Differential Transition-State Stabilization in Enzyme Catalysis:  Quantum Chemical Analysis of Interactions in the Chorismate Mutase Reaction and Prediction of the Optimal Catalytic Field

Abstract

Chorismate mutase is a key model system in the development of theories of enzyme catalysis. To analyze the physical nature of catalytic interactions within the enzyme active site and to estimate the stabilization of the transition state (TS) relative to the substrate (differential transition state stabilization, DTSS), we have carried out nonempirical variation-perturbation analysis of the electrostatic, exchange, delocalization, and correlation interactions of the enzyme-bound substrate and transition-state structures derived from ab initio QM/MM modeling of Bacillus subtilis chorismate mutase. Significant TS stabilization by approximately -23 kcal/mol [MP2/6-31G(d)] relative to the bound substrate is in agreement with that of previous QM/MM modeling and contrasts with suggestions that catalysis by this enzyme arises purely from conformational selection effects. The most important contributions to DTSS come from the residues, Arg90, Arg7, Glu78, a crystallographic water molecule, Arg116, and Arg63, and are dominated by electrostatic effects. Analysis of the differential electrostatic potential of the TS and substrate allows calculation of the catalytic field, predicting the optimal location of charged groups to achieve maximal DTSS. Comparison with the active site of the enzyme from those of several species shows that the positions of charged active site residues correspond closely to the optimal catalytic field, showing that the enzyme has evolved specifically to stabilize the TS relative to the substrate.

Applications of large-scale density functional theory in biology

“…It was found that significant orbital overlap between the substrate and a number of charged active site residues act to stabilise the transition state (relative to the reactant and product states). This picture is supported by a previous study, which demonstrated the importance of electrostatic interactions in the active site to TS stabilisation in chorismate mutase [225].…”

Understanding the role of carbamate reactivity in fatty acid amide hydrolase inhibition by QM/MM mechanistic modelling

“…1). Furthermore, differential transition state stabilization (DTSS) analysis, 14 an emerging approach for identifying important interactions in enzyme-catalysed reactions, 15 was also performed to identify crucial residues involved in FAAH inhibition.…”

Tracking molecular charge distribution along reaction paths with atomic multipole moments

“…Fortunately, the redistribution of molecular charge density can also be monitored more directly through the multipole expansion of any well-defined molecular property, such as the MEP or electric fields. In their case, the arbitrary character of a particular atomic charge definition is, to a large degree, eliminated, yielding static or dynamic catalytic fields [2] and aiding de novo catalyst design.…”

“…Finally, we turn to two reactions involving neutral reactants, namely the second phase of the reaction of CO 2 with water during which a CO double bond is formed (Fig. 6) and the isomerisation of HCN to HNC (Fig.…”

“…The electron redistribution around reactants defines catalytic fields which have been shown to be useful indicators for de novo catalyst design [1,2]. In general, static catalytic fields are defined as molecular electrostatic potential changes during reaction progress [1,2].…”