The intramolecular mechanism for the second proton transfer in triosephosphate isomerase (TIM): A QM/FE approach

Abstract

The intramolecular mechanism we earlier proposed [Alagona, G.; Desmeules, P.; Ghio, C.; Kollman, P. A. J Am Chem Soc 1984, 106, 3623] for the second proton transfer of the reaction catalyzed by triosephosphate isomerase (TIM) is examined ab initio at the HF and MP2/6-31+G** levels in vacuo for two conformers of the enediolate phosphate (ENEP), with the ethereal oxygen of the phosphate group either syn (X), as in the crystal structure, or anti (Y) with respect to the enediolate carbonyl O. The barrier height for the intramolecular proton transfer occurring in enediolate is very sensitive to electron correlation corrections. The MP2 internal energy barrier is much lower than the HF one, while the free energy (FE) barrier is even more favorable, indicating that the enzyme presence is not requested to speed up that step. An investigation of the dynamical aspects of the mechanism, along the pathway from ENEP A (with H on O(1)) to TS and from TS to ENEP B (with H on O(2)), was, however, carried out in the presence of the enzyme field while using a neutral His-95 with its proton on Ndelta. To perform the FE simulations, it was necessary to parametrize in the AMBER force-field the ENEP A, TS and B species, whose partial charges have been determined with the RESP procedure, with the X and Y arrangements of the phosphate head. Actually, the FE/QM approach produced a low barrier and a substantial balance between A and B, especially at the MP2 level. The trajectories, analyzed paying a particular attention to the positions assumed by His-95 and by the other active site residues, put forward somewhat different H-bond patterns around the X or Y enediolate phosphate.

Free Energies of Chemical Reactions in Solution and in Enzymes with Ab Initio Quantum Mechanics/Molecular Mechanics Methods

“…The mechanism has been examined by semiempirical QM/MM methods [115,116]. Later, several DFT-based QM/MM studies were been carried out [14,117,17,118]. With a higher resolution structure of the enzyme, Friesner's group modeled the reaction process and obtained results in good agreement with experimental data [119].…”

Ab Initio Quantum Chemical and Mixed Quantum Mechanics/Molecular Mechanics (Qm/Mm) Methods for Studying Enzymatic Catalysis

“…Several theoretical studies, using semiempirical and DFT-based QM/MM methods to study TIM catalysis, have provided an initial atomic-level picture of the various reaction steps (70,(134)(135)(136)(137)(138). Three different paths, involving the key catalytic residues, Glu165 and His95 have been proposed and discussed by several experimental and theoretical groups.…”

Computational Modeling of the Catalytic Reaction in Triosephosphate Isomerase

“…The protonation state of His95 has been the subject of an active experimental and theoretical discussion. 13,16 NMR studies demonstrated that the imidazole group is neutral at physiological pH values. 32 In the TIM-DHAP Michaelis crystal structure at near-atomic resolution, 1NEY.pdb, the imino N d forms a hydrogen bond with an amidic NH backbone group, and N 1 is tightly hydrogen bonding the substrate O1 and O2, accounting for the repulsive interaction observed in this and previous studies.…”