Enzymatic Kinetic Isotope Effects from First-Principles Path Sampling Calculations

Varga, Matthew J.; Schwartz, Steven D.

doi:10.1021/acs.jctc.5b01169

Cited by 7 publications

(11 citation statements)

References 61 publications

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“…In recent work, we developed a method to calculate KIEs from first principle path sampling calculations (Varga & Schwartz, 2016). As in the above described study, TPS and CMD were utilized to circumvent limitations of other techniques dealing with the transfer of quantum particles.…”

Section: New Methods For Calculation Of Values Relevant To Enzyme Mmentioning

confidence: 99%

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Path Sampling Methods for Enzymatic Quantum Particle Transfer Reactions

Dzierlenga

Varga

Schwartz

2016

Methods in Enzymology

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The mechanisms of enzymatic reactions are studied via a host of computational techniques. While previous methods have been used successfully, many fail to incorporate the full dynamical properties of enzymatic systems. This can lead to misleading results in cases where enzyme motion plays a significant role in the reaction coordinate, which is especially relevant in particle transfer reactions where nuclear tunneling may occur. In this chapter, we outline previous methods, as well as discuss newly developed dynamical methods to interrogate mechanisms of enzymatic particle transfer reactions. These new methods allow for the calculation of free energy barriers and kinetic isotope effects (KIEs) with the incorporation of quantum effects through centroid molecular dynamics (CMD) and the full complement of enzyme dynamics through transition path sampling (TPS). Recent work, summarized in this chapter, applied the method for calculation of free energy barriers to reaction in lactate dehydrogenase (LDH) and yeast alcohol dehydrogenase (YADH). It was found that tunneling plays an insignificant role in YADH but plays a more significant role in LDH, though not dominant over classical transfer. Additionally, we summarize the application of a TPS algorithm for the calculation of reaction rates in tandem with CMD to calculate the primary H/D KIE of YADH from first principles. It was found that the computationally obtained KIE is within the margin of error of experimentally determined KIEs, and corresponds to the KIE of particle transfer in the enzyme. These methods provide new ways to investigate enzyme mechanism with the inclusion of protein and quantum dynamics.

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Section: New Methods For Calculation Of Values Relevant To Enzyme Mmentioning

confidence: 99%

“…In recent work, the rate algorithm with CMD was applied to the calculation of the primary H/D KIE in yeast alcohol dehydrogenase (Varga & Schwartz, 2016). This is the first application of the Chandler rate algorithm to an enzyme, as well as the first application in tandem with CMD.…”

Section: New Methods For Calculation Of Values Relevant To Enzyme Mmentioning

confidence: 99%

Path Sampling Methods for Enzymatic Quantum Particle Transfer Reactions

Dzierlenga

Varga

Schwartz

2016

Methods in Enzymology

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“…[51,52] Trajectorybased dynamics has also been applied to investigate H/D isotope effect on an ESPT. [53] However, the application of such a method to the present solution system is computationally too demanding because of the conformational flexibility of heptane and the need to model the solute by DFT.…”

Section: Differences In Gspt Reaction In An Isolated Cluster and Inmentioning

confidence: 99%

Reaction pathway and H/D kinetic isotope effects of the triple proton transfer in a 7‐hydroxyquinoline‐methanol complex in the ground state: A computational approach

Mori

2017

J of Physical Organic Chem

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Multiple proton transfer (PT) is an essential process in long-range proton transport such as proton relay in enzymes. 7-Hydroxyquinoline (7HQ) undergoes alcohol-mediated PT in both the excited and ground states, and this system has been investigated as a biomimetic model. In the present study, the reaction pathway of triple PT in a 7HQ-methanol cluster, 7HQ·(MeOH) 2 , in the ground state has been investigated using density functional theory calculations to clarify the reaction mechanism and the origin of the experimentally observed kinetic isotope effect (KIE). The PT takes place in an asynchronous concerted fashion, in which the oxygen atom in 7HQ first accepts a proton from the directly hydrogen-bonded MeOH. The rate constants and primary H/D KIEs have been estimated with canonical variational transition state theory in combination with the small curvature tunneling approximation. The tunneling effect on the PT rate is significant, and the KIE is much greater than 1 at room temperature. The rule of the geometric mean for the KIEs breaks down because of the asynchronicity in the motions of 3 protons and tunneling effect. In addition, the rate constant is smaller, the KIE is larger, and the activation energy is higher compared with the experimental values in heptane solution, suggesting that the PT dynamics in solution is governed by not only the intrinsic PT process but also thermal fluctuation of the solute and solvent molecules, which plays an important role in the configurational change of the 7HQ·(MeOH) 2 complex.

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“…They identified a conserved evolutionary motif in horse liver ADH that spans the catalytic and coenzyme binding domains (including Ser‐144, Gly‐181, Val‐203, Gly‐204, Val‐207, Glu‐267, Ile‐269, and Val‐292) and could participate in catalysis. They used transition path sampling to conclude that “protein compression” in the homologous yeast ADH “mediates a near barrier‐less hydride transfer.” They suggested that “slight changes in promoting vibrations (in lactate dehydrogenase) result in dramatic changes in enzyme chemistry.” The contribution of such fast dynamics to catalysis of hydride transfer by ADH needs experimental evaluation.…”

Section: Introductionmentioning

confidence: 99%

“…They used transition path sampling to conclude that "protein compression" in the homologous yeast ADH 51 "mediates a near barrier-less hydride transfer." 52,53 They suggested that "slight changes in promoting vibrations (in lactate dehydrogenase) result in dramatic changes in enzyme chemistry." 54,55 The contribution of such fast dynamics to catalysis of hydride transfer by ADH needs experimental evaluation.…”

Section: Introductionmentioning

confidence: 99%

Contribution of buried distal amino acid residues in horse liver alcohol dehydrogenase to structure and catalysis

Shanmuganatham¹,

Wallace²,

Lee³

et al. 2018

Protein Science

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The dynamics of enzyme catalysis range from the slow time scale (∼ms) for substrate binding and conformational changes to the fast time (∼ps) scale for reorganization of substrates in the chemical step. The contribution of global dynamics to catalysis by alcohol dehydrogenase was tested by substituting five different, conserved amino acid residues that are distal from the active site and located in the hinge region for the conformational change or in hydrophobic clusters. X-ray crystallography shows that the structures for the G173A, V197I, I220 (V, L, or F), V222I, and F322L enzymes complexed with NAD and an analogue of benzyl alcohol are almost identical, except for small perturbations at the sites of substitution. The enzymes have very similar kinetic constants for the oxidation of benzyl alcohol and reduction of benzaldehyde as compared to the wild-type enzyme, and the rates of conformational changes are not altered. Less conservative substitutions of these amino acid residues, such as G173(V, E, K, or R), V197(G, S, or T), I220(G, S, T, or N), and V222(G, S, or T) produced unstable or poorly expressed proteins, indicating that the residues are critical for global stability. The enzyme scaffold accommodates conservative substitutions of distal residues, and there is no evidence that fast, global dynamics significantly affect the rate constants for hydride transfers. In contrast, other studies show that proximal residues significantly participate in catalysis.

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Enzymatic Kinetic Isotope Effects from First-Principles Path Sampling Calculations

Cited by 7 publications

References 61 publications

Path Sampling Methods for Enzymatic Quantum Particle Transfer Reactions

Path Sampling Methods for Enzymatic Quantum Particle Transfer Reactions

Reaction pathway and H/D kinetic isotope effects of the triple proton transfer in a 7‐hydroxyquinoline‐methanol complex in the ground state: A computational approach

Contribution of buried distal amino acid residues in horse liver alcohol dehydrogenase to structure and catalysis

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