Reaction Coordinate, Free Energy, and Rate of Intramolecular Proton Transfer in Human Carbonic Anhydrase II

The Journal of Physical Chemistry. B
Sanjib PaulSrabani Taraphder

Abstract

The role of structure and dynamics of an enzyme has been investigated at three different stages of its function including the chemical event it catalyzes. A one-pot computational method has been designed for each of these stages on the basis of classical and/or quantum mechanical-molecular mechanical molecular dynamics and transition path sampling simulations. For a pair of initial and final states A and B separated by a high free-energy barrier, using a two-stage selection process, several collective variables (CVs) are identified that can delineate A and B. However, these CVs are found to exhibit strong cross-coupling over the transition paths. A set of mutually orthogonal order parameters is then derived from these CVs and an optimal reaction coordinate, r, determined applying half-trajectory likelihood maximization along with a Bayesian information criterion. The transition paths are also used to project the multidimensional free energy surface and barrier crossing dynamics along r. The proposed scheme has been applied to the rate-determining intramolecular proton transfer reaction of the well-known enzyme human carbonic anhydrase II. The potential of mean force, F( r), in the absence of the chemical step is found to reprod...Continue Reading

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Citations

Apr 25, 2020·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Tanmoy Kumar Paul, Srabani Taraphder
Feb 18, 2021·Journal of Chemical Theory and Computation·Lev LevintovHarish Vashisth
Oct 31, 2019·Journal of Chemical Theory and Computation·Diego Soler-PoloJosé Ortega
Jan 17, 2019·The Journal of Physical Chemistry Letters·Abhishek Bagusetty, J Karl Johnson

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