A hybrid elastic band string algorithm for studies of enzymatic reactions

Physical Chemistry Chemical Physics : PCCP
Alexey Aleksandrov, Martin J Field

Abstract

A common challenge in theoretical biophysics is the identification of a minimum energy path (MEP) for the rearrangement of a group of atoms from one stable configuration to another. The structure with maximum energy along the MEP approximates the transition state for the process and the energy profile itself permits estimation of the transition rates. In this work we describe a computationally efficient algorithm for the identification of minimum energy paths in complicated biosystems. The algorithm is a hybrid of the nudged elastic band (NEB) and string methods. It has been implemented in the pDynamo simulation program and tested by examining elementary steps in the reaction mechanisms of three enzymes: citrate synthase, RasGAP, and lactate dehydrogenase. Good agreement is found for the energies and geometries of the species along the reaction profiles calculated using the new algorithm and previous versions of the NEB and string techniques, and also those obtained by the common method of adiabatic exploration of the potential energy surface as a function of predefined reaction coordinates. Precisely refined structures of the saddle points along the paths may be subsequently obtained with the climbing image variant of the NEB ...Continue Reading

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Citations

Apr 12, 2014·The Journal of Physical Chemistry. B·Alexey AleksandrovMartin Field
Oct 13, 2014·Journal of Molecular Graphics & Modelling·Alexandra T P CarvalhoShina Caroline Lynn Kamerlin
Feb 19, 2015·Nucleic Acids Research·Etienne DubiezEmmanuelle Schmitt
May 20, 2016·The Journal of Physical Chemistry. B·Nicholus BhattacharjeeCatherine M Bougault
Dec 28, 2016·The Journal of Physical Chemistry. B·Nicholus BhattacharjeeMartin J Field
Jul 12, 2017·The Journal of Physical Chemistry Letters·Elena E ZverevaAlexey V Aleksandrov
May 8, 2018·Scientific Reports·Emmanuelle SchmittAlexey Aleksandrov
Jul 26, 2017·Scientific Reports·Christina DiederichWulf Blankenfeldt
Mar 3, 2020·Inorganic Chemistry·Nicolás O FogliaDarío A Estrin
Feb 7, 2015·The Journal of Physical Chemistry. B·Cui WangJie-Lou Liao
Oct 7, 2014·The Journal of Physical Chemistry. B·Melchor Sanchez-MartinezRamon Crehuet
Feb 6, 2020·Journal of Chemical Theory and Computation·David K WolfeEdward P O'Brien

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