the current MTD simulations. We also discuss the problems with current studies that challenge the phosphate as a base mechanism and emphasize that all recent studies found associative/concerted paths (although many have not realized the meaning of their results). Finally, although we clearly do not have the last word about the 1W versus 2W paths we believe that we illustrated that the crucial mechanistic problems with alternative pathways should not be resolved by just running black box search approaches.
ISSN	15206106
e-ISSN	15205207
Journal	The Journal of Physical Chemistry B
Issue Number	1
Volume Number	117
Language	English
Publisher	American Chemical Society (United States)
Publisher Date	2013-01-10
Publisher Place	United States
Access Restriction	Open
Subject Keyword	Phosphates Chemistry Hydrolysis Quantum Theory Research Support, N.I.H., Extramural Research Support, U.S. Gov't, Non-P.H.S. Physical chemistry
Content Type	Text
Resource Type	Article
Subject	Surfaces, Coatings and Films Materials Chemistry Medicine Physical and Theoretical Chemistry

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