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

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- 3 H 3 and 14 C α 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-T 3 IPFR values from the full-subset Hessians of all the TSs but not the α- 14 CIPFRs. Average AM1/OPLS-AA harmonic frequencies and mean-square amplitudes are presented for the 12 normal modes of the α-CH 3 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- 14 C tends toward a limiting minimum whereas that for α-T 3 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 SC α and C α O 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.

Factors That Determine the Variation of Equilibrium and Kinetic Properties of QM/MM Enzyme Simulations: QM Region, Conformation, and Boundary Condition

“…As COMT provides a rich base for theoretical models, energy and free energy surfaces have been computed using multiple levels of theory, ranging from full ab initio quantum mechanical active site models to QM/MM free energy simulations. ,,,,− However, seemingly disparate results were obtained between different studies, leading to discussions of error sources between methods. To date, there has been much disagreement in how large the QM region should be for reliable free energy results.…”

Improving the Accuracy of Quantum Mechanics/Molecular Mechanics (QM/MM) Models with Polarized Fragment Charges

“…To further complicate matters, the QM region can be defined using different schemes ( e.g ., based on the distance from the reaction center, atomic charges, or chemical intuition), and the QM/MM models may be implemented using different pairings of QM methods and MM potentials, choice of embedding scheme, methods to treat the QM/MM boundary, and whether periodic boundary conditions are used. , Additionally, QM/MM energies may be calculated based on static geometries derived from crystal structures or an ensemble of configurations sampled from molecular dynamics simulations. − These choices could affect the accuracy and convergence of QM/MM reaction barriers and energies with respect to the QM region size and may explain some of the conflicting observations made by different research groups regarding the convergence behavior of their QM/MM models. ,, Notably, the catechol- O -methyltransferase (COMT) enzyme has been used as a model system by several groups to study the effect of the QM region size on the calculated reaction barriers and energies. ,,,− The most recent study by Cui and co-workers indicates that with extensive configurational sampling, the structural characteristics and energetics of the enzymatic reaction become less sensitive to the QM region size . However, due to the high computational cost of these studies, they are invariably limited to a specific QM and MM pairing ( e.g,.…”

High‐throughput computational investigation of protein electrostatics and cavity for SAM‐dependent methyltransferases

“…MTases catalyzing small molecules (i.e., molecular weight ≤582.9 g/mol), proteins, and catechol each contribute 11.0%, 7.7%, and 3.3% of the structures, respectively. We isolated catechol from the small molecule category because of its high abundance and well‐established existing studies elucidating its mechanism (Jindal & Warshel, 2016; Kulik et al, 2016; Männistö & Kaakkola, 1999; Patra et al, 2016; Roca & Williams, 2020; Ruggiero et al, 2004; Yang et al, 2019; Zhang et al, 2015). The distributions of cavity volumes and EF values are displayed in Figure 1b.…”

“…SAM MTases target various types of atoms, including carbon, nitrogen, oxygen, and sulfur (Scheme 1). Enabled by advances in structural determination, kinetic studies, and multiscale molecular modeling (Patra et al, 2016; Ruggiero et al, 2004; Soriano et al, 2006; Zhang et al, 2015), the mechanistic details of SAM MTases have been unveiled (Horowitz et al, 2014; Roca & Williams, 2020; Świderek et al, 2018). The combination of binding isotope effect experiments and large‐scale quantum mechanical calculations shows the dependence of ground state donor‐acceptor distance on the catalytic efficiency of catechol‐O‐methyltransferase (Zhang et al, 2020; Zhang & Klinman, 2016; Zhang et al, 2015).…”