Literature DB >> 18666265

Associative versus dissociative mechanisms of phosphate monoester hydrolysis: on the interpretation of activation entropies.

Shina C L Kamerlin1, Jan Florián, Arieh Warshel.   

Abstract

Phosphate monoester and anhydride hydrolysis is ubiquitous in biology, being involved in, amongst other things, signal transduction, energy production, and the regulation of protein function. Therefore, this reaction has understandably been the focus of intensive research. Nevertheless, the precise mechanism by which phosphate monoester hydrolysis proceeds remains controversial. Traditionally, it has been assumed and frequently implied that a near-zero activation entropy is indicative of a dissociative pathway. Herein, we examine free-energy surfaces for the hydrolysis of the methyl phosphate dianion and the methyl pyrophosphate trianion in aqueous solution. In both cases, the reaction can proceed through either compact or expansive concerted (A(N)D(N)) transition states, with fairly similar barriers. We have evaluated the activation entropies for each transition state and demonstrate that both associative and dissociative transition states have near-zero entropies of activation that are in good agreement with experimental values. Therefore, we believe that the activation entropy alone is not a useful diagnostic tool, as it depends not only on bond orders at the transition state, but also on other issues that include (but are not limited to) steric factors determining the configurational volumes available to reactants during the reaction, solvation and desolvation effects that may be associated with charge redistribution upon approaching the transition state and entropy changes associated with intramolecular degrees of freedom as the transition state is approached.

Entities:  

Mesh:

Substances:

Year:  2008        PMID: 18666265     DOI: 10.1002/cphc.200800356

Source DB:  PubMed          Journal:  Chemphyschem        ISSN: 1439-4235            Impact factor:   3.102


  24 in total

1.  ATP hydrolysis in Eg5 kinesin involves a catalytic two-water mechanism.

Authors:  Courtney L Parke; Edward J Wojcik; Sunyoung Kim; David K Worthylake
Journal:  J Biol Chem       Date:  2009-12-15       Impact factor: 5.157

2.  Absolute binding free energy calculations: on the accuracy of computational scoring of protein-ligand interactions.

Authors:  Nidhi Singh; Arieh Warshel
Journal:  Proteins       Date:  2010-05-15

3.  Paradynamics: an effective and reliable model for ab initio QM/MM free-energy calculations and related tasks.

Authors:  Nikolay V Plotnikov; Shina C L Kamerlin; Arieh Warshel
Journal:  J Phys Chem B       Date:  2011-05-27       Impact factor: 2.991

4.  The control of the discrimination between dNTP and rNTP in DNA and RNA polymerase.

Authors:  Hanwool Yoon; Arieh Warshel
Journal:  Proteins       Date:  2016-08-10

5.  Does water relay play an important role in phosphoryl transfer reactions? Insights from theoretical study of a model reaction in water and tert-butanol.

Authors:  Yang Yang; Qiang Cui
Journal:  J Phys Chem B       Date:  2009-04-09       Impact factor: 2.991

6.  Overview of simulation studies on the enzymatic activity and conformational dynamics of the GTPase Ras.

Authors:  Priyanka Prakash; Alemayehu A Gorfe
Journal:  Mol Simul       Date:  2014-03-19       Impact factor: 2.178

Review 7.  Why nature really chose phosphate.

Authors:  Shina C L Kamerlin; Pankaz K Sharma; Ram B Prasad; Arieh Warshel
Journal:  Q Rev Biophys       Date:  2013-01-15       Impact factor: 5.318

8.  Quantum mechanics/molecular mechanics investigation of the mechanism of phosphate transfer in human uridine-cytidine kinase 2.

Authors:  Adam J T Smith; Ying Li; K N Houk
Journal:  Org Biomol Chem       Date:  2009-05-06       Impact factor: 3.876

9.  The hydrolysis activity of adenosine triphosphate in myosin: a theoretical analysis of anomeric effects and the nature of the transition state.

Authors:  Yang Yang; Qiang Cui
Journal:  J Phys Chem A       Date:  2009-11-12       Impact factor: 2.781

10.  Hyperconjugation-mediated solvent effects in phosphoanhydride bonds.

Authors:  Jean C Summerton; Jeffrey D Evanseck; Michael S Chapman
Journal:  J Phys Chem A       Date:  2012-10-09       Impact factor: 2.781

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.