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González PJ, Rivas MG, Ferroni FM, Rizzi AC, Brondino CD. Electron transfer pathways and spin–spin interactions in Mo- and Cu-containing oxidoreductases. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.214202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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2
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Sequential and Coupled Proton and Electron Transfer Events in the S2 → S3 Transition of Photosynthetic Water Oxidation Revealed by Time-Resolved X-ray Absorption Spectroscopy. Biochemistry 2016; 55:6996-7004. [DOI: 10.1021/acs.biochem.6b01078] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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3
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Zhu H, Sommerhalter M, Nguy AKL, Klinman JP. Solvent and Temperature Probes of the Long-Range Electron-Transfer Step in Tyramine β-Monooxygenase: Demonstration of a Long-Range Proton-Coupled Electron-Transfer Mechanism. J Am Chem Soc 2015; 137:5720-9. [PMID: 25919134 PMCID: PMC4970857 DOI: 10.1021/ja512388n] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
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Tyramine
β-monooxygenase (TβM) belongs to a family
of physiologically important dinuclear copper monooxygenases that
function with a solvent-exposed active site. To accomplish each enzymatic
turnover, an electron transfer (ET) must occur between two solvent-separated
copper centers. In wild-type TβM, this event is too fast to
be rate limiting. However, we have recently shown [Osborne, R. L.;
et al. Biochemistry2013, 52, 1179] that the Tyr216Ala variant of TβM leads to rate-limiting
ET. In this study, we present a pH–rate profile study of Tyr216Ala,
together with deuterium oxide solvent kinetic isotope effects (KIEs).
A solvent KIE of 2 on kcat is found in
a region where kcat is pH/pD independent.
As a control, the variant Tyr216Trp, for which ET is not rate determining,
displays a solvent KIE of unity. We conclude, therefore, that the
observed solvent KIE arises from the rate-limiting ET step in the
Tyr216Ala variant, and show
how small solvent KIEs (ca. 2) can be fully accommodated from equilibrium effects within the Marcus equation. To gain insight into the role of the enzyme in the long-range
ET step, a temperature dependence study was also pursued. The small
enthalpic barrier of ET (Ea = 3.6 kcal/mol)
implicates a significant entropic barrier, which is attributed to
the requirement for extensive rearrangement of the inter-copper environment
during PCET catalyzed by the Tyr216Ala variant. The data lead to the
proposal of a distinct inter-domain pathway for PCET in the dinuclear
copper monooxygenases.
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Affiliation(s)
| | - Monika Sommerhalter
- #Department of Chemistry and Biochemistry, California State University, East Bay, 25800 Carlos Bee Boulevard, Hayward, California 94542, United States
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4
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Cong Z, Kinemuchi H, Kurahashi T, Fujii H. Factors affecting hydrogen-tunneling contribution in hydroxylation reactions promoted by oxoiron(IV) porphyrin π-cation radical complexes. Inorg Chem 2014; 53:10632-41. [PMID: 25222493 DOI: 10.1021/ic501737j] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Hydrogen atom transfer with a tunneling effect (H-tunneling) has been proposed to be involved in aliphatic hydroxylation reactions catalyzed by cytochrome P450 and synthetic heme complexes as a result of the observation of large hydrogen/deuterium kinetic isotope effects (KIEs). In the present work, we investigate the factors controlling the H-tunneling contribution to the H-transfer process in hydroxylation reaction by examining the kinetics of hydroxylation reactions at the benzylic positions of xanthene and 1,2,3,4-tetrahydronaphthalene by oxoiron(IV) 5,10,15,20-tetramesitylporphyrin π-cation radical complexes ((TMP(+•))Fe(IV)O(L)) under single-turnover conditions. The Arrhenius plots for these hydroxylation reactions of H-isotopomers have upwardly concave profiles. The Arrhenius plots of D-isotopomers, clear isosbestic points, and product analysis rule out the participation of thermally dependent other reaction processes in the concave profiles. These results provide evidence for the involvement of H-tunneling in the rate-limiting H-transfer process. These profiles are simulated using an equation derived from Bell's tunneling model. The temperature dependence of the KIE values (k(H)/k(D)) determined for these reactions indicates that the KIE value increases as the reaction temperature becomes lower, the bond dissociation energy (BDE) of the C-H bond of a substrate becomes higher, and the reactivity of (TMP(+•))Fe(IV)O(L) decreases. In addition, we found correlation of the slope of the ln(k(H)/k(D)) - 1/T plot and the bond strengths of the Fe═O bond of (TMP(+•))Fe(IV)O(L) estimated from resonance Raman spectroscopy. These observations indicate that these factors modulate the extent of the H-tunneling contribution by modulating the ratio of the height and thickness of the reaction barrier.
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Affiliation(s)
- Zhiqi Cong
- Department of Chemistry, Biology and Environmental Science, Faculty of Science, Nara Women's University , Kitauoyanishi, Nara 830-8506, Japan
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5
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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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6
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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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7
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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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8
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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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9
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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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10
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Dynamics and mechanism of repair of ultraviolet-induced (6-4) photoproduct by photolyase. Nature 2010; 466:887-890. [PMID: 20657578 PMCID: PMC3018752 DOI: 10.1038/nature09192] [Citation(s) in RCA: 165] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2010] [Revised: 08/12/2010] [Accepted: 05/20/2010] [Indexed: 01/02/2023]
Abstract
One of the detrimental effects of UV radiation on DNA is the formation of the (6-4) photoproduct (6-4PP) between two adjacent pyrimidines1. This lesion interferes with replication and transcription and may result in mutation and cell death2. In many organisms a flavoenzyme called photolyase uses blue light energy to repair the 6-4PP3. The molecular mechanism of the repair reaction is poorly understood. Here, we use ultrafast spectroscopy to show that the key step in the repair photocycle is a cyclic proton transfer between the enzyme and the substrate. By femtosecond synchronization of the enzymatic dynamics with the repair function, we followed the function evolution and observed direct electron transfer from the excited flavin cofactor to the 6-4PP in 225 ps but surprisingly fast back electron transfer in 50 ps without repair. Strikingly, we found that the catalytic proton transfer between a histidine residue in the active site and the 6-4PP, induced by the initial photoinduced electron transfer from the excited flavin cofactor to 6-4PP, occurs in 425 ps and leads to 6-4PP repair in tens of nanoseconds. These key dynamics define the repair photocycle and explain the underlying molecular mechanism of the enzyme’s modest efficiency.
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11
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Sen A, Kohen A. Enzymatic tunneling and kinetic isotope effects: chemistry at the crossroads. J PHYS ORG CHEM 2009. [DOI: 10.1002/poc.1633] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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12
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Quaye O, Cowins S, Gadda G. Contribution of flavin covalent linkage with histidine 99 to the reaction catalyzed by choline oxidase. J Biol Chem 2009; 284:16990-16997. [PMID: 19398559 DOI: 10.1074/jbc.m109.003715] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The FAD-dependent choline oxidase has a flavin cofactor covalently attached to the protein via histidine 99 through an 8alpha-N(3)-histidyl linkage. The enzyme catalyzes the four-electron oxidation of choline to glycine betaine, forming betaine aldehyde as an enzyme-bound intermediate. The variant form of choline oxidase in which the histidine residue has been replaced with asparagine was used to investigate the contribution of the 8alpha-N(3)-histidyl linkage of FAD to the protein toward the reaction catalyzed by the enzyme. Decreases of 10-fold and 30-fold in the k(cat)/K(m) and k(cat) values were observed as compared with wild-type choline oxidase at pH 10 and 25 degrees C, with no significant effect on k(cat)/K(O) using choline as substrate. Both the k(cat)/K(m) and k(cat) values increased with increasing pH to limiting values at high pH consistent with the participation of an unprotonated group in the reductive half-reaction and the overall turnover of the enzyme. The pH independence of both (D)(k(cat)/K(m)) and (D)k(cat), with average values of 9.2 +/- 3.3 and 7.4 +/- 0.5, respectively, is consistent with absence of external forward and reverse commitments to catalysis, and the chemical step of CH bond cleavage being rate-limiting for both the reductive half-reaction and the overall enzyme turnover. The temperature dependence of the (D)k(red) values suggests disruption of the preorganization in the asparagine variant enzyme. Altogether, the data presented in this study are consistent with the FAD-histidyl covalent linkage being important for the optimal positioning of the hydride ion donor and acceptor in the tunneling reaction catalyzed by choline oxidase.
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Affiliation(s)
- Osbourne Quaye
- From the Departments of Chemistry, Atlanta, Georgia 30302-4098
| | - Sharonda Cowins
- From the Departments of Chemistry, Atlanta, Georgia 30302-4098; Department of Chemistry, Albany State University, Albany, Georgia 31705
| | - Giovanni Gadda
- From the Departments of Chemistry, Atlanta, Georgia 30302-4098; Biology, Atlanta, Georgia 30302-4098; The Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302-4098.
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Wu A, Mayer JM. Hydrogen atom transfer reactions of a ruthenium imidazole complex: hydrogen tunneling and the applicability of the Marcus cross relation. J Am Chem Soc 2008; 130:14745-54. [PMID: 18841973 PMCID: PMC2633126 DOI: 10.1021/ja805067h] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The reaction of Ru(II)(acac)2(py-imH) (Ru(II)imH) with TEMPO(*) (2,2,6,6-tetramethylpiperidine-1-oxyl radical) in MeCN quantitatively gives Ru(III)(acac)2(py-im) (Ru(III)im) and the hydroxylamine TEMPO-H by transfer of H(*) (H(+) + e(-)) (acac = 2,4-pentanedionato, py-imH = 2-(2'-pyridyl)imidazole). Kinetic measurements of this reaction by UV-vis stopped-flow techniques indicate a bimolecular rate constant k(3H) = 1400 +/- 100 M(-1) s(-1) at 298 K. The reaction proceeds via a concerted hydrogen atom transfer (HAT) mechanism, as shown by ruling out the stepwise pathways of initial proton or electron transfer due to their very unfavorable thermochemistry (Delta G(o)). Deuterium transfer from Ru(II)(acac)2(py-imD) (Ru(II)imD) to TEMPO(*) is surprisingly much slower at k(3D) = 60 +/- 7 M(-1) s(-1), with k(3H)/k(3D) = 23 +/- 3 at 298 K. Temperature-dependent measurements of this deuterium kinetic isotope effect (KIE) show a large difference between the apparent activation energies, E(a3D) - E(a3H) = 1.9 +/- 0.8 kcal mol(-1). The large k(3H)/k(3D) and DeltaE(a) values appear to be greater than the semiclassical limits and thus suggest a tunneling mechanism. The self-exchange HAT reaction between Ru(II)imH and Ru(III)im, measured by (1)H NMR line broadening, occurs with k(4H) = (3.2 +/- 0.3) x 10(5) M(-1) s(-1) at 298 K and k(4H)/k(4D) = 1.5 +/- 0.2. Despite the small KIE, tunneling is suggested by the ratio of Arrhenius pre-exponential factors, log(A(4H)/A(4D)) = -0.5 +/- 0.3. These data provide a test of the applicability of the Marcus cross relation for H and D transfers, over a range of temperatures, for a reaction that involves substantial tunneling. The cross relation calculates rate constants for Ru(II)imH(D) + TEMPO(*) that are greater than those observed: k(3H,calc)/k(3H) = 31 +/- 4 and k(3D,calc)/k(3D) = 140 +/- 20 at 298 K. In these rate constants and in the activation parameters, there is a better agreement with the Marcus cross relation for H than for D transfer, despite the greater prevalence of tunneling for H. The cross relation does not explicitly include tunneling, so close agreement should not be expected. In light of these results, the strengths and weaknesses of applying the cross relation to HAT reactions are discussed.
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Affiliation(s)
- Adam Wu
- Department of Chemistry, University of Washington, Campus Box 351700, Seattle, WA, 98195-1700, USA
| | - James M. Mayer
- Department of Chemistry, University of Washington, Campus Box 351700, Seattle, WA, 98195-1700, USA
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Hay S, Scrutton NS. Incorporation of hydrostatic pressure into models of hydrogen tunneling highlights a role for pressure-modulated promoting vibrations. Biochemistry 2008; 47:9880-7. [PMID: 18717597 DOI: 10.1021/bi8005972] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Hydrostatic pressure offers an alternative to temperature as an experimental probe of hydrogen-transfer reactions. H tunneling reactions have been shown to exhibit kinetic isotope effects (KIEs) that are sensitive to pressure, and environmentally coupled H tunneling reactions, those reactions in which H transfer is coupled to atomic fluctuations (a promoting vibration) along the reaction coordinate, often have quite temperature-dependent KIEs. We present here a theoretical treatment of the combined effect of temperature and pressure on environmentally coupled H tunneling reactions. We develop a generalized expression for the KIE, which can be used as a simple fitting function for combined experimental temperature- and pressure-dependent KIE data sets. With this expression, we are able to extract information about the pressure dependence of both the apparent tunneling distance and the frequency of the promoting vibration. The KIE expression is tested on two data sets {the reduction of chloranil by leuco crystal violet [Isaacs, N. S., Javaid, K., and Rannala, E. (1998) J. Chem. Soc., Perkin Trans. 2, 709-711] and the reduction of morphinone reductase by NADH [Hay, S., Sutcliffe, M. J., and Scrutton, N. S. (2007) Proc. Natl. Acad. Sci. U.S.A. 104, 507-512]} and suggests that hydrostatic pressure is a sensitive probe of nuclear quantum mechanical effects in H-transfer reactions.
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Affiliation(s)
- Sam Hay
- Manchester Interdisciplinary Biocentre and Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
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15
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Markle T, Mayer J. Concerted Proton–Electron Transfer in Pyridylphenols: The Importance of the Hydrogen Bond. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200702486] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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16
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Markle T, Mayer J. Concerted Proton–Electron Transfer in Pyridylphenols: The Importance of the Hydrogen Bond. Angew Chem Int Ed Engl 2008; 47:738-40. [DOI: 10.1002/anie.200702486] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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17
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Karyagina I, Pushkar Y, Stehlik D, van der Est A, Ishikita H, Knapp EW, Jagannathan B, Agalarov R, Golbeck JH. Contributions of the Protein Environment to the Midpoint Potentials of the A1 Phylloquinones and the FX Iron−Sulfur Cluster in Photosystem I. Biochemistry 2007; 46:10804-16. [PMID: 17725326 DOI: 10.1021/bi700846z] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Electrostatic calculations have predicted that the partial negative charge associated with D575PsaB plays a significant role in modulating the midpoint potentials of the A1A and A1B phylloquinones in photosystem I. To test this prediction, the side chain of residue 575PsaB was changed from negatively charged (D) to neutral (A) and to positively charged (K). D566PsaB, which is located at a considerable distance from either A1A or A1B, and should affect primarily the midpoint potential of FX, was similarly changed. In the 575PsaB variants, the rate of electron transfer from A1A to FX is observed to decrease slightly according to the sequence D/A/K. In the 566PsaB variants, the opposite effect of a slight increase in the rate is observed according to the same sequence D/A/K. These results are consistent with the expectation that changing these residues will shift the midpoint potentials of nearby cofactors to more positive values and that the magnitude of this shift will depend on the distance between the cofactors and the residues being changed. Thus, the midpoint potentials of A1A and A1B should experience a larger shift than will FX in the 575PsaB variants, while FX should experience a larger shift than will either A1A or A1B in the 566PsaB variants. As a result, the driving energy for electron transfer from A1A and A1B to FX will be decreased in the former and increased in the latter. This rationalization of the changes in kinetics is compared with the results of electrostatic calculations. While the altered amino acids shift the midpoint potentials of A1A, A1B, and FX by different amounts, the difference in the shifts between A1A and FX or between A1B and FX is small so that the overall effect on the electron transfer rate between A1A and FX or between A1B and FX is predicted to be small. These conclusions are borne out by experiment.
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Affiliation(s)
- Irina Karyagina
- Institut für Experimentalphysik, Freie Universität Berlin, Arnimallee 14, D-14195, Berlin, Germany
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18
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Marcus RA. H and other transfers in enzymes and in solution: theory and computations, a unified view. 2. Applications to experiment and computations. J Phys Chem B 2007; 111:6643-54. [PMID: 17497918 DOI: 10.1021/jp071589s] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Equations obtained in part I for the free-energy barrier to one-step enzymatic reactions between bound reactants are discussed. The rate is expressed in terms of lambdao (protein reorganization energy), DeltaG(o) (standard free energy of reaction of the H-transfer step), bond breaking/bond forming term, w (work terms), and H-transmission property. Two alternative approximations for the coupling of the bond breaking/bond forming and protein are distinguished experimentally in favorable cases by the DeltaG(o) where the maximum deuterium kinetic isotope effect occurs. Plots of log rate versus DeltaG(o) and properties such as DeltaS* and DeltaS(o) are discussed. The weak or zero T-dependence of the kinetic isotope effect for wild-type enzymes operating under physiological conditions is interpreted in terms of vanishing (or isotopically insensitive) w plus transfer from the lowest H-state. Static and dynamic protein flexibility is discussed. While the many correlations accessible for electron transfers are not available for H-transfers in enzymes, a combination of experiment, computation, and analytical approaches can assist in evaluating the utility of the present equations and in suggesting further experiments and computations. A protein reorganization energy lambdao is obtained in the literature from the extended valence bond formalism where diabatic electronic states are used. A method is suggested for extracting it when instead a bond distance difference coordinate is used. The results may provide a bridge between the two approaches.
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Affiliation(s)
- R A Marcus
- Noyes Laboratory of Chemical Physics, MC 127-72, California Institute of Technology, Pasadena, California 91125-0072, USA.
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19
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Marcus RA. Enzymatic catalysis and transfers in solution. I. Theory and computations, a unified view. J Chem Phys 2006; 125:194504. [PMID: 17129120 DOI: 10.1063/1.2372496] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The transfer of hydride, proton, or H atom between substrate and cofactor in enzymes has been extensively studied for many systems, both experimentally and computationally. A simple equation for the reaction rate, an analog of an equation obtained earlier for electron transfer rates, is obtained, but now containing an approximate analytic expression for the bond rupture-bond forming feature of these H transfers. A "symmetrization," of the potential energy surfaces is again introduced [R. A. Marcus, J. Chem. Phys. 43, 679 (1965); J. Phys. Chem. 72, 891 (1968)], together with Gaussian fluctuations of the remaining coordinates of the enzyme and solution needed for reaching the transition state. Combining the two expressions for the changes in the difference of the two bond lengths of the substrate-cofactor subsystem and in the fluctuation coordinates of the protein leading to the transition state, an expression is obtained for the free energy barrier. To this end a two-dimensional reaction space (m,n) is used that contains the relative coordinates of the H in the reactants, the heavy atoms to which it is bonded, and the protein/solution reorganization coordinate, all leading to the transition state. The resulting expression may serve to characterize in terms of specific parameters (two "reorganization" terms, thermodynamics, and work terms), experimental and computational data for different enzymes, and different cofactor-substrate systems. A related characterization was used for electron transfers. To isolate these factors from nuclear tunneling, when the H-tunneling effect is large, use of deuterium and tritium transfers is of course helpful, although tunneling has frequently and understandably dominated the discussions. A functional form is suggested for the dependence of the deuterium kinetic isotope effect (KIE) on DeltaG degrees and a different form for the 13C KIE. Pressure effects on deuterium and 13C KIEs are also discussed. Although formulated for a one-step transfer of a light particle in an enzyme, the results would also apply to single-step transfers of other atoms and groups in enzymes and in solution.
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Affiliation(s)
- R A Marcus
- Noyes Laboratory of Chemical Physics, MC 127-72, California Institute of Technology, Pasadena, California 91125-0072, USA.
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20
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Dutton PL, Munro AW, Scrutton NS, Sutcliffe MJ. Introduction. Quantum catalysis in enzymes: beyond the transition state theory paradigm. Philos Trans R Soc Lond B Biol Sci 2006. [DOI: 10.1098/rstb.2006.1879] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- P. Leslie Dutton
- Department of Biochemistry and Biophysics, University of PennsylvaniaPhiladelphia, PA 19104-6059, USA
| | - Andrew W Munro
- Manchester Interdisciplinary Biocentre, University of Manchester131 Princess Street, Manchester M1 7ND, UK
- School of Chemical Engineering and Analytical Science, University of Manchester131 Princess Street, Manchester M1 7ND, UK
| | - Nigel S Scrutton
- Faculty of Life Sciences, University of Manchester131 Princess Street, Manchester M1 7ND, UK
| | - Michael J Sutcliffe
- Manchester Interdisciplinary Biocentre, University of Manchester131 Princess Street, Manchester M1 7ND, UK
- School of Chemical Engineering and Analytical Science, University of Manchester131 Princess Street, Manchester M1 7ND, UK
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