Proton transport in carbonic anhydrase: Insights from molecular simulation

Abstract

Summary This article reviews the insights gained from molecular simulations of human carbonic anhydrase II (HCA II) utilizing non-reactive and reactive force fields. The simulations with a reactive force field explore protein transfer and transport via Grotthuss shuttling, while the non-reactive simulations probe the larger conformational dynamics that underpin the various contributions to the rate-limiting proton transfer event. Specific attention is given to the orientational stability of the His64 group and the characteristics of the active site water cluster, in an effort to determine both of their impact on the maximal catalytic rate. The explicit proton transfer and transport events are described by the multistate empirical valence bond (MS-EVB) method, as are alternative pathways for the excess proton charge defect to enter/leave the active site. The simulation results are interpreted in light of experimental results on the wild-type enzyme and various site-specific mutations of HCA II in order to better elucidate the key factors that contribute to its exceptional efficiency.

Proton Transport in a Membrane Protein Channel: Two-Dimensional Infrared Spectrum Modeling

“…Proton transport in membrane proteins has been intensively studied by different simulation approaches, including MS-EVB, 45,90,91 CPMD, 92,93 path-integral, 51 semiclassical, 37 and Monte Carlo 43 methods, in order to derive the free energy surface for proton translocation along these channels. However, due to the limited simulation time (from ps to tens of ns), the PT rate along the channel is difficult to determine.…”

“…Besides proton channels, some other systems involving proton transport, such as enzyme families, 91 condensed phase crystals, 95,96 carbon nanotubes, 94 and fuel cell electrolyte membranes, 82,97 are also under investigation to understand the proton transport process and determine rate limiting steps. Combining MD simulation and 2DIR spectrum modeling offers a promising tool to study proton transport in these novel systems.…”

Where does charge reside in amino acids? The effect of side-chain protonation state on the atomic charges of Asp, Glu, Lys, His and Arg

“…For example, the rate limiting step in the conversion of CO 2 þ H 2 O ! HCO À 3 þ H þ by the enzyme carbonic anhydrase is a proton transfer involving the residue His64 [1,2]. Similarly, a proton transfer mechanism involving a Glu residue in the active site is found to be the ratedetermining step in the mechanism of the enzyme glutaminylcyclase [3].…”

Chemical Rescue of Enzymes: Proton Transfer in Mutants of Human Carbonic Anhydrase II

“…19 For additional information on the computational studies of HCA II the readers are referred to a recent review. 17 …”

“…The optimal region corresponds to a separation distance that would place the imidazole ring at a distance no greater than ~ 8 Å from the catalytic zinc. 17,19,43 This separation distance favors smaller, more stable water clusters connecting the proton donor/acceptor and would therefore have a positive impact on the PT event. 9,17,18 Computational studies of plausible hydrogen bonded water cluster pathways for H64A HCA II, with and without 4MI, have been conducted on the static crystallographic structure and its variants.…”