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Beach A, Adhikari P, Singh G, Song M, DeGroot N, Lu Y. Structural Effects on the Temperature Dependence of Hydride Kinetic Isotope Effects of the NADH/NAD + Model Reactions in Acetonitrile: Charge-Transfer Complex Tightness Is a Key. J Org Chem 2024; 89:3184-3193. [PMID: 38364859 PMCID: PMC10913049 DOI: 10.1021/acs.joc.3c02562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 01/12/2024] [Accepted: 01/18/2024] [Indexed: 02/18/2024]
Abstract
It has recently frequently been found that the kinetic isotope effect (KIE) is independent of temperature (T) in H-tunneling reactions in enzymes but becomes dependent on T in their mutants. Many enzymologists found that the trend is related to different donor-acceptor distances (DADs) at tunneling-ready states (TRSs), which could be sampled by protein dynamics. That is, a more rigid system of densely populated short DADs gives rise to a weaker T dependence of KIEs. Theoreticians have attempted to develop H-tunneling theories to explain the observations, but none have been universally accepted. It is reasonable to assume that the DAD sampling concept, if it exists, applies to the H-transfer reactions in solution, as well. In this work, we designed NADH/NAD+ model reactions to investigate their structural effects on the T dependence of hydride KIEs in acetonitrile. Hammett correlations together with N-CH3/CD3 secondary KIEs were used to provide the electronic structure of the TRSs and thus the rigidity of their charge-transfer complexation vibrations. In all three pairs of reactions, a weaker T dependence of KIEs always corresponds to a steeper Hammett slope on the substituted hydride acceptors. It was found that a tighter/rigid charge-transfer complexation system corresponds with a weaker T dependence of KIEs, consistent with the observations in enzymes.
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Affiliation(s)
- Amanda Beach
- Department of Chemistry, Southern
Illinois University Edwardsville, Edwardsville, Illinois 62026, United States
| | - Pratichhya Adhikari
- Department of Chemistry, Southern
Illinois University Edwardsville, Edwardsville, Illinois 62026, United States
| | - Grishma Singh
- Department of Chemistry, Southern
Illinois University Edwardsville, Edwardsville, Illinois 62026, United States
| | - Meimei Song
- Department of Chemistry, Southern
Illinois University Edwardsville, Edwardsville, Illinois 62026, United States
| | - Nicholas DeGroot
- Department of Chemistry, Southern
Illinois University Edwardsville, Edwardsville, Illinois 62026, United States
| | - Yun Lu
- Department of Chemistry, Southern
Illinois University Edwardsville, Edwardsville, Illinois 62026, United States
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2
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Johannissen LO, Iorgu AI, Scrutton NS, Hay S. What are the signatures of tunnelling in enzyme-catalysed reactions? Faraday Discuss 2020; 221:367-378. [DOI: 10.1039/c9fd00044e] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Computed tunnelling contributions and correlations between apparent activation enthalpy and entropy are explored for the interpretation of enzyme-catalysed H-transfer reactions.
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Affiliation(s)
- Linus O. Johannissen
- Manchester Institute of Biotechnology (MIB)
- School of Chemistry
- University of Manchester
- Manchester
- UK
| | - Andreea I. Iorgu
- Manchester Institute of Biotechnology (MIB)
- School of Chemistry
- University of Manchester
- Manchester
- UK
| | - Nigel S. Scrutton
- Manchester Institute of Biotechnology (MIB)
- School of Chemistry
- University of Manchester
- Manchester
- UK
| | - Sam Hay
- Manchester Institute of Biotechnology (MIB)
- School of Chemistry
- University of Manchester
- Manchester
- UK
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3
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Eriksson A, Kürten C, Syrén P. Protonation-Initiated Cyclization by a Class II Terpene Cyclase Assisted by Tunneling. Chembiochem 2017; 18:2301-2305. [PMID: 28980755 PMCID: PMC5725671 DOI: 10.1002/cbic.201700443] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Indexed: 02/03/2023]
Abstract
Terpenes represent one of the most diversified classes of natural products with potent biological activities. The key to the myriad of polycyclic terpene skeletons with crucial functions in organisms from all kingdoms of life are terpene cyclase enzymes. These biocatalysts enable stereospecific cyclization of relatively simple, linear, prefolded polyisoprenes by highly complex, partially concerted, electrophilic cyclization cascades that remain incompletely understood. Herein, additional mechanistic light is shed on terpene biosynthesis by kinetic studies in mixed H2 O/D2 O buffers of a class II bacterial ent-copalyl diphosphate synthase. Mass spectrometry determination of the extent of deuterium incorporation in the bicyclic product, reminiscent of initial carbocation formation by protonation, resulted in a large kinetic isotope effect of up to seven. Kinetic analysis at different temperatures confirmed that the isotope effect was independent of temperature, which is consistent with hydrogen tunneling.
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Affiliation(s)
- Adam Eriksson
- School of Chemical Science and EngineeringKTH Royal Institute of Technology100 44StockholmSweden
| | - Charlotte Kürten
- Science for Life LaboratoryKTH Royal Institute of TechnologySchool of BiotechnologyDivision of Proteomics171 21StockholmSweden
| | - Per‐Olof Syrén
- School of Chemical Science and EngineeringKTH Royal Institute of Technology100 44StockholmSweden
- Science for Life LaboratoryKTH Royal Institute of TechnologySchool of BiotechnologyDivision of Proteomics171 21StockholmSweden
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4
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Geddes A, Paul CE, Hay S, Hollmann F, Scrutton NS. Donor–Acceptor Distance Sampling Enhances the Performance of “Better than Nature” Nicotinamide Coenzyme Biomimetics. J Am Chem Soc 2016; 138:11089-92. [DOI: 10.1021/jacs.6b05625] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Alexander Geddes
- BBSRC/EPSRC
Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM),
Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Caroline E. Paul
- Department
of Biotechnology, Delft University of Technology, Julianalaan 136, 2628BL Delft, The Netherlands
| | - Sam Hay
- BBSRC/EPSRC
Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM),
Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Frank Hollmann
- Department
of Biotechnology, Delft University of Technology, Julianalaan 136, 2628BL Delft, The Netherlands
| | - Nigel S. Scrutton
- BBSRC/EPSRC
Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM),
Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
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5
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Wu W, Zhang J, Fan W, Li Z, Wang L, Li X, Wang Y, Wang R, Zheng J, Wu M, Zeng H. Remedying Defects in Carbon Nitride To Improve both Photooxidation and H2 Generation Efficiencies. ACS Catal 2016. [DOI: 10.1021/acscatal.6b00879] [Citation(s) in RCA: 127] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Wenting Wu
- State
Key Laboratory of Heavy Oil Processing, School of Chemical Engineering, China University of Petroleum, Qingdao 266580, People’s Republic of China
- Institute of Optoelectronics & Nanomaterials, Herbert Gleiter Institute of Nanoscience, School of Materials Science and Engineering, Nanjing University of Science and Technology, Nanjing 210094, People’s Republic of China
| | - Jinqiang Zhang
- State
Key Laboratory of Heavy Oil Processing, School of Chemical Engineering, China University of Petroleum, Qingdao 266580, People’s Republic of China
| | - Weiyu Fan
- State
Key Laboratory of Heavy Oil Processing, School of Chemical Engineering, China University of Petroleum, Qingdao 266580, People’s Republic of China
| | - Zhongtao Li
- State
Key Laboratory of Heavy Oil Processing, School of Chemical Engineering, China University of Petroleum, Qingdao 266580, People’s Republic of China
| | - Lizhuo Wang
- State
Key Laboratory of Heavy Oil Processing, School of Chemical Engineering, China University of Petroleum, Qingdao 266580, People’s Republic of China
| | - Xiaoming Li
- Institute of Optoelectronics & Nanomaterials, Herbert Gleiter Institute of Nanoscience, School of Materials Science and Engineering, Nanjing University of Science and Technology, Nanjing 210094, People’s Republic of China
| | - Yang Wang
- State
Key Laboratory of Heavy Oil Processing, School of Chemical Engineering, China University of Petroleum, Qingdao 266580, People’s Republic of China
| | - Ruiqin Wang
- State
Key Laboratory of Heavy Oil Processing, School of Chemical Engineering, China University of Petroleum, Qingdao 266580, People’s Republic of China
| | - Jingtang Zheng
- State
Key Laboratory of Heavy Oil Processing, School of Chemical Engineering, China University of Petroleum, Qingdao 266580, People’s Republic of China
| | - Mingbo Wu
- State
Key Laboratory of Heavy Oil Processing, School of Chemical Engineering, China University of Petroleum, Qingdao 266580, People’s Republic of China
| | - Haibo Zeng
- Institute of Optoelectronics & Nanomaterials, Herbert Gleiter Institute of Nanoscience, School of Materials Science and Engineering, Nanjing University of Science and Technology, Nanjing 210094, People’s Republic of China
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6
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Hoeven R, Heyes DJ, Hay S, Scrutton NS. Does the pressure dependence of kinetic isotope effects report usefully on dynamics in enzyme H-transfer reactions? FEBS J 2015; 282:3243-55. [PMID: 25581554 PMCID: PMC4949571 DOI: 10.1111/febs.13193] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 12/15/2014] [Accepted: 01/08/2015] [Indexed: 11/30/2022]
Abstract
The temperature dependence of kinetic isotope effects (KIEs) has emerged as the main experimental probe of enzymatic H-transfer by quantum tunnelling. Implicit in the interpretation is a presumed role for dynamic coupling of H-transfer chemistry to the protein environment, the so-called 'promoting motions/vibrations hypothesis'. This idea remains contentious, and others have questioned the importance and/or existence of promoting motions/vibrations. New experimental methods of addressing this problem are emerging, including use of mass-modulated enzymes and time-resolved spectroscopy. The pressure dependence of KIEs has been considered as a potential probe of quantum tunnelling reactions, because semi-classical KIEs, which are defined by differences in zero-point vibrational energy, are relatively insensitive to kbar changes in pressure. Reported combined pressure and temperature (p-T) dependence studies of H-transfer reactions are, however, limited. Here, we extend and review the available p-T studies that have utilized well-defined experimental systems in which quantum mechanical tunnelling is established. These include flavoproteins, quinoproteins, light-activated enzymes and chemical model systems. We show that there is no clear general trend between the p-T dependencies of the KIEs in these systems. Given the complex nature of p-T studies, we conclude that computational simulations using determined (e.g. X-ray) structures are also needed alongside experimental measurements of reaction rates/KIEs to guide the interpretation of p-T effects. In providing new insight into H-transfer/environmental coupling, combined approaches that unite both atomistic understanding with experimental rate measurements will require careful evaluation on a case-by-case basis. Although individually informative, we conclude that p-T studies do not provide the more generalized insight that has come from studies of the temperature dependence of KIEs.
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Affiliation(s)
- Robin Hoeven
- Manchester Institute of Biotechnology and Faculty of Life Sciences, The University of Manchester, UK
| | - Derren J Heyes
- Manchester Institute of Biotechnology and Faculty of Life Sciences, The University of Manchester, UK
| | - Sam Hay
- Manchester Institute of Biotechnology and Faculty of Life Sciences, The University of Manchester, UK
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology and Faculty of Life Sciences, The University of Manchester, UK
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7
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Frank O, Kreissl JK, Daschner A, Hofmann T. Accurate determination of reference materials and natural isolates by means of quantitative (1)h NMR spectroscopy. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:2506-2515. [PMID: 24559241 DOI: 10.1021/jf405529b] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
A fast and precise proton nuclear magnetic resonance (qHNMR) method for the quantitative determination of low molecular weight target molecules in reference materials and natural isolates has been validated using ERETIC 2 (Electronic REference To access In vivo Concentrations) based on the PULCON (PULse length based CONcentration determination) methodology and compared to the gravimetric results. Using an Avance III NMR spectrometer (400 MHz) equipped with a broad band observe (BBO) probe, the qHNMR method was validated by determining its linearity, range, precision, and accuracy as well as robustness and limit of quantitation. The linearity of the method was assessed by measuring samples of l-tyrosine, caffeine, or benzoic acid in a concentration range between 0.3 and 16.5 mmol/L (r(2) ≥ 0.99), whereas the interday and intraday precisions were found to be ≤2%. The recovery of a range of reference compounds was ≥98.5%, thus demonstrating the qHNMR method as a precise tool for the rapid quantitation (~15 min) of food-related target compounds in reference materials and natural isolates such as nucleotides, polyphenols, or cyclic peptides.
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Affiliation(s)
- Oliver Frank
- Chair of Food Chemistry and Molecular Sensory Science, Technische Universität München , Lise-Meitner-Strasse 34, D-85354 Freising-Weihenstephan, Germany
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8
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Pudney CR, Lane RSK, Fielding AJ, Magennis SW, Hay S, Scrutton NS. Enzymatic single-molecule kinetic isotope effects. J Am Chem Soc 2013; 135:3855-64. [PMID: 23402437 DOI: 10.1021/ja309286r] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Ensemble-based measurements of kinetic isotope effects (KIEs) have advanced physical understanding of enzyme-catalyzed reactions, but controversies remain. KIEs are used as reporters of rate-limiting H-transfer steps, quantum mechanical tunnelling, dynamics and multiple reactive states. Single molecule (SM) enzymatic KIEs could provide new information on the physical basis of enzyme catalysis. Here, single pair fluorescence energy transfer (spFRET) was used to measure SM enzymatic KIEs on the H-transfer catalyzed by the enzyme pentaerythritol tetranitrate reductase. We evaluated a range of methods for extracting the SM KIE from single molecule spFRET time traces. The SM KIE enabled separation of contributions from nonenzymatic protein and fluorophore processes and H-transfer reactions. Our work demonstrates SM KIE analysis as a new method for deconvolving reaction chemistry from intrinsic dynamics.
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Affiliation(s)
- Christopher R Pudney
- Manchester Institute of Biotechnology and Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
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9
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Lobo IA, Wilson DJD, Bieske E, Robertson EG. A sting in the tail of flexible molecules: spectroscopic and energetic challenges in the case of p-aminophenethylamine. Phys Chem Chem Phys 2012; 14:9219-29. [PMID: 22644595 DOI: 10.1039/c2cp40828g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The neurotransmitter analogue p-aminophenethylamine (APEA) illustrates many of the pitfalls and challenges associated with spectroscopic and conformational analysis of flexible molecules. The combined experimental-theoretical study presented here resolves a long-standing controversy over its conformational energetic preferences. Jet-cooled resonance enhanced two-photon ionisation (R2PI) and IR-UV ion depletion techniques enabled conformer-specific IR spectra in the NH-CH stretch region to be measured for four distinct conformers of APEA. Comparison of spectra with theoretical calculations (including MP2, M06-2X and B3LYP with aug-cc-pVTZ basis sets) allows the two most populated conformers to be unambiguously identified as those having a gauche arrangement of the side chain, which facilitates an NH···π type hydrogen bond. The other two observed conformers are assigned to structures with an anti-side chain. A fifth gauche conformer, predicted to be least stable, is not observed. Comparison with published conformer specific IR spectra of tyramine (Makara et al., J. Phys. Chem. A, 2008, 112, 13463-13469) and Raman spectra of phenylethylamine (Golan et al., J. Chem. Phys., 2009, 131, 024305) reveals an entirely consistent pattern of spectral signatures associated with the four specific conformations of the ethylamine side chain evident in APEA, and aids assignment of the associated CH and NH stretch fundamentals, some of which have very weak IR intensities. Extensive calculations of the relative energetic trends of the five conformers have been carried out. In comparison to the highest level of theory considered, CCSD(T)-F12b/cc-pVDZ-F12, MP2 overestimate the energy difference, whereas DFT significantly underestimates the energetic preference for NH···π stabilised gauche conformers, although inclusion of dispersion (M06-2X, B3LYP-D3) improves the DFT results.
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Affiliation(s)
- Isabella A Lobo
- Department of Chemistry and La Trobe Institute for Molecular Sciences (LIMS), La Trobe University, Bundoora, Victoria, 3086, Australia
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10
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Hay S, Johannissen LO, Hothi P, Sutcliffe MJ, Scrutton NS. Pressure Effects on Enzyme-Catalyzed Quantum Tunneling Events Arise from Protein-Specific Structural and Dynamic Changes. J Am Chem Soc 2012; 134:9749-54. [DOI: 10.1021/ja3024115] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sam Hay
- Manchester
Interdisciplinary Biocentre, ‡Faculty of Life Sciences, and §School of Chemical Engineering and
Analytical Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Linus O. Johannissen
- Manchester
Interdisciplinary Biocentre, ‡Faculty of Life Sciences, and §School of Chemical Engineering and
Analytical Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Parvinder Hothi
- Manchester
Interdisciplinary Biocentre, ‡Faculty of Life Sciences, and §School of Chemical Engineering and
Analytical Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Michael J. Sutcliffe
- Manchester
Interdisciplinary Biocentre, ‡Faculty of Life Sciences, and §School of Chemical Engineering and
Analytical Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Nigel S. Scrutton
- Manchester
Interdisciplinary Biocentre, ‡Faculty of Life Sciences, and §School of Chemical Engineering and
Analytical Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
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11
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Heuts DPHM, Gummadova JO, Pang J, Rigby SEJ, Scrutton NS. Reaction of vascular adhesion protein-1 (VAP-1) with primary amines: mechanistic insights from isotope effects and quantitative structure-activity relationships. J Biol Chem 2011; 286:29584-93. [PMID: 21737458 DOI: 10.1074/jbc.m111.232850] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Human vascular adhesion protein-1 (VAP-1) is an endothelial copper-dependent amine oxidase involved in the recruitment and extravasation of leukocytes at sites of inflammation. VAP-1 is an important therapeutic target for several pathological conditions. We expressed soluble VAP-1 in HEK293 EBNA1 cells at levels suitable for detailed mechanistic studies with model substrates. Using the model substrate benzylamine, we analyzed the steady-state kinetic parameters of VAP-1 as a function of solution pH. We found two macroscopic pK(a) values that defined a bell-shaped plot of turnover number k(cat,app) as a function of pH, representing ionizable groups in the enzyme-substrate complex. The dependence of (k(cat)/K(m))(app) on pH revealed a single pK(a) value (∼9) that we assigned to ionization of the amine group in free benzylamine substrate. A kinetic isotope effect (KIE) of 6 to 7.6 on (k(cat)/K(m))(app) over the pH range of 6 to 10 was observed with d(2)-benzylamine. Over the same pH range, the KIE on k(cat) was found to be close to unity. The unusual KIE values on (k(cat)/K(m))(app) were rationalized using a mechanistic scheme that includes the possibility of multiple isotopically sensitive steps. We also report the analysis of quantitative structure-activity relationships (QSAR) using para-substituted protiated and deuterated phenylethylamines. With phenylethylamines we observed a large KIE on k(cat,app) (8.01 ± 0.28 with phenylethylamine), indicating that C-H bond breakage is limiting for 2,4,5-trihydroxyphenylalanine quinone reduction. Poor correlations were observed between steady-state rate constants and QSAR parameters. We show the importance of combining KIE, QSAR, and structural studies to gain insight into the complexity of the VAP-1 steady-state mechanism.
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Affiliation(s)
- Dominic P H M Heuts
- Manchester Interdisciplinary Biocentre, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
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13
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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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14
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Pudney CR, Hay S, Levy C, Pang J, Sutcliffe MJ, Leys D, Scrutton NS. Evidence to support the hypothesis that promoting vibrations enhance the rate of an enzyme catalyzed H-tunneling reaction. J Am Chem Soc 2010; 131:17072-3. [PMID: 19891489 DOI: 10.1021/ja908469m] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In recent years there has been a shift away from transition state theory models for H-transfer reactions. Models that incorporate tunneling as the mechanism of H-transfer are now recognized as a better description of such reactions. Central to many models of H-tunneling is the notion that specific vibrational modes of the protein and/or substrate can increase the probability of a H-tunneling reaction, modes that are termed promoting vibrations. Thus far there has been limited evidence that promoting vibrations can increase the rate of H-transfer. In the present communication we examine the single hydride transfer from both NADPH and NADH to FMN in the reductive half-reaction of pentaerythritol tetranitrate reductase (PETNR). We find that there is a significant promoting vibration with NADPH but not with NADH and that the observed rate of hydride transfer is significantly (approximately 15x) faster with NADPH. We rule out differences in rate due to variation in driving force and the donor-acceptor distance, suggesting it is the promoting vibration with NADPH that is the origin of the increased observed rate. This study therefore provides direct evidence that promoting vibrations can lead to an increase in rate.
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Affiliation(s)
- Christopher R Pudney
- Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
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15
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Yahashiri A, Nimrod G, Ben-Tal N, Howell EE, Kohen A. The effect of electrostatic shielding on H tunneling in R67 dihydrofolate reductase. Chembiochem 2010; 10:2620-3. [PMID: 19774544 DOI: 10.1002/cbic.200900451] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Atsushi Yahashiri
- Department of Chemistry, The University of Iowa, Iowa City, IA 52242, USA
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16
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Hay S, Pudney CR, Scrutton NS. Structural and mechanistic aspects of flavoproteins: probes of hydrogen tunnelling. FEBS J 2009; 276:3930-41. [DOI: 10.1111/j.1742-4658.2009.07121.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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18
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Abstract
Now, more than ever, enzymology and its development can be considered of vital importance to the progression of the biological sciences. With an increase in the numbers of enzymes being identified from genomic studies, enzymology is key to defining the structural and functional properties of these enzymes in order to establish their mechanisms of action and how they fit into metabolic networks. Along with the efforts of the bioinformaticians and systems biologists, such studies will ultimately lead to detailed descriptions of intricate biochemical pathways and allow identification of the most appropriate target enzymes for intervention in disease therapy. Thus the timing for the recent Biochemical Society Focused Meeting entitled 'Enzyme Mechanisms: Fast Reaction and Computational Approaches' was highly appropriate. The present paper represents an overview of this meeting, which was held at the Manchester Interdisciplinary Biocentre on 9-10 October 2008.
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