1
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Pusuluk O, Farrow T, Deliduman C, Burnett K, Vedral V. Proton tunnelling in hydrogen bonds and its implications in an induced-fit model of enzyme catalysis. Proc Math Phys Eng Sci 2018. [DOI: 10.1098/rspa.2018.0037] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The role of proton tunnelling in biological catalysis is investigated here within the frameworks of quantum information theory and thermodynamics. We consider the quantum correlations generated through two hydrogen bonds between a substrate and a prototypical enzyme that first catalyses the tautomerization of the substrate to move on to a subsequent catalysis, and discuss how the enzyme can derive its catalytic potency from these correlations. In particular, we show that classical changes induced in the binding site of the enzyme spreads the quantum correlations among all of the four hydrogen-bonded atoms thanks to the directionality of hydrogen bonds. If the enzyme rapidly returns to its initial state after the binding stage, the substrate ends in a new transition state corresponding to a quantum superposition. Open quantum system dynamics can then naturally drive the reaction in the forward direction from the major tautomeric form to the minor tautomeric form without needing any additional catalytic activity. We find that in this scenario the enzyme lowers the activation energy so much that there is no energy barrier left in the tautomerization, even if the quantum correlations quickly decay.
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Affiliation(s)
- Onur Pusuluk
- Department of Physics, İstanbul Technical University, Maslak, Istanbul 34469, Turkey
| | - Tristan Farrow
- Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, UK
- Centre for Quantum Technologies, National University of Singapore, 3 Science Drive 2, Singapore 117543, Singapore
| | - Cemsinan Deliduman
- Department of Physics, Mimar Sinan Fine Arts University, Bomonti, Istanbul 34380, Turkey
| | - Keith Burnett
- University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Vlatko Vedral
- Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, UK
- Centre for Quantum Technologies, National University of Singapore, 3 Science Drive 2, Singapore 117543, Singapore
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2
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Ranaghan KE, Morris WG, Masgrau L, Senthilkumar K, Johannissen LO, Scrutton NS, Harvey JN, Manby FR, Mulholland AJ. Ab Initio QM/MM Modeling of the Rate-Limiting Proton Transfer Step in the Deamination of Tryptamine by Aromatic Amine Dehydrogenase. J Phys Chem B 2017; 121:9785-9798. [PMID: 28930453 DOI: 10.1021/acs.jpcb.7b06892] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Aromatic amine dehydrogenase (AADH) and related enzymes are at the heart of debates on the roles of quantum tunneling and protein dynamics in catalysis. The reaction of tryptamine in AADH involves significant quantum tunneling in the rate-limiting proton transfer step, shown by large H/D primary kinetic isotope effects (KIEs), with unusual temperature dependence. We apply correlated ab initio combined quantum mechanics/molecular mechanics (QM/MM) methods, at levels up to local coupled cluster theory (LCCSD(T)/(aug)-cc-pVTZ), to calculate accurate potential energy surfaces for this reaction, which are necessary for quantitative analysis of tunneling contributions and reaction dynamics. Different levels of QM/MM treatment are tested. Multiple pathways are calculated with fully flexible transition state optimization by the climbing-image nudged elastic band method at the density functional QM/MM level. The average LCCSD(T) potential energy barriers to proton transfer are 16.7 and 14.0 kcal/mol for proton transfer to the two carboxylate atoms of the catalytic base, Asp128β. The results show that two similar, but distinct pathways are energetically accessible. These two pathways have different barriers, exothermicity and curvature, and should be considered in analyses of the temperature dependence of reaction and KIEs in AADH and other enzymes. These results provide a benchmark for this prototypical enzyme reaction and will be useful for developing empirical models, and analyzing experimental data, to distinguish between different conceptual models of enzyme catalysis.
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Affiliation(s)
- Kara E Ranaghan
- Centre for Computational Chemistry, School of Chemistry, University of Bristol , Cantock's Close, Bristol BS8 1TS, U.K
| | - William G Morris
- Centre for Computational Chemistry, School of Chemistry, University of Bristol , Cantock's Close, Bristol BS8 1TS, U.K
| | - Laura Masgrau
- Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona , 08193 Bellaterra (Barcelona), Spain
- Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona , 08193 Bellaterra (Barcelona), Spain
| | | | - Linus O Johannissen
- Manchester Institute of Biotechnology, University of Manchester , Manchester M13 9PL, U.K
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology, University of Manchester , Manchester M13 9PL, U.K
| | - Jeremy N Harvey
- Department of Chemistry, KU Leuven , Celestijnenlaan 200F, B-3001 Heverlee, Belgium
| | - Frederick R Manby
- Centre for Computational Chemistry, School of Chemistry, University of Bristol , Cantock's Close, Bristol BS8 1TS, U.K
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol , Cantock's Close, Bristol BS8 1TS, U.K
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3
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Tormos JR, Suarez MB, Fitzpatrick PF. 13C kinetic isotope effects on the reaction of a flavin amine oxidase determined from whole molecule isotope effects. Arch Biochem Biophys 2016; 612:115-119. [PMID: 27815088 PMCID: PMC5257176 DOI: 10.1016/j.abb.2016.10.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 10/26/2016] [Accepted: 10/27/2016] [Indexed: 12/14/2022]
Abstract
A large number of flavoproteins catalyze the oxidation of amines. Because of the importance of these enzymes in metabolism, their mechanisms have previously been studied using deuterium, nitrogen, and solvent isotope effects. While these results have been valuable for computational studies to distinguish among proposed mechanisms, a measure of the change at the reacting carbon has been lacking. We describe here the measurement of a 13C kinetic isotope effect for a representative amine oxidase, polyamine oxidase. The isotope effect was determined by analysis of the isotopic composition of the unlabeled substrate, N, N'-dibenzyl-1,4-diaminopropane, to obtain a pH-independent value of 1.025. The availability of a 13C isotope effect for flavoprotein-catalyzed amine oxidation provides the first measure of the change in bond order at the carbon involved in this carbon-hydrogen bond cleavage and will be of value to understanding the transition state structure for this class of enzymes.
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Affiliation(s)
- José R Tormos
- Department of Chemistry and Biochemistry, St. Mary's University, San Antonio, TX 78228, United States
| | - Marina B Suarez
- Department of Geological Sciences, University of Texas-San Antonio, San Antonio, TX 78249, United States
| | - Paul F Fitzpatrick
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229, United States.
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4
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Zelleke T, Marx D. Free-Energy Landscape and Proton Transfer Pathways in Oxidative Deamination by Methylamine Dehydrogenase. Chemphyschem 2016; 18:208-222. [DOI: 10.1002/cphc.201601113] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Indexed: 12/26/2022]
Affiliation(s)
- Theodros Zelleke
- Lehrstuhl für Theoretische Chemie; Ruhr-Universität Bochum; 44780 Bochum Germany
| | - Dominik Marx
- Lehrstuhl für Theoretische Chemie; Ruhr-Universität Bochum; 44780 Bochum Germany
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5
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Reinhardt CR, Jaglinski TC, Kastenschmidt AM, Song EH, Gross AK, Krause AJ, Gollmar JM, Meise KJ, Stenerson ZS, Weibel TJ, Dison A, Finnegan MR, Griesi DS, Heltne MD, Hughes TG, Hunt CD, Jansen KA, Xiong AH, Hati S, Bhattacharyya S. Insight into the kinetics and thermodynamics of the hydride transfer reactions between quinones and lumiflavin: a density functional theory study. J Mol Model 2016; 22:199. [PMID: 27491848 DOI: 10.1007/s00894-016-3074-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 07/17/2016] [Indexed: 12/14/2022]
Abstract
The kinetics and equilibrium of the hydride transfer reaction between lumiflavin and a number of substituted quinones was studied using density functional theory. The impact of electron withdrawing/donating substituents on the redox potentials of quinones was studied. In addition, the role of these substituents on the kinetics of the hydride transfer reaction with lumiflavin was investigated in detail under the transition state (TS) theory assumption. The hydride transfer reactions were found to be more favorable for an electron-withdrawing substituent. The activation barrier exhibited a quadratic relationship with the driving force of these reactions as derived under the formalism of modified Marcus theory. The present study found a significant extent of electron delocalization in the TS that is stabilized by enhanced electrostatic, polarization, and exchange interactions. Analysis of geometry, bond-orders, and energetics revealed a predominant parallel (Leffler-Hammond) effect on the TS. Closer scrutiny reveals that electron-withdrawing substituents, although located on the acceptor ring, reduce the N-H bond order of the donor fragment in the precursor complex. Carried out in the gas-phase, this is the first ever report of a theoretical study of flavin's hydride transfer reactions with quinones, providing an unfiltered view of the electronic effect on the nuclear reorganization of donor-acceptor complexes.
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Affiliation(s)
- Clorice R Reinhardt
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Tanner C Jaglinski
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Ashly M Kastenschmidt
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Eun H Song
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Adam K Gross
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Alyssa J Krause
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Jonathan M Gollmar
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Kristin J Meise
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Zachary S Stenerson
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Tyler J Weibel
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Andrew Dison
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Mackenzie R Finnegan
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Daniel S Griesi
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Michael D Heltne
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Tom G Hughes
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Connor D Hunt
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Kayla A Jansen
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Adam H Xiong
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Sanchita Hati
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Sudeep Bhattacharyya
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA.
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6
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Wide-dynamic-range kinetic investigations of deep proton tunnelling in proteins. Nat Chem 2016; 8:874-80. [PMID: 27554414 DOI: 10.1038/nchem.2527] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 04/14/2016] [Indexed: 11/08/2022]
Abstract
Directional proton transport along 'wires' that feed biochemical reactions in proteins is poorly understood. Amino-acid residues with high pKa are seldom considered as active transport elements in such wires because of their large classical barrier for proton dissociation. Here, we use the light-triggered proton wire of the green fluorescent protein to study its ground-electronic-state proton-transport kinetics, revealing a large temperature-dependent kinetic isotope effect. We show that 'deep' proton tunnelling between hydrogen-bonded oxygen atoms with a typical donor-acceptor distance of 2.7-2.8 Å fully accounts for the rates at all temperatures, including the unexpectedly large value (2.5 × 10(9) s(-1)) found at room temperature. The rate-limiting step in green fluorescent protein is assigned to tunnelling of the ionization-resistant serine hydroxyl proton. This suggests how high-pKa residues within a proton wire can act as a 'tunnel diode' to kinetically trap protons and control the direction of proton flow.
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7
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Ghosh AK, Islam Z, Krueger J, Abeysinghe T, Kohen A. The general base in the thymidylate synthase catalyzed proton abstraction. Phys Chem Chem Phys 2015; 17:30867-75. [PMID: 25912171 PMCID: PMC4624062 DOI: 10.1039/c5cp01246e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The enzyme thymidylate synthase (TSase), an important chemotherapeutic drug target, catalyzes the formation of 2'-deoxythymidine-5'-monophosphate (dTMP), a precursor of one of the DNA building blocks. TSase catalyzes a multi-step mechanism that includes the abstraction of a proton from the C5 of the substrate 2'-deoxyuridine-5'-monophosphate (dUMP). Previous studies on ecTSase proposed that an active-site residue, Y94 serves the role of the general base abstracting this proton. However, since Y94 is neither very basic, nor connected to basic residues, nor located close enough to the pyrimidine proton to be abstracted, the actual identity of this base remains enigmatic. Based on crystal structures, an alternative hypothesis is that the nearest potential proton-acceptor of C5 of dUMP is a water molecule that is part of a hydrogen bond (H-bond) network comprised of several water molecules and several protein residues including H147, E58, N177, and Y94. Here, we examine the role of the residue Y94 in the proton abstraction step by removing its hydroxyl group (Y94F mutant). We investigated the effect of the mutation on the temperature dependence of intrinsic kinetic isotope effects (KIEs) and found that these KIEs are more temperature dependent than those of the wild-type enzyme (WT). These results suggest that the phenolic -OH of Y94 is a component of the transition state for the proton abstraction step. The findings further support the hypothesis that no single functional group is the general base, but a network of bases and hydroxyls (from water molecules and tyrosine) sharing H-bonds across the active site can serve the role of the general base to remove the pyrimidine proton.
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Affiliation(s)
- Ananda K Ghosh
- Department of Chemistry, University of Iowa, Iowa City, IA 52242, USA.
| | - Zahidul Islam
- Department of Chemistry, University of Iowa, Iowa City, IA 52242, USA.
| | - Jonathan Krueger
- Department of Chemistry, University of Iowa, Iowa City, IA 52242, USA.
| | - Thelma Abeysinghe
- Department of Chemistry, University of Iowa, Iowa City, IA 52242, USA.
| | - Amnon Kohen
- Department of Chemistry, University of Iowa, Iowa City, IA 52242, USA.
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8
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Benabbas A, Salna B, Sage JT, Champion PM. Deep proton tunneling in the electronically adiabatic and non-adiabatic limits: comparison of the quantum and classical treatment of donor-acceptor motion in a protein environment. J Chem Phys 2015; 142:114101. [PMID: 25796225 DOI: 10.1063/1.4913591] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Analytical models describing the temperature dependence of the deep tunneling rate, useful for proton, hydrogen, or hydride transfer in proteins, are developed and compared. Electronically adiabatic and non-adiabatic expressions are presented where the donor-acceptor (D-A) motion is treated either as a quantized vibration or as a classical "gating" distribution. We stress the importance of fitting experimental data on an absolute scale in the electronically adiabatic limit, which normally applies to these reactions, and find that vibrationally enhanced deep tunneling takes place on sub-ns timescales at room temperature for typical H-bonding distances. As noted previously, a small room temperature kinetic isotope effect (KIE) does not eliminate deep tunneling as a major transport channel. The quantum approach focuses on the vibrational sub-space composed of the D-A and hydrogen atom motions, where hydrogen bonding and protein restoring forces quantize the D-A vibration. A Duschinsky rotation is mandated between the normal modes of the reactant and product states and the rotation angle depends on the tunneling particle mass. This tunnel-mass dependent rotation contributes substantially to the KIE and its temperature dependence. The effect of the Duschinsky rotation is solved exactly to find the rate in the electronically non-adiabatic limit and compared to the Born-Oppenheimer (B-O) approximation approach. The B-O approximation is employed to find the rate in the electronically adiabatic limit, where we explore both harmonic and quartic double-well potentials for the hydrogen atom bound states. Both the electronically adiabatic and non-adiabatic rates are found to diverge at high temperature unless the proton coupling includes the often neglected quadratic term in the D-A displacement from equilibrium. A new expression is presented for the electronically adiabatic tunnel rate in the classical limit for D-A motion that should be useful to experimentalists working near room temperature. This expression also holds when a broad protein conformational distribution of D-A equilibrium distances dominates the spread of the D-A vibrational wavefunction.
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Affiliation(s)
- Abdelkrim Benabbas
- Department of Physics and Center for Interdisciplinary Research on Complex Systems,Northeastern University, Boston, Massachusetts 02115, USA
| | - Bridget Salna
- Department of Physics and Center for Interdisciplinary Research on Complex Systems,Northeastern University, Boston, Massachusetts 02115, USA
| | - J Timothy Sage
- Department of Physics and Center for Interdisciplinary Research on Complex Systems,Northeastern University, Boston, Massachusetts 02115, USA
| | - Paul M Champion
- Department of Physics and Center for Interdisciplinary Research on Complex Systems,Northeastern University, Boston, Massachusetts 02115, USA
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9
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Abeysinghe T, Kohen A. Role of long-range protein dynamics in different thymidylate synthase catalyzed reactions. Int J Mol Sci 2015; 16:7304-19. [PMID: 25837629 PMCID: PMC4425018 DOI: 10.3390/ijms16047304] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 03/26/2015] [Accepted: 03/30/2015] [Indexed: 02/01/2023] Open
Abstract
Recent studies of Escherichia coli thymidylate synthase (ecTSase) showed that a highly conserved residue, Y209, that is located 8 Å away from the reaction site, plays a key role in the protein’s dynamics. Those crystallographic studies indicated that Y209W mutant is a structurally identical but dynamically altered relative to the wild type (WT) enzyme, and that its turnover catalytic rate governed by a slow hydride-transfer has been affected. The most challenging test of an examination of a fast chemical conversion that precedes the rate-limiting step has been achieved here. The physical nature of both fast and slow C-H bond activations have been compared between the WT and mutant by means of observed and intrinsic kinetic isotope effects (KIEs) and their temperature dependence. The findings indicate that the proton abstraction step has not been altered as much as the hydride transfer step. Additionally, the comparison indicated that other kinetic steps in the TSase catalyzed reaction were substantially affected, including the order of the substrate binding. Enigmatically, although Y209 is H-bonded to 3'-OH of 2'-deoxyuridine-5'-monophosphate (dUMP), its altered dynamics is more pronounced on the binding of the remote cofactor, (6R)-N5,N10-methylene-5,6,7,8-tetrahydrofolate (CH2H4folate), revealing the importance of long-range dynamics of the enzymatic complex and its catalytic function.
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Affiliation(s)
- Thelma Abeysinghe
- Department of Chemistry, University of Iowa, Iowa City, IA 52242-1727, USA.
| | - Amnon Kohen
- Department of Chemistry, University of Iowa, Iowa City, IA 52242-1727, USA.
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10
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Francis K, Kohen A. Protein motions and the activation of the CH bond catalyzed by dihydrofolate reductase. Curr Opin Chem Biol 2014; 21:19-24. [PMID: 24742825 PMCID: PMC4149937 DOI: 10.1016/j.cbpa.2014.03.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2014] [Revised: 03/03/2014] [Accepted: 03/05/2014] [Indexed: 11/28/2022]
Abstract
The role of protein motions in enzymatic CH→C transfer is an area of great contemporary debate. An effective tool in probing such a role is the temperature dependence of the intrinsic kinetic isotope effects for the enzyme-catalyzed reaction. The outcome of those experiments is interpreted within the context of phenomenological Marcus-like models of hydrogen tunneling. The current review focuses on recent studies of dihydrofolate reductase (DHFR) and how the role of protein motions in the catalyzed reaction has been demonstrated. The motions in DHFR are controlled by local effects of active site residues, global effects involving remote residues across the enzyme and appear to be preserved during the evolution of the enzyme from bacteria to human.
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Affiliation(s)
- Kevin Francis
- Department of Chemistry, The University of Iowa, Iowa City, IA 52242, United States
| | - Amnon Kohen
- Department of Chemistry, The University of Iowa, Iowa City, IA 52242, United States.
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11
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Islam Z, Strutzenberg TS, Gurevic I, Kohen A. Concerted versus stepwise mechanism in thymidylate synthase. J Am Chem Soc 2014; 136:9850-3. [PMID: 24949852 PMCID: PMC4105062 DOI: 10.1021/ja504341g] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Thymidylate synthase (TSase) catalyzes the intracellular de novo formation of thymidylate (a DNA building block) in most living organisms, making it a common target for chemotherapeutic and antibiotic drugs. Two mechanisms have been proposed for the rate-limiting hydride transfer step in TSase catalysis: a stepwise mechanism in which the hydride transfer precedes the cleavage of the covalent bond between the enzymatic cysteine and the product and a mechanism where both happen concertedly. Striking similarities between the enzyme-bound enolate intermediates formed in the initial and final step of the reaction supported the first mechanism, while QM/MM calculations favored the concerted mechanism. Here, we experimentally test these two possibilities using secondary kinetic isotope effect (KIE), mutagenesis study, and primary KIEs. The findings support the concerted mechanism and demonstrate the critical role of an active site arginine in substrate binding, activation of enzymatic nucleophile, and the hydride transfer studied here. The elucidation of this reduction/substitution sheds light on the critical catalytic step in TSase and may aid future drug or biomimetic catalyst design.
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Affiliation(s)
- Zahidul Islam
- Department of Chemistry, The University of Iowa , Iowa City, Iowa 52242-1727, United States
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12
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Francis K, Kohen A. Standards for the reporting of kinetic isotope effects in enzymology. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.pisc.2014.02.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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13
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Migliore A, Polizzi NF, Therien M, Beratan DN. Biochemistry and theory of proton-coupled electron transfer. Chem Rev 2014; 114:3381-465. [PMID: 24684625 PMCID: PMC4317057 DOI: 10.1021/cr4006654] [Citation(s) in RCA: 350] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Indexed: 02/01/2023]
Affiliation(s)
- Agostino Migliore
- Department
of Chemistry, Department of Biochemistry, and Department of Physics, Duke University, Durham, North Carolina 27708, United States
| | - Nicholas F. Polizzi
- Department
of Chemistry, Department of Biochemistry, and Department of Physics, Duke University, Durham, North Carolina 27708, United States
| | - Michael
J. Therien
- Department
of Chemistry, Department of Biochemistry, and Department of Physics, Duke University, Durham, North Carolina 27708, United States
| | - David N. Beratan
- Department
of Chemistry, Department of Biochemistry, and Department of Physics, Duke University, Durham, North Carolina 27708, United States
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14
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Kryvohuz M. Calculation of Kinetic Isotope Effects for Intramolecular Hydrogen Shift Reactions Using Semiclassical Instanton Approach. J Phys Chem A 2014; 118:535-44. [DOI: 10.1021/jp4099073] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Maksym Kryvohuz
- Chemical Sciences and Engineering
Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
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15
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Francis K, Stojković V, Kohen A. Preservation of protein dynamics in dihydrofolate reductase evolution. J Biol Chem 2013; 288:35961-8. [PMID: 24158440 PMCID: PMC3861645 DOI: 10.1074/jbc.m113.507632] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 10/09/2013] [Indexed: 11/06/2022] Open
Abstract
The hydride transfer reaction catalyzed by dihydrofolate reductase (DHFR) is a model for examining how protein dynamics contribute to enzymatic function. The relationship between functional motions and enzyme evolution has attracted significant attention. Recent studies on N23PP Escherichia coli DHFR (ecDHFR) mutant, designed to resemble parts of the human enzyme, indicated a reduced single turnover rate. NMR relaxation dispersion experiments with that enzyme showed rigidification of millisecond Met-20 loop motions (Bhabha, G., Lee, J., Ekiert, D. C., Gam, J., Wilson, I. A., Dyson, H. J., Benkovic, S. J., and Wright, P. E. (2011) Science 332, 234-238). A more recent study of this mutant, however, indicated that fast motions along the reaction coordinate are actually more dispersed than for wild-type ecDHFR (WT). Furthermore, a double mutant (N23PP/G51PEKN) that better mimics the human enzyme seems to restore both the single turnover rates and narrow distribution of fast dynamics (Liu, C. T., Hanoian, P., French, T. H., Hammes-Schiffer, S., and Benkovic, S. J. (2013) Proc. Natl. Acad. Sci. U.S.A. 110, 10159-11064). Here, we measured intrinsic kinetic isotope effects for both N23PP and N23PP/G51PEKN double mutant DHFRs over a temperature range. The findings indicate that although the C-H→C transfer and dynamics along the reaction coordinate are impaired in the altered N23PP mutant, both seem to be restored in the N23PP/G51PEKN double mutant. This indicates that the evolution of G51PEKN, although remote from the Met-20 loop, alleviated the loop rigidification that would have been caused by N23PP, enabling WT-like H-tunneling. The correlation between the calculated dynamics, the nature of C-H→C transfer, and a phylogenetic analysis of DHFR sequences are consistent with evolutionary preservation of the protein dynamics to enable H-tunneling from well reorganized active sites.
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Affiliation(s)
- Kevin Francis
- From the Department of Chemistry, The University of Iowa, Iowa City, Iowa 52242
| | - Vanja Stojković
- From the Department of Chemistry, The University of Iowa, Iowa City, Iowa 52242
| | - Amnon Kohen
- From the Department of Chemistry, The University of Iowa, Iowa City, Iowa 52242
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16
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Kryvohuz M. On the derivation of semiclassical expressions for quantum reaction rate constants in multidimensional systems. J Chem Phys 2013; 138:244114. [DOI: 10.1063/1.4811221] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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17
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Liuni P, Olkhov-Mitsel E, Orellana A, Wilson DJ. Measuring kinetic isotope effects in enzyme reactions using time-resolved electrospray mass spectrometry. Anal Chem 2013; 85:3758-64. [PMID: 23461634 DOI: 10.1021/ac400191t] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Kinetic isotope effect (KIE) measurements are a powerful tool for studying enzyme mechanisms; they can provide insights into microscopic catalytic processes and even structural constraints for transition states. However, KIEs have not come into widespread use in enzymology, due in large part to the requirement for prohibitively cumbersome experimental procedures and daunting analytical frameworks. In this work, we introduce time-resolved electrospray ionization mass spectrometry (TRESI-MS) as a straightforward, precise, and inexpensive method for measuring KIEs. Neither radioisotopes nor large amounts of material are needed and kinetic measurements for isotopically "labeled" and "unlabeled" species are acquired simultaneously in a single "competitive" assay. The approach is demonstrated first using a relatively large isotope effect associated with yeast alcohol dehydrogenase (YADH) catalyzed oxidation of ethanol. The measured macroscopic KIE of 2.19 ± 0.05 is consistent with comparable measurements in the literature but cannot be interpreted in a way that provides insights into isotope effects in individual microscopic steps. To demonstrate the ability of TRESI-MS to directly measure intrinsic KIEs and to characterize the precision of the technique, we measure a much smaller (12)C/(13)C KIE associated specifically with presteady state acylation of chymotrypsin during hydrolysis of an ester substrate.
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Affiliation(s)
- Peter Liuni
- Department of Chemistry, York University, Toronto, ON, Canada
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18
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Abstract
Techniques for modelling enzyme-catalyzed reaction mechanisms are making increasingly important contributions to biochemistry. They can address fundamental questions in enzyme catalysis and have the potential to contribute to practical applications such as drug development.
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19
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Kryvohuz M. Calculation of chemical reaction rate constants using on-the-fly high level electronic structure computations with account of multidimensional tunneling. J Chem Phys 2012; 137:234304. [DOI: 10.1063/1.4769195] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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20
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Wang Z, Abeysinghe T, Finer-Moore JS, Stroud RM, Kohen A. A remote mutation affects the hydride transfer by disrupting concerted protein motions in thymidylate synthase. J Am Chem Soc 2012; 134:17722-30. [PMID: 23034004 DOI: 10.1021/ja307859m] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The role of protein flexibility in enzyme-catalyzed activation of chemical bonds is an evolving perspective in enzymology. Here we examine the role of protein motions in the hydride transfer reaction catalyzed by thymidylate synthase (TSase). Being remote from the chemical reaction site, the Y209W mutation of Escherichia coli TSase significantly reduces the protein activity, despite the remarkable similarity between the crystal structures of the wild-type and mutant enzymes with ligands representing their Michaelis complexes. The most conspicuous difference between these two crystal structures is in the anisotropic B-factors, which indicate disruption of the correlated atomic vibrations of protein residues in the mutant. This dynamically altered mutant allows a variety of small thiols to compete for the reaction intermediate that precedes the hydride transfer, indicating disruption of motions that preorganize the protein environment for this chemical step. Although the mutation causes higher enthalpy of activation of the hydride transfer, it only shows a small effect on the temperature dependence of the intrinsic KIE, suggesting marginal changes in the geometry and dynamics of the H-donor and -acceptor at the tunneling ready state. These observations suggest that the mutation disrupts the concerted motions that bring the H-donor and -acceptor together during the pre- and re-organization of the protein environment. The integrated structural and kinetic data allow us to probe the impact of protein motions on different time scales of the hydride transfer reaction within a complex enzymatic mechanism.
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Affiliation(s)
- Zhen Wang
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242-1727, USA
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21
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Kryvohuz M, Marcus RA. Semiclassical evaluation of kinetic isotope effects in 13-atomic system. J Chem Phys 2012; 137:134107. [DOI: 10.1063/1.4754660] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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22
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Hernández-Ortega A, Ferreira P, Merino P, Medina M, Guallar V, Martínez AT. Stereoselective Hydride Transfer by Aryl-Alcohol Oxidase, a Member of the GMC Superfamily. Chembiochem 2012; 13:427-35. [PMID: 22271643 DOI: 10.1002/cbic.201100709] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Indexed: 11/06/2022]
Affiliation(s)
- Aitor Hernández-Ortega
- Centro de Investigaciones Biológicas (CIB), Consejo Superior de Investigaciones Científicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
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23
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Kaspera R, Sahele T, Lakatos K, Totah RA. Cytochrome P450BM-3 reduces aldehydes to alcohols through a direct hydride transfer. Biochem Biophys Res Commun 2012; 418:464-8. [PMID: 22281497 DOI: 10.1016/j.bbrc.2012.01.040] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Accepted: 01/09/2012] [Indexed: 12/15/2022]
Abstract
Cytochrome P450BM-3 catalyzed the reduction of lipophilic aldehydes to alcohols efficiently. A k(cat) of ∼25 min(-1) was obtained for the reduction of methoxy benzaldehyde with wild type P450BM-3 protein which was higher than in the isolated reductase domain (BMR) alone and increased in specific P450-domain variants. The reduction was caused by a direct hydride transfer from preferentially R-NADP(2)H to the carbonyl moiety of the substrate. Weak substrate-P450-binding of the aldehyde, turnover with the reductase domain alone, a deuterium incorporation in the product from NADP(2)H but not D(2)O, and no inhibition by imidazole suggests the reductase domain of P450BM-3 as the potential catalytic site. However, increased aldehyde reduction by P450 domain variants (P450BM-3 F87A T268A) may involve allosteric or redox mechanistic interactions between heme and reductase domains. This is a novel reduction of aldehydes by P450BM-3 involving a direct hydride transfer and could have implications for the metabolism of endogenous substrates or xenobiotics.
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Affiliation(s)
- Rüdiger Kaspera
- Department of Medicinal Chemistry, University of Washington, Box 357610, Seattle, WA 98195-7610, USA
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24
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Stojković V, Perissinotti LL, Willmer D, Benkovic SJ, Kohen A. Effects of the donor-acceptor distance and dynamics on hydride tunneling in the dihydrofolate reductase catalyzed reaction. J Am Chem Soc 2012; 134:1738-45. [PMID: 22171795 DOI: 10.1021/ja209425w] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A significant contemporary question in enzymology involves the role of protein dynamics and hydrogen tunneling in enhancing enzyme catalyzed reactions. Here, we report a correlation between the donor-acceptor distance (DAD) distribution and intrinsic kinetic isotope effects (KIEs) for the dihydrofolate reductase (DHFR) catalyzed reaction. This study compares the nature of the hydride-transfer step for a series of active-site mutants, where the size of a side chain that modulates the DAD (I14 in E. coli DHFR) is systematically reduced (I14V, I14A, and I14G). The contributions of the DAD and its dynamics to the hydride-transfer step were examined by the temperature dependence of intrinsic KIEs, hydride-transfer rates, activation parameters, and classical molecular dynamics (MD) simulations. Results are interpreted within the framework of the Marcus-like model where the increase in the temperature dependence of KIEs arises as a direct consequence of the deviation of the DAD from its distribution in the wild type enzyme. Classical MD simulations suggest new populations with larger average DADs, as well as broader distributions, and a reduction in the population of the reactive conformers correlated with the decrease in the size of the hydrophobic residue. The more flexible active site in the mutants required more substantial thermally activated motions for effective H-tunneling, consistent with the hypothesis that the role of the hydrophobic side chain of I14 is to restrict the distribution and dynamics of the DAD and thus assist the hydride-transfer. These studies establish relationships between the distribution of DADs, the hydride-transfer rates, and the DAD's rearrangement toward tunneling-ready states. This structure-function correlation shall assist in the interpretation of the temperature dependence of KIEs caused by mutants far from the active site in this and other enzymes, and may apply generally to C-H→C transfer reactions.
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Affiliation(s)
- Vanja Stojković
- Department of Chemistry, The University of Iowa, Iowa City, Iowa 52242, USA
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25
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In Silico Strategies Toward Enzyme Function and Dynamics. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2012. [DOI: 10.1016/b978-0-12-398312-1.00009-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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26
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Karković A, Brala CJ, Pilepić V, Uršić S. Solvent-induced hydrogen tunnelling in ascorbate proton-coupled electron transfers. Tetrahedron Lett 2011. [DOI: 10.1016/j.tetlet.2011.01.142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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27
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de la Lande A, Řezáč J, Lévy B, Sanders BC, Salahub DR. Transmission coefficients for chemical reactions with multiple states: role of quantum decoherence. J Am Chem Soc 2011; 133:3883-94. [PMID: 21344903 DOI: 10.1021/ja107950m] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Transition-state theory (TST) is a widely accepted paradigm for rationalizing the kinetics of chemical reactions involving one potential energy surface (PES). Multiple PES reaction rate constants can also be estimated within semiclassical approaches provided the hopping probability between the quantum states is taken into account when determining the transmission coefficient. In the Marcus theory of electron transfer, this hopping probability was historically calculated with models such as Landau-Zener theory. Although the hopping probability is intimately related to the question of the transition from the fully quantum to the semiclassical description, this issue is not adequately handled in physicochemical models commonly in use. In particular, quantum nuclear effects such as decoherence or dephasing are not present in the rate constant expressions. Retaining the convenient semiclassical picture, we include these effects through the introduction of a phenomenological quantum decoherence function. A simple modification to the usual TST rate constant expression is proposed: in addition to the electronic coupling, a characteristic decoherence time τ(dec) now also appears as a key parameter of the rate constant. This new parameter captures the idea that molecular systems, although intrinsically obeying quantum mechanical laws, behave semiclassically after a finite but nonzero amount of time (τ(dec)). This new degree of freedom allows a fresh look at the underlying physics of chemical reactions involving more than one quantum state. The ability of the proposed formula to describe the main physical lines of the phenomenon is confirmed by comparison with results obtained from density functional theory molecular dynamics simulations for a triplet to singlet transition within a copper dioxygen adduct relevant to the question of dioxygen activation by copper monooxygenases.
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Affiliation(s)
- Aurélien de la Lande
- Laboratoire de Chimie Physique-CNRS UMR 8000, Université Paris-Sud 11, Bât. 349, Campus d'Orsay, 15 rue Jean Perrin, 91 405 Orsay Cedex, France.
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28
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Klinman JP. The widespread occurrence of enzymatic hydrogen tunneling, andits unique properties, lead to a new physical model for the origins of enzyme catalysis. ACTA ACUST UNITED AC 2011. [DOI: 10.1016/j.proche.2011.08.037] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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29
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McGeagh JD, Ranaghan KE, Mulholland AJ. Protein dynamics and enzyme catalysis: insights from simulations. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1814:1077-92. [PMID: 21167324 DOI: 10.1016/j.bbapap.2010.12.002] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2010] [Revised: 11/25/2010] [Accepted: 12/03/2010] [Indexed: 10/18/2022]
Abstract
The role of protein dynamics in enzyme catalysis is one of the most active and controversial areas in enzymology today. Some researchers claim that protein dynamics are at the heart of enzyme catalytic efficiency, while others state that dynamics make no significant contribution to catalysis. What is the biochemist - or student - to make of the ferocious arguments in this area? Protein dynamics are complex and fascinating, as molecular dynamics simulations and experiments have shown. The essential question is: do these complex motions have functional significance? In particular, how do they affect or relate to chemical reactions within enzymes, and how are chemical and conformational changes coupled together? Biomolecular simulations can analyse enzyme reactions and dynamics in atomic detail, beyond that achievable in experiments: accurate atomistic modelling has an essential part to play in clarifying these issues. This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches.
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Affiliation(s)
- John D McGeagh
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, BS8 1TS, United Kingdom
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30
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Wang Z, Kohen A. Thymidylate synthase catalyzed H-transfers: two chapters in one tale. J Am Chem Soc 2010; 132:9820-5. [PMID: 20575541 DOI: 10.1021/ja103010b] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Examination of the nature of different bond activations along the same catalytic path is of general interest in chemistry and biology. In this report, we compare the physical nature of two sequential H-transfers in the same enzymatic reaction. Thymidylate synthase (TSase) catalyzes a complex reaction that involves many chemical transformations including two different C-H bond cleavages, a rate-limiting C-H-C hydride transfer and a non-rate-limiting C-H-O proton transfer. Although the large kinetic complexity imposes difficulties in studying the proton transfer catalyzed by TSase, we are able to experimentally extract the intrinsic kinetic isotope effects (KIEs) on both steps. In contrast with the hydride transfer, the intrinsic KIEs of the proton transfer are temperature dependent. The results are interpreted within the framework of the Marcus-like model. This interpretation suggests that TSase optimizes the donor-acceptor geometries for the slower and overall rate-limiting hydride transfer but not for the faster proton transfer.
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Affiliation(s)
- Zhen Wang
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, USA
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31
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Characterizing the dynamics of functionally relevant complexes of formate dehydrogenase. Proc Natl Acad Sci U S A 2010; 107:17974-9. [PMID: 20876138 DOI: 10.1073/pnas.0912190107] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The potential for femtosecond to picosecond time-scale motions to influence the rate of the intrinsic chemical step in enzyme-catalyzed reactions is a source of significant controversy. Among the central challenges in resolving this controversy is the difficulty of experimentally characterizing thermally activated motions at this time scale in functionally relevant enzyme complexes. We report a series of measurements to address this problem using two-dimensional infrared spectroscopy to characterize the time scales of active-site motions in complexes of formate dehydrogenase with the transition-state-analog inhibitor azide (N(3)(-)). We observe that the frequency-frequency time correlation functions (FFCF) for the ternary complexes with NAD(+) and NADH decay completely with slow time constants of 3.2 ps and 4.6 ps, respectively. This result suggests that in the vicinity of the transition state, the active-site enzyme structure samples a narrow and relatively rigid conformational distribution indicating that the transition-state structure is well organized for the reaction. In contrast, for the binary complex, we observe a significant static contribution to the FFCF similar to what is seen in other enzymes, indicating the presence of the slow motions that occur on time scales longer than our measurement window.
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32
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Williams IH. Quantum catalysis? A comment on tunnelling contributions for catalysed and uncatalysed reactions. J PHYS ORG CHEM 2010. [DOI: 10.1002/poc.1658] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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33
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Hay S, Johannissen LO, Sutcliffe MJ, Scrutton NS. Barrier compression and its contribution to both classical and quantum mechanical aspects of enzyme catalysis. Biophys J 2010; 98:121-8. [PMID: 20085724 DOI: 10.1016/j.bpj.2009.09.045] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2009] [Revised: 09/23/2009] [Accepted: 09/24/2009] [Indexed: 12/01/2022] Open
Abstract
It is generally accepted that enzymes catalyze reactions by lowering the apparent activation energy by transition state stabilization or through destabilization of ground states. A more controversial proposal is that enzymes can also accelerate reactions through barrier compression-an idea that has emerged from studies of H-tunneling reactions in enzyme systems. The effects of barrier compression on classical (over-the-barrier) reactions, and the partitioning between tunneling and classical reaction paths, have largely been ignored. We performed theoretical and computational studies on the effects of barrier compression on the shape of potential energy surfaces/reaction barriers for model (malonaldehyde and methane/methyl radical anion) and enzymatic (aromatic amine dehydrogenase) proton transfer systems. In all cases, we find that barrier compression is associated with an approximately linear decrease in the activation energy. For partially nonadiabatic proton transfers, we show that barrier compression enhances, to similar extents, the rate of classical and proton tunneling reactions. Our analysis suggests that barrier compression-through fast promoting vibrations, or other means-could be a general mechanism for enhancing the rate of not only tunneling, but also classical, proton transfers in enzyme catalysis.
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Affiliation(s)
- Sam Hay
- Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, United Kingdom
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34
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Computer simulations of quantum tunnelling in enzyme-catalysed hydrogen transfer reactions. Interdiscip Sci 2010; 2:78-97. [DOI: 10.1007/s12539-010-0093-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Revised: 12/04/2009] [Accepted: 12/06/2009] [Indexed: 10/19/2022]
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35
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Murdock D, Burns LA, Vaccaro PH. Vibrational specificity of proton-transfer dynamics in ground-state tropolone. Phys Chem Chem Phys 2010; 12:8285-99. [DOI: 10.1039/c003140b] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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36
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37
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Backstrom N, Burton NA, Watt CIF. Primary kinetic hydrogen isotope effects in deprotonations of a nitroalkane by intramolecular phenolate groups. J PHYS ORG CHEM 2009. [DOI: 10.1002/poc.1631] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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38
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Bandaria JN, Cheatum CM, Kohen A. Examination of enzymatic H-tunneling through kinetics and dynamics. J Am Chem Soc 2009; 131:10151-5. [PMID: 19621965 DOI: 10.1021/ja902120t] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In recent years, kinetic measurements of isotope effects of enzyme-catalyzed reactions and their temperature dependence led to the development of theoretical models that were used to rationalize the findings. These models suggested that motions at the femto- to picosecond (fs to ps) time scale modulate the environment of the catalyzed reaction. Due to the fast nature of motions that directly affect the cleavage of a covalent bond, it is challenging to correlate the enzyme kinetics and dynamics related to that step. We report a study of formate dehydrogenase (FDH) that compares the temperature dependence of intrinsic kinetic isotope effects (KIEs) to measurements of the environmental dynamics at the fs-ps time scale (Bandaria et al. J. Am. Chem. Soc. 2008, 130, 22-23). The findings from this comparison of experimental kinetics and dynamics are consistent with models of environmentally coupled H-tunneling models, also known as Marcus-like models. Apparently, at tunneling ready conformations, the donor-acceptor distance, orientation, and fluctuations seems to be well tuned for H-transfer and are not affected by thermal fluctuations slower than 10 ps. This phenomenon has been suggested in the past to be quite general in enzymatic reactions. Here, the kinetics and the dynamics measurements on a single chemical step and on fs-ps time scale, respectively, provide new insight and support for the relevant theoretical models. Furthermore, this methodology could be applied to other systems and be used to examine mutants for which the organization of the donor and acceptor is not ideal, or enzymes with different rigidity and different temperature optimum.
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Affiliation(s)
- Jigar N Bandaria
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, USA
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39
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Quaye O, Gadda G. Effect of a conservative mutation of an active site residue involved in substrate binding on the hydride tunneling reaction catalyzed by choline oxidase. Arch Biochem Biophys 2009; 489:10-4. [DOI: 10.1016/j.abb.2009.07.021] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2009] [Revised: 07/30/2009] [Accepted: 07/30/2009] [Indexed: 11/29/2022]
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40
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Wu A, Mader EA, Datta A, Hrovat DA, Borden WT, Mayer JM. Nitroxyl radical plus hydroxylamine pseudo self-exchange reactions: tunneling in hydrogen atom transfer. J Am Chem Soc 2009; 131:11985-97. [PMID: 19618933 PMCID: PMC2775461 DOI: 10.1021/ja904400d] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bimolecular rate constants have been measured for reactions that involve hydrogen atom transfer (HAT) from hydroxylamines to nitroxyl radicals, using the stable radicals TEMPO(*) (2,2,6,6-tetramethylpiperidine-1-oxyl radical), 4-oxo-TEMPO(*) (2,2,6,6-tetramethyl-4-oxo-piperidine-1-oxyl radical), di-tert-butylnitroxyl ((t)Bu(2)NO(*)), and the hydroxylamines TEMPO-H, 4-oxo-TEMPO-H, 4-MeO-TEMPO-H (2,2,6,6-tetramethyl-N-hydroxy-4-methoxy-piperidine), and (t)Bu(2)NOH. The reactions have been monitored by UV-vis stopped-flow methods, using the different optical spectra of the nitroxyl radicals. The HAT reactions all have |DeltaG (o)| < or = 1.4 kcal mol(-1) and therefore are close to self-exchange reactions. The reaction of 4-oxo-TEMPO(*) + TEMPO-H --> 4-oxo-TEMPO-H + TEMPO(*) occurs with k(2H,MeCN) = 10 +/- 1 M(-1) s(-1) in MeCN at 298 K (K(2H,MeCN) = 4.5 +/- 1.8). Surprisingly, the rate constant for the analogous deuterium atom transfer reaction is much slower: k(2D,MeCN) = 0.44 +/- 0.05 M(-1) s(-1) with k(2H,MeCN)/k(2D,MeCN) = 23 +/- 3 at 298 K. The same large kinetic isotope effect (KIE) is found in CH(2)Cl(2), 23 +/- 4, suggesting that the large KIE is not caused by solvent dynamics or hydrogen bonding to solvent. The related reaction of 4-oxo-TEMPO(*) with 4-MeO-TEMPO-H(D) also has a large KIE, k(3H)/k(3D) = 21 +/- 3 in MeCN. For these three reactions, the E(aD) - E(aH) values, between 0.3 +/- 0.6 and 1.3 +/- 0.6 kcal mol(-1), and the log(A(H)/A(D)) values, between 0.5 +/- 0.7 and 1.1 +/- 0.6, indicate that hydrogen tunneling plays an important role. The related reaction of (t)Bu(2)NO(*) + TEMPO-H(D) in MeCN has a large KIE, 16 +/- 3 in MeCN, and very unusual isotopic activation parameters, E(aD) - E(aH) = -2.6 +/- 0.4 and log(A(H)/A(D)) = 3.1 +/- 0.6. Computational studies, using POLYRATE, also indicate substantial tunneling in the (CH(3))(2)NO(*) + (CH(3))(2)NOH model reaction for the experimental self-exchange processes. Additional calculations on TEMPO((*)/H), (t)Bu(2)NO((*)/H), and Ph(2)NO((*)/H) self-exchange reactions reveal why the phenyl groups make the last of these reactions several orders of magnitude faster than the first two. By inference, the calculations also suggest why tunneling appears to be more important in the self-exchange reactions of dialkylhydroxylamines than of arylhydroxylamines.
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Affiliation(s)
- Adam Wu
- Department of Chemistry, Campus Box 351700, University of Washington, Seattle, Washington 98195-1700, USA
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41
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Hill SE, Bandaria JN, Fox M, Vanderah E, Kohen A, Cheatum CM. Exploring the molecular origins of protein dynamics in the active site of human carbonic anhydrase II. J Phys Chem B 2009; 113:11505-10. [PMID: 19637848 PMCID: PMC2736349 DOI: 10.1021/jp901321m] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We present three-pulse vibrational echo measurements of azide ion bound to the active site Zn of human carbonic anhydrase II (HCA II) and of two separate active-site mutants Thr199 --> Ala (T199A) and Leu198 --> Phe (L198F). Because structural motions of the protein active site influence the frequency of bound ligands, the differences in the time scales of the frequency-frequency correlation functions (FFCFs) obtained from global fits to each set of data allow us to make inferences about the time scales of the active site dynamics of HCA II. Surprisingly, the deletion of a potential electrostatic interaction in results in very little change in the FFCF, but the insertion of the bulky phenylalanine ring in causes much faster dynamics. We conclude that the fast, sub-picosecond time scale in the correlation function is attributable to hydrogen bond dynamics, and the slow, apparently static contribution is due to the conformational flexibility of Zn-bound azide in the active site.
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Affiliation(s)
- Sarah E Hill
- Department of Chemistry and Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, USA.
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42
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Reece SY, Nocera DG. Proton-coupled electron transfer in biology: results from synergistic studies in natural and model systems. Annu Rev Biochem 2009; 78:673-99. [PMID: 19344235 DOI: 10.1146/annurev.biochem.78.080207.092132] [Citation(s) in RCA: 361] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Proton-coupled electron transfer (PCET) underpins energy conversion in biology. PCET may occur with the unidirectional or bidirectional transfer of a proton and electron and may proceed synchronously or asynchronously. To illustrate the role of PCET in biology, this review presents complementary biological and model systems that explore PCET in electron transfer (ET) through hydrogen bonds [azurin as compared to donor-acceptor (D-A) hydrogen-bonded networks], the activation of C-H bonds [alcohol dehydrogenase and soybean lipoxygenase (SLO) as compared to Fe(III) metal complexes], and the generation and transport of amino acid radicals [photosystem II (PSII) and ribonucleotide reductase (RNR) as compared to tyrosine-modified photoactive Re(I) and Ru(II) complexes]. In providing these comparisons, the fundamental principles of PCET in biology are illustrated in a tangible way.
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Affiliation(s)
- Steven Y Reece
- Department of Chemistry, Massachusetts Institutes of Technology, Cambridge, MA 02139-4307, USA
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Hay S, Sutcliffe MJ, Scrutton NS. Probing Coupled Motions in Enzymatic Hydrogen Tunnelling Reactions: Beyond Temperature-Dependence Studies of Kinetic Isotope Effects. QUANTUM TUNNELLING IN ENZYME-CATALYSED REACTIONS 2009. [DOI: 10.1039/9781847559975-00199] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Sam Hay
- Faculty of Life Sciences, Manchester Interdisciplinary Biocentre, University of Manchester 131 Princess Street Manchester M1 7DN UK
| | - Michael J. Sutcliffe
- School of Chemical Engineering and Analytical Science, Manchester Interdisciplinary Biocentre, University of Manchester 131 Princess Street Manchester M1 7DN UK
| | - Nigel S. Scrutton
- Faculty of Life Sciences, Manchester Interdisciplinary Biocentre, University of Manchester 131 Princess Street Manchester M1 7DN UK
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Abstract
'Everything that living things do can be understood in terms of the jigglings and wigglings of atoms' as Richard Feynman provocatively stated nearly 50 years ago. But how can we 'see' this wiggling and jiggling and understand how it drives biology? Increasingly, computer simulations of biological macromolecules are helping to meet this challenge.
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Affiliation(s)
- Adrian J Mulholland
- School of Chemistry, Centre for Computational Chemistry, University of Bristol, Bristol, UK.
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Hay S, Pang J, Monaghan PJ, Wang X, Evans RM, Sutcliffe MJ, Allemann RK, Scrutton NS. Secondary kinetic isotope effects as probes of environmentally-coupled enzymatic hydrogen tunneling reactions. Chemphyschem 2008; 9:1536-9. [PMID: 18613201 DOI: 10.1002/cphc.200800291] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Sam Hay
- Manchester Interdisciplinary Biocentre, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
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Hay S, Scrutton NS. H-transfers in Photosystem II: what can we learn from recent lessons in the enzyme community? PHOTOSYNTHESIS RESEARCH 2008; 98:169-177. [PMID: 18766465 DOI: 10.1007/s11120-008-9326-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2008] [Accepted: 06/28/2008] [Indexed: 05/26/2023]
Abstract
Over the last 10 years, studies of enzyme systems have demonstrated that, in many cases, H-transfers occur by a quantum mechanical tunneling mechanism analogous to long-range electron transfer. H-transfer reactions can be described by an extension of Marcus theory and, by substituting hydrogen with deuterium (or even tritium), it is possible to explore this theory in new ways by employing kinetic isotope effects. Because hydrogen has a relatively short deBroglie wavelength, H-transfers are controlled by the width of the reaction barrier. By coupling protein dynamics to the reaction coordinate, enzymes have the potential ability to facilitate more efficient H-tunneling by modulating barrier properties. In this review, we describe recent advances in both experimental and theoretical studies of enzymatic H-transfer, in particular the role of protein dynamics or promoting motions. We then discuss possible consequences with regard to tyrosine oxidation/reduction kinetics in Photosystem II.
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Affiliation(s)
- Sam Hay
- Manchester Interdisciplinary Biocentre and Faculty of Life Sciences, University of Manchester, Manchester, UK.
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Malmquist NA, Gujjar R, Rathod PK, Phillips MA. Analysis of flavin oxidation and electron-transfer inhibition in Plasmodium falciparum dihydroorotate dehydrogenase. Biochemistry 2008; 47:2466-75. [PMID: 18225919 DOI: 10.1021/bi702218c] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Plasmodium falciparum dihydroorotate dehydrogenase (pfDHODH) is a flavin-dependent mitochondrial enzyme that provides the only route to pyrimidine biosynthesis in the parasite. Clinically significant inhibitors of human DHODH (e.g., A77 1726) bind to a pocket on the opposite face of the flavin cofactor from dihydroorotate (DHO). This pocket demonstrates considerable sequence variability, which has allowed species-specific inhibitors of the malarial enzyme to be identified. Ubiquinone (CoQ), the physiological oxidant in the reaction, has been postulated to bind this site despite a lack of structural evidence. To more clearly define the residues involved in CoQ binding and catalysis, we undertook site-directed mutagenesis of seven residues in the structurally defined A77 1726 binding site, which we term the species-selective inhibitor site. Mutation of several of these residues (H185, F188, and F227) to Ala substantially decreased the affinity of pfDHODH-specific inhibitors (40-240-fold). In contrast, only a modest increase in the Kmapp for CoQ was observed, although mutation of Y528 in particular caused a substantial reduction in kcat (40-100-fold decrease). Pre-steady-state kinetic analysis by single wavelength stopped-flow spectroscopy showed that the mutations had no effect on the rate of the DHO-dependent reductive half-reaction, but most reduced the rate of the CoQ-dependent flavin oxidation step (3-20-fold decrease), while not significantly altering the Kdox for CoQ. As with the mutants, inhibitors that bind this site block the CoQ-dependent oxidative half-reaction without affecting the DHO-dependent step. These results identify residues involved in inhibitor binding and electron transfer to CoQ. Importantly, the data provide compelling evidence that the binding sites for CoQ and species-selective site inhibitors do not overlap, and they suggest instead that inhibitors act either by blocking the electron path between flavin and CoQ or by stabilizing a conformation that excludes CoQ binding.
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Affiliation(s)
- Nicholas A Malmquist
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park Boulevard, Dallas, Texas 75390-9041, USA
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48
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Atomistic insight into the origin of the temperature-dependence of kinetic isotope effects and H-tunnelling in enzyme systems is revealed through combined experimental studies and biomolecular simulation. Biochem Soc Trans 2008; 36:16-21. [DOI: 10.1042/bst0360016] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The physical basis of the catalytic power of enzymes remains contentious despite sustained and intensive research efforts. Knowledge of enzyme catalysis is predominantly descriptive, gained from traditional protein crystallography and solution studies. Our goal is to understand catalysis by developing a complete and quantitative picture of catalytic processes, incorporating dynamic aspects and the role of quantum tunnelling. Embracing ideas that we have spearheaded from our work on quantum mechanical tunnelling effects linked to protein dynamics for H-transfer reactions, we review our recent progress in mapping macroscopic kinetic descriptors to an atomistic understanding of dynamics linked to biological H-tunnelling reactions.
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van der Kamp MW, Mulholland AJ. Computational enzymology: insight into biological catalysts from modelling. Nat Prod Rep 2008; 25:1001-14. [DOI: 10.1039/b600517a] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Pudney CR, Hay S, Pang J, Costello C, Leys D, Sutcliffe MJ, Scrutton NS. Mutagenesis of morphinone reductase induces multiple reactive configurations and identifies potential ambiguity in kinetic analysis of enzyme tunneling mechanisms. J Am Chem Soc 2007; 129:13949-56. [PMID: 17939663 DOI: 10.1021/ja074463h] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have identified multiple reactive configurations (MRCs) of an enzyme-coenzyme complex that have measurably different kinetic properties. In the complex formed between morphinone reductase (MR) and the NADH analogue 1,4,5,6-tetrahydro-NADH (NADH4) the nicotinamide moiety is restrained close to the FMN isoalloxazine ring by hydrogen bonds from Asn-189 and His-186 as determined from the X-ray crystal structure. Molecular dynamic simulations indicate that removal of one of these hydrogen bonds in the N189A MR mutant allows the nicotinamide moiety to occupy a region of configurational space not accessible in wild-type enzyme. Using stopped-flow spectroscopy, we show that reduction of the FMN cofactor by NADH in N189A MR is multiphasic, identifying at least four different reactive configurations of the MR-NADH complex. This contrasts with wild-type MR in which hydride transfer occurs by environmentally coupled tunneling in a single kinetic phase [Pudney et al. J. Am. Chem. Soc. 2006, 128, 14053-14058]. Values for primary and alpha-secondary kinetic isotope effects, and their temperature dependence, for three of the kinetic phases in the N189A MR are consistent with hydride transfer by tunneling. Our analysis enables derivation of mechanistic information concerning different reactive configurations of the same enzyme-coenzyme complex using ensemble stopped-flow methods. Implications for the interpretation from kinetic data of tunneling mechanisms in enzymes are discussed.
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Affiliation(s)
- Christopher R Pudney
- Manchester Interdisciplinary Biocentre, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester, M1 7DN, U.K
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