Transition-State Vibrational Analysis and Isotope Effects for COMT-Catalyzed Methyl Transfer.

Maite Roca,Ian H Williams

doi:10.1021/jacs.0c07344

Abstract

Isotopic partition-function ratios (IPFRs) computed for transition structures (TSs) of the methyl-transfer reaction catalyzed by catechol O-methyltransferase and modeled by hybrid QM/MM methods are analyzed. The ability of smaller Hessians to reproduce trends in α-3H3 and 14Cα IPFRs as obtained using the much larger subset QM/MM Hessians from which they are extracted is investigated critically. A 6-atom-extracted Hessian reproduces perfectly the α-T3 IPFR values from the full-subset Hessians of all the TSs but not the α-14CIPFRs. Average AM1/OPLS-AA harmonic frequencies and mean-square amplitudes are presented for the 12 normal modes of the α-CH3 moiety within the active site of several enzymic transition structures, together with QM/MM potential energy scans along each of these modes to assess the degree of anharmonicity. A novel investigation of ponderal effects upon IPFRs suggests that the value for α-14C tends toward a limiting minimum whereas that for α-T3 tends toward a limiting maximum as the mass of the rest of the system increases. The transition vector is dominated by motions of atoms within the donor and acceptor moieties and is very well described as a simple combination of Walden-inversion “umbrella” bending and asymmetric stretching of the SCα and CαO bonds. The contribution of atoms of the protein residues Met40, Tyr68, and Asp141 to the transition vector is extremely small. Average valence force constants for the COMT TS show significant differences from early BEBOVIB estimates which were used in support of the compression hypothesis for catalysis. There is no correlation between TS IPFRs and the nonbonded distances for close contacts between the S atom of SAM and Tyr68 or between any of the H atoms of the transferring methyl group and either Met40 or Asp141.

Highlights

The transition state (TS) has been a cornerstone of physical organic chemistry for many years and has provided a useful foundation for discussions of reaction mechanisms in solution and in enzymes
(1) The ability of 6-atom-extracted Hessian to reproduce perfectly the α-T3 Isotopic partition-function ratios (IPFRs) values from the full-subset Hessians of all the TSs demonstrates that the origin of variation in these IPFRs for systems of any size is entirely due to changes in the isotopic sensitivity of the vibrational frequencies of the extracted 6-atom core
This result is consistent with the traditional rule that isotope effects are well approximated by truncated models including only atoms two bonds removed from the site of isotopic substitution; this is expected to be a general result for isotopes of hydrogen

Summary

Introduction

The transition state (TS) has been a cornerstone of physical organic chemistry for many years and has provided a useful foundation for discussions of reaction mechanisms in solution and in enzymes. For example, derives from the interaction of enzyme and substrate structures in the transition state, so that an understanding of this power must grow from a knowledge of these structures and interactions.”[1] These authors acknowledged that the form of any complete description might need to go beyond “present-day” TS theory, and the concept of the TS has recently been reassessed in the light of developments of computer simulations of chemical reactions in condensedphase systems,[2] but the elegance and economy of Schowen’s “fundamentalist” view remains: the entire and sole source of catalytic power is TS stabilization.[3] from this point of view, details of specific structures and pathways encountered between the reactant state (RS) and TS (as described by socalled “canonical” formulations of enzyme catalysis)[3] are unimportant, just as the difference between two thermodynamic functions of state is independent of the path that connects those states. Hybrid quantummechanics/molecular mechanics (QM/MM) calculations reproduced the trend in the 2° α-D3 KIEs without evidence

Objectives

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Results

Conclusion