1
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Mhashal AR, Major DT. Temperature-Dependent Kinetic Isotope Effects in R67 Dihydrofolate Reductase from Path-Integral Simulations. J Phys Chem B 2021; 125:1369-1377. [PMID: 33522797 PMCID: PMC7883348 DOI: 10.1021/acs.jpcb.0c10318] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/05/2021] [Indexed: 11/28/2022]
Abstract
Calculation of temperature-dependent kinetic isotope effects (KIE) in enzymes presents a significant theoretical challenge. Additionally, it is not trivial to identify enzymes with available experimental accurate intrinsic KIEs in a range of temperatures. In the current work, we present a theoretical study of KIEs in the primitive R67 dihydrofolate reductase (DHFR) enzyme and compare with experimental work. The advantage of R67 DHFR is its significantly lower kinetic complexity compared to more evolved DHFR isoforms. We employ mass-perturbation-based path-integral simulations in conjunction with umbrella sampling and a hybrid quantum mechanics-molecular mechanics Hamiltonian. We obtain temperature-dependent KIEs in good agreement with experiments and ascribe the temperature-dependent KIEs primarily to zero-point energy effects. The active site in the primitive enzyme is found to be poorly preorganized, which allows excessive water access to the active site and results in loosely bound reacting ligands.
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Affiliation(s)
- Anil R. Mhashal
- Department of Chemistry and Institute
for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Dan Thomas Major
- Department of Chemistry and Institute
for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
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2
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The Hydride Transfer Process in NADP-dependent Methylene-tetrahydromethanopterin Dehydrogenase. J Mol Biol 2020; 432:2042-2054. [PMID: 32061937 DOI: 10.1016/j.jmb.2020.01.042] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 01/24/2020] [Accepted: 01/28/2020] [Indexed: 11/22/2022]
Abstract
NADP-dependent methylene-tetrahydromethanopterin (methylene-H4MPT) dehydrogenase (MtdA) catalyzes the reversible dehydrogenation of methylene-H4MPT to form methenyl-H4MPT+ by using NADP+ as a hydride acceptor. This hydride transfer reaction is involved in the oxidative metabolism from formaldehyde to CO2 in methylotrophic and methanotrophic bacteria. Here, we report on the crystal structures of the ternary MtdA-substrate complexes from Methylorubrum extorquens AM1 obtained in open and closed forms. Their conversion is accomplished by opening/closing the active site cleft via a 15° rotation of the NADP, relative to the pterin domain. The 1.08 Å structure of the closed and active enzyme-NADP-methylene-H4MPT complex allows a detailed geometric analysis of the bulky substrates and a precise prediction of the hydride trajectory. Upon domain closure, the bulky substrate rings become compressed resulting in a tilt of the imidazolidine group of methylene-H4MPT that optimizes the geometry for hydride transfer. An additional 1.5 Å structure of MtdA in complex with the nonreactive NADP+ and methenyl-H4MPT+ revealed an extremely short distance between nicotinamide-C4 and imidazoline-C14a of 2.5 Å, which demonstrates the strong pressure imposed. The pterin-imidazolidine-phenyl butterfly angle of methylene-H4MPT bound to MtdA is smaller than that in the enzyme-free state but is similar to that in H2- and F420-dependent methylene-H4MPT dehydrogenases. The concept of compression-driven hydride transfer including quantum mechanical hydrogen tunneling effects, which are established for flavin- and NADP-dependent enzymes, can be expanded to hydride-transferring H4MPT-dependent enzymes.
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3
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Howe GW, van der Donk WA. Temperature-Independent Kinetic Isotope Effects as Evidence for a Marcus-like Model of Hydride Tunneling in Phosphite Dehydrogenase. Biochemistry 2019; 58:4260-4268. [PMID: 31535852 PMCID: PMC6852621 DOI: 10.1021/acs.biochem.9b00732] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Phosphite dehydrogenase catalyzes the transfer of a hydride from phosphite to NAD+, producing phosphate and NADH. We have evaluated the role of hydride tunneling in a thermostable variant of this enzyme (17X-PTDH) by measuring the temperature dependence of the primary 2H kinetic isotope effects (KIEs) between 5 and 45 °C. Pre-steady-state kinetic measurements were used to demonstrate that the hydride transfer is rate-determining across this temperature range and that the observed KIEs are equal to the intrinsic isotope effect on the chemical step. The KIEs on the pre-exponential factor (AH/AD) and the activation energy (ΔEa) were 1.6 ± 0.1 and 0.21 ± 0.05 kcal/mol, respectively, suggesting that 17X-PTDH facilitates extensive tunneling of both isotopes via a Marcus-like model. Site-directed mutagenesis was used to evaluate the role of an active site threonine (Thr104) found on the back face of the nicotinamide in promoting the close packing of the substrates. In mutants with reduced steric bulk at this position, values of AH/AD and ΔEa fall within the range describing semiclassical "over the barrier" reactivity, suggesting that Thr104 acts as a steric backstop to promote tunneling in 17X-PTDH. Whereas hydrogen tunneling is now a widely appreciated feature of C-H activating enzymes, these observations with a P-H activating system are consistent with the proposal that tunneling is likely to be a common feature on all enzymes that catalyze hydrogen transfers.
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Affiliation(s)
- Graeme W Howe
- Department of Chemistry , University of Illinois at Urbana-Champaign , 600 South Mathews Avenue , Urbana , Illinois 61801 , United States.,Carl R. Woese Institute for Genomic Biology , University of Illinois at Urbana-Champaign , 1206 West Gregory Drive , Urbana , Illinois 61801 , United States
| | - Wilfred A van der Donk
- Department of Chemistry , University of Illinois at Urbana-Champaign , 600 South Mathews Avenue , Urbana , Illinois 61801 , United States.,Carl R. Woese Institute for Genomic Biology , University of Illinois at Urbana-Champaign , 1206 West Gregory Drive , Urbana , Illinois 61801 , United States.,Howard Hughes Medical Institute , University of Illinois at Urbana-Champaign , 1206 West Gregory Drive , Urbana , Illinois 61801 , United States
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4
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On the use of noncompetitive kinetic isotope effects to investigate flavoenzyme mechanism. Methods Enzymol 2019; 620:115-143. [PMID: 31072484 DOI: 10.1016/bs.mie.2019.03.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
This account describes the application of kinetic isotope effects (KIEs) to investigate the mechanistic properties of flavin dependent enzymes. Assays can be conducted during steady-state catalytic turnover of the flavoenzyme with its substrate or by using rapid-kinetic techniques to measure either the reductive or oxidative half-reactions of the enzyme. Great care should be taken to ensure that the observed effects are due to isotopic substitution and not other factors such as pH effects or changes in the solvent viscosity of the reaction mixture. Different types of KIEs are described along with a physical description of their origins and the unique information each can provide about the mechanism of an enzyme. Detailed experimental techniques are outlined with special emphasis on the proper controls and data analysis that must be carried out to avoid erroneous conclusions. Examples are provided for each type of KIE measurement from references in the literature. It is our hope that this article will clarify any confusion concerning the utility of KIEs in the study of flavoprotein mechanism and encourage their use by the community.
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5
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Iorgu AI, Cliff MJ, Waltho JP, Scrutton NS, Hay S. Isotopically labeled flavoenzymes and their uses in probing reaction mechanisms. Methods Enzymol 2019; 620:145-166. [PMID: 31072485 DOI: 10.1016/bs.mie.2019.03.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The incorporation of stable isotopes into proteins is beneficial or essential for a range of experiments, including NMR, neutron scattering and reflectometry, proteomic mass spectrometry, vibrational spectroscopy and "heavy" enzyme kinetic isotope effect (KIE) measurements. Here, we present detailed protocols for the stable isotopic labeling of pentaerythritol tetranitrate reductase (PETNR) via recombinant expression in E. coli. PETNR is an ene-reductase belonging to the Old Yellow Enzyme (OYE) family of flavoenzymes, and is regarded as a model system for studying hydride transfer reactions. Included is a discussion of how efficient back-exchange of amide protons in the protein core can be achieved and how the intrinsic flavin mononucleotide (FMN) cofactor can be exchanged, allowing the production of isotopologues with differentially labeled protein and cofactor. In addition to a thorough description of labeling strategies, we briefly exemplify how data analysis and interpretation of "heavy" enzyme KIEs can be performed.
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Affiliation(s)
- Andreea I Iorgu
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, United Kingdom
| | - Matthew J Cliff
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, United Kingdom
| | - Jonathan P Waltho
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, United Kingdom
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, United Kingdom
| | - Sam Hay
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, United Kingdom.
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6
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Iorgu AI, Baxter NJ, Cliff MJ, Levy C, Waltho JP, Hay S, Scrutton NS. Nonequivalence of Second Sphere "Noncatalytic" Residues in Pentaerythritol Tetranitrate Reductase in Relation to Local Dynamics Linked to H-Transfer in Reactions with NADH and NADPH Coenzymes. ACS Catal 2018; 8:11589-11599. [PMID: 31119061 PMCID: PMC6516726 DOI: 10.1021/acscatal.8b02810] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 10/23/2018] [Indexed: 11/28/2022]
Abstract
![]()
Many enzymes that
catalyze hydride transfer reactions work via
a mechanism dominated by quantum mechanical tunneling. The involvement
of fast vibrational modes of the reactive complex is often inferred
in these reactions, as in the case of the NAD(P)H-dependent pentaerythritol
tetranitrate reductase (PETNR). Herein, we interrogated the H-transfer
mechanism in PETNR by designing conservative (L25I and I107L) and
side chain shortening (L25A and I107A) PETNR variants and using a
combination of experimental approaches (stopped-flow rapid kinetics,
X-ray crystallography, isotope/temperature dependence studies of H-transfer
and NMR spectroscopy). X-ray data show subtle changes in the local
environment of the targeted side chains but no major structural perturbation
caused by mutagenesis of these two second sphere active site residues.
However, temperature dependence studies of H-transfer revealed a coenzyme-specific
and complex thermodynamic equilibrium between different reactive configurations
in PETNR–coenzyme complexes. We find that mutagenesis of these
second sphere “noncatalytic” residues affects differently
the reactivity of PETNR with NADPH and NADH coenzymes. We attribute
this to subtle, dynamic structural changes in the PETNR active site,
the effects of which impact differently in the nonequivalent reactive
geometries of PETNR−NADH and PETNR−NADPH complexes.
This inference is confirmed through changes observed in the NMR chemical
shift data for PETNR complexes with unreactive 1,4,5,6-tetrahydro-NAD(P)
analogues. We show that H-transfer rates can (to some extent) be buffered
through entropy–enthalpy compensation, but that use of integrated
experimental tools reveals hidden complexities that implicate a role
for dynamics in this relatively simple H-transfer reaction. Similar
approaches are likely to be informative in other enzymes to understand
the relative importance of (distal) hydrophobic side chains and dynamics
in controlling the rates of enzymatic H-transfer.
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Affiliation(s)
- Andreea I. Iorgu
- Manchester Institute of Biotechnology and School of Chemistry, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Nicola J. Baxter
- Manchester Institute of Biotechnology and School of Chemistry, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, United Kingdom
| | - Matthew J. Cliff
- Manchester Institute of Biotechnology and School of Chemistry, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Colin Levy
- Manchester Institute of Biotechnology and School of Chemistry, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Jonathan P. Waltho
- Manchester Institute of Biotechnology and School of Chemistry, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, United Kingdom
| | - Sam Hay
- Manchester Institute of Biotechnology and School of Chemistry, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Nigel S. Scrutton
- Manchester Institute of Biotechnology and School of Chemistry, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
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7
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Boehr DD, D'Amico RN, O'Rourke KF. Engineered control of enzyme structural dynamics and function. Protein Sci 2018; 27:825-838. [PMID: 29380452 DOI: 10.1002/pro.3379] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Revised: 01/20/2018] [Accepted: 01/24/2018] [Indexed: 12/20/2022]
Abstract
Enzymes undergo a range of internal motions from local, active site fluctuations to large-scale, global conformational changes. These motions are often important for enzyme function, including in ligand binding and dissociation and even preparing the active site for chemical catalysis. Protein engineering efforts have been directed towards manipulating enzyme structural dynamics and conformational changes, including targeting specific amino acid interactions and creation of chimeric enzymes with new regulatory functions. Post-translational covalent modification can provide an additional level of enzyme control. These studies have not only provided insights into the functional role of protein motions, but they offer opportunities to create stimulus-responsive enzymes. These enzymes can be engineered to respond to a number of external stimuli, including light, pH, and the presence of novel allosteric modulators. Altogether, the ability to engineer and control enzyme structural dynamics can provide new tools for biotechnology and medicine.
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Affiliation(s)
- David D Boehr
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, 16802, USA
| | - Rebecca N D'Amico
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, 16802, USA
| | - Kathleen F O'Rourke
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, 16802, USA
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8
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Jevtic S, Anders J. A qualitative quantum rate model for hydrogen transfer in soybean lipoxygenase. J Chem Phys 2017; 147:114108. [PMID: 28938801 DOI: 10.1063/1.4998941] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The hydrogen transfer reaction catalysed by soybean lipoxygenase (SLO) has been the focus of intense study following observations of a high kinetic isotope effect (KIE). Today high KIEs are generally thought to indicate departure from classical rate theory and are seen as a strong signature of tunnelling of the transferring particle, hydrogen or one of its isotopes, through the reaction energy barrier. In this paper, we build a qualitative quantum rate model with few free parameters that describes the dynamics of the transferring particle when it is exposed to energetic potentials exerted by the donor and the acceptor. The enzyme's impact on the dynamics is modelled by an additional energetic term, an oscillatory contribution known as "gating." By varying two key parameters, the gating frequency and the mean donor-acceptor separation, the model is able to reproduce well the KIE data for SLO wild-type and a variety of SLO mutants over the experimentally accessible temperature range. While SLO-specific constants have been considered here, it is possible to adapt these for other enzymes.
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Affiliation(s)
- S Jevtic
- Department of Mathematics, Huxley Building, Imperial College, London SW7 2AZ, United Kingdom
| | - J Anders
- CEMPS, Physics and Astronomy, University of Exeter, Exeter EX4 4QL, United Kingdom
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9
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Leys D, Scrutton NS. Sweating the assets of flavin cofactors: new insight of chemical versatility from knowledge of structure and mechanism. Curr Opin Struct Biol 2016; 41:19-26. [DOI: 10.1016/j.sbi.2016.05.014] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 05/24/2016] [Indexed: 10/21/2022]
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10
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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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11
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Romero E, Ladani ST, Hamelberg D, Gadda G. Solvent-Slaved Motions in the Hydride Tunneling Reaction Catalyzed by Human Glycolate Oxidase. ACS Catal 2016. [DOI: 10.1021/acscatal.5b02889] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Elvira Romero
- Department of Chemistry, ¶Department of Biology, ∥Center for Biotechnology
and Drug
Design, and #Center
for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Safieh Tork Ladani
- Department of Chemistry, ¶Department of Biology, ∥Center for Biotechnology
and Drug
Design, and #Center
for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Donald Hamelberg
- Department of Chemistry, ¶Department of Biology, ∥Center for Biotechnology
and Drug
Design, and #Center
for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Giovanni Gadda
- Department of Chemistry, ¶Department of Biology, ∥Center for Biotechnology
and Drug
Design, and #Center
for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30302-3965, United States
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12
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Johannissen LO, Hay S, Scrutton NS. Nuclear quantum tunnelling in enzymatic reactions – an enzymologist's perspective. Phys Chem Chem Phys 2015; 17:30775-82. [DOI: 10.1039/c5cp00614g] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The roles of nuclear quantum tunnelling and dynamics in enzyme reactions are discussed in this perspective on H-transfer reactions.
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Affiliation(s)
- Linus O. Johannissen
- SYNBIOCHEM
- Manchester Institute of Biotechnology
- Faculty of Life Sciences
- The University of Manchester
- Manchester M1 7DN
| | - Sam Hay
- SYNBIOCHEM
- Manchester Institute of Biotechnology
- Faculty of Life Sciences
- The University of Manchester
- Manchester M1 7DN
| | - Nigel S. Scrutton
- SYNBIOCHEM
- Manchester Institute of Biotechnology
- Faculty of Life Sciences
- The University of Manchester
- Manchester M1 7DN
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13
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Practical aspects on the use of kinetic isotope effects as probes of flavoprotein enzyme mechanisms. Methods Mol Biol 2014; 1146:161-75. [PMID: 24764092 DOI: 10.1007/978-1-4939-0452-5_8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The measurement of kinetic isotope effects (KIEs) has proved useful in many mechanistic studies of enzyme activity, most notably in enzyme-catalyzed hydrogen-transfer reactions. Primary KIEs (1° KIE) greater than unity indicate that transfer of the hydrogen species of interest is partially or fully rate limiting, and studies of the magnitude of the temperature and pressure dependence of these KIEs can inform on the mechanism of transfer. For example, KIE measurements have proved crucial in understanding the role of quantum mechanical tunneling in enzyme systems. The measurement of secondary KIEs (2° KIEs) is also informative and can be used to infer a significant tunneling contribution and details of transition state geometry. Here the deuterium label is introduced next to that of the transferred hydrogen. Measurements of 1° and 2° KIEs are being used increasingly in studies of H-transfer in flavoprotein enzymes and this requires the preparation of high purity and stereospecific labeled isotopologues. Strategies for the synthesis of labeled substrates are dependent on the enzyme system being studied. However, the nicotinamide coenzymes are often used in studies of flavoprotein enzyme mechanisms. Here, we provide practical details for the enzymatic synthesis of high purity deuterated isotopologues of the common biological coenzymes NADH and NADPH as well as the corresponding nonreactive mimics, tetrahydroNAD(P)H. Both forms of the coenzyme have proven useful in the study of mechanisms, particularly in relation to the involvement of quantum mechanical tunneling and dynamics in enzymatic H-transfer chemistry. The focus here is on practical considerations in the synthesis of these compounds. We also provide an abbreviated description of how measurements of KIEs can inform on flavoprotein mechanisms. The aim of this contribution is not to give a detailed description of the underlying theory (which has been reviewed extensively in the literature), but to provide a basic introduction and practical considerations for nonexpert readers who wish to incorporate such measurements in studies of enzyme mechanisms.
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14
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Hardman SJO, Pudney CR, Hay S, Scrutton NS. Excited state dynamics can be used to probe donor-acceptor distances for H-tunneling reactions catalyzed by flavoproteins. Biophys J 2014; 105:2549-58. [PMID: 24314085 DOI: 10.1016/j.bpj.2013.10.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Revised: 10/09/2013] [Accepted: 10/21/2013] [Indexed: 10/26/2022] Open
Abstract
In enzyme systems where fast motions are thought to contribute to H-transfer efficiency, the distance between hydrogen donor and acceptor is a very important factor. Sub-ångstrom changes in donor-acceptor distance can have a large effect on the rate of reaction, so a sensitive probe of these changes is a vital tool in our understanding of enzyme function. In this study we use ultrafast transient absorption spectroscopy to investigate the photoinduced electron transfer rates, which are also very sensitive to small changes in distance, between coenzyme analog, NAD(P)H4, and the isoalloxazine center in the model flavoenzymes morphinone reductase (wild-type and selected variants) and pentaerythritol tetranitrate reductase (wild-type). It is shown that upon addition of coenzyme to the protein the rate of photoinduced electron transfer is increased. By comparing the magnitude of this increase with existing values for NAD(P)H4-FMN distances, based on charge-transfer complex absorbance and experimental kinetic isotope effect reaction data, we show that this method can be used as a sensitive probe of donor-acceptor distance in a range of enzyme systems.
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Affiliation(s)
- Samantha J O Hardman
- Manchester Institute of Biotechnology and Photon Science Institute, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
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15
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Ruiz-Pernia JJ, Luk LYP, García-Meseguer R, Martí S, Loveridge EJ, Tuñón I, Moliner V, Allemann RK. Increased dynamic effects in a catalytically compromised variant of Escherichia coli dihydrofolate reductase. J Am Chem Soc 2013; 135:18689-96. [PMID: 24252106 PMCID: PMC3949409 DOI: 10.1021/ja410519h] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Indexed: 01/19/2023]
Abstract
Isotopic substitution ((15)N, (13)C, (2)H) of a catalytically compromised variant of Escherichia coli dihydrofolate reductase, EcDHFR-N23PP/S148A, has been used to investigate the effect of these mutations on catalysis. The reduction of the rate constant of the chemical step in the EcDHFR-N23PP/S148A catalyzed reaction is essentially a consequence of an increase of the quasi-classical free energy barrier and to a minor extent of an increased number of recrossing trajectories on the transition state dividing surface. Since the variant enzyme is less well set up to catalyze the reaction, a higher degree of active site reorganization is needed to reach the TS. Although millisecond active site motions are lost in the variant, there is greater flexibility on the femtosecond time scale. The "dynamic knockout" EcDHFR-N23PP/S148A is therefore a "dynamic knock-in" at the level of the chemical step, and the increased dynamic coupling to the chemical coordinate is in fact detrimental to catalysis. This finding is most likely applicable not just to hydrogen transfer in EcDHFR but also to other enzymatic systems.
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Affiliation(s)
- J. Javier Ruiz-Pernia
- Departament
de Química Física i Analítica, Universitat Jaume I, 12071 Castello, Spain
| | - Louis Y. P. Luk
- School
of Chemistry & Cardiff Catalysis Institute, Cardiff University, Park Place, Cardiff, CF10
3AT, U.K.
| | | | - Sergio Martí
- Departament
de Química Física i Analítica, Universitat Jaume I, 12071 Castello, Spain
| | - E. Joel Loveridge
- School
of Chemistry & Cardiff Catalysis Institute, Cardiff University, Park Place, Cardiff, CF10
3AT, U.K.
| | - Iñaki Tuñón
- Departament
de Química Física, Universitat
de València, 46100 Burjassot, Spain
| | - Vicent Moliner
- Departament
de Química Física i Analítica, Universitat Jaume I, 12071 Castello, Spain
| | - Rudolf K. Allemann
- School
of Chemistry & Cardiff Catalysis Institute, Cardiff University, Park Place, Cardiff, CF10
3AT, U.K.
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16
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Wiebe H, Prachnau M, Weinberg N. Hydrogen transfer reactions in viscous media — Potential and free energy surfaces in solvent–solute coordinates and their kinetic implications. CAN J CHEM 2013. [DOI: 10.1139/cjc-2012-0554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Two-dimensional potential energy and free energy surfaces are obtained using quantum mechanical and molecular dynamics calculations for four hydrogen transfer reactions in n-hexane solvent: the methyl–methane, n-propyl–n-propane, n-pentyl–n-pentane, and t-butyl–isobutane systems. The resultant surfaces have similar landscapes despite the fact the equilibrated solvent cavities for these systems are notably different in size and shape. The kinetic implications of these landscapes are discussed. The Arrhenius and tunneling kinetics of hydrogen transfer in nonpolar hydrocarbon solute–solvent systems are not expected to show any significant viscosity dependence.
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Affiliation(s)
- Heather Wiebe
- Department of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Melissa Prachnau
- Department of Chemistry, University of the Fraser Valley, Abbotsford, BC V2S 7M8, Canada
| | - Noham Weinberg
- Department of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
- Department of Chemistry, University of the Fraser Valley, Abbotsford, BC V2S 7M8, Canada
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Loveridge EJ, Behiry EM, Guo J, Allemann RK. Evidence that a 'dynamic knockout' in Escherichia coli dihydrofolate reductase does not affect the chemical step of catalysis. Nat Chem 2012; 4:292-7. [PMID: 22437714 DOI: 10.1038/nchem.1296] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Accepted: 02/06/2012] [Indexed: 12/16/2022]
Abstract
The question of whether protein motions play a role in the chemical step of enzymatic catalysis has generated much controversy in recent years. Debate has recently reignited over possible dynamic contributions to catalysis in dihydrofolate reductase, following conflicting conclusions from studies of the N23PP/S148A variant of the Escherichia coli enzyme. By investigating the temperature dependence of kinetic isotope effects, we present evidence that the reduction in the hydride transfer rate constants in this variant is not a direct result of impairment of conformational fluctuations. Instead, the conformational state of the enzyme immediately before hydride transfer, which determines the electrostatic environment of the active site, affects the rate constant for the reaction. Although protein motions are clearly important for binding and release of substrates and products, there appears to be no detectable dynamic coupling of protein motions to the hydride transfer step itself.
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Affiliation(s)
- E Joel Loveridge
- School of Chemistry, Cardiff University, Park Place, Cardiff, CF10 3AT, UK
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18
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Abstract
Fast motions (femtosecond to picosecond) and their potential involvement during enzyme-catalysed reactions have ignited considerable interest in recent years. Their influence on reaction chemistry has been inferred indirectly from studies of the anomalous temperature dependence of kinetic isotope effects and computational simulations. But can such motion reduce the width and height of energy barriers along the reaction coordinate, and contribute to quantum mechanical and/or classical nuclear-transfer chemistry? Here we discuss contemporary ideas for enzymatic reactions invoking a role for fast 'promoting' (or 'compressive') motions that, in principle, can aid hydrogen-transfer reactions. Of key importance is the direct demonstration of a role for compressive motions and the ability to understand in atomic detail the structural origin of these fast motions, but so far this has not been achieved. Here we discuss both indirect experimental evidence that supports a role for compressive motion and the additional insight gained from computational simulations.
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Affiliation(s)
- Sam Hay
- Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
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Loveridge EJ, Allemann RK. Effect of pH on hydride transfer by Escherichia coli dihydrofolate reductase. Chembiochem 2011; 12:1258-62. [PMID: 21506230 DOI: 10.1002/cbic.201000794] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2010] [Indexed: 11/07/2022]
Abstract
The kinetic isotope effect (KIE) on hydride transfer in the reaction catalysed by dihydrofolate reductase from Escherichia coli (EcDHFR) is known to be temperature dependent at pH 7, but essentially independent of temperature at elevated pH. Here, we show that the transition from the temperature-dependent regime to the temperature-independent regime occurs sharply between pH 7.5 and 8. The activation energy for hydride transfer is independent of pH. The mechanism leading to the change in behaviour of the KIEs is not clear, but probably involves a conformational change in the enzyme brought about by deprotonation of a key residue (or residues) at high pH. The KIE on hydride transfer at low pH suggests that the rate constant for the reaction is not limited by a conformational change to the enzyme under these conditions. The effect of pH on the temperature dependence of the rate constants and KIEs for hydride transfer catalysed by EcDHFR suggests that enzyme motions and conformational changes do not directly influence the chemistry, but that the reaction conditions affect the conformational ensemble of the enzyme prior to reaction and control the reaction though this route.
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Affiliation(s)
- E Joel Loveridge
- School of Chemistry, Cardiff University, Park Place, Cardiff, UK
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20
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Schittmayer M, Glieder A, Uhl MK, Winkler A, Zach S, Schrittwieser JH, Kroutil W, Macheroux P, Gruber K, Kambourakis S, Rozzell JD, Winkler M. Old Yellow Enzyme-Catalyzed Dehydrogenation of Saturated Ketones. Adv Synth Catal 2011. [DOI: 10.1002/adsc.201000862] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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21
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Stenuit BA, Agathos SN. Microbial 2,4,6-trinitrotoluene degradation: could we learn from (bio)chemistry for bioremediation and vice versa? Appl Microbiol Biotechnol 2010; 88:1043-64. [DOI: 10.1007/s00253-010-2830-x] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2010] [Revised: 08/06/2010] [Accepted: 08/08/2010] [Indexed: 12/11/2022]
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22
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Pudney CR, Johannissen LO, Sutcliffe MJ, Hay S, Scrutton NS. Direct Analysis of Donor−Acceptor Distance and Relationship to Isotope Effects and the Force Constant for Barrier Compression in Enzymatic H-Tunneling Reactions. J Am Chem Soc 2010; 132:11329-35. [DOI: 10.1021/ja1048048] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Christopher R. Pudney
- Manchester Interdisciplinary Biocentre, Faculty of Life Sciences, and School of Chemical Engineering and Analytical Science, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Linus O. Johannissen
- Manchester Interdisciplinary Biocentre, Faculty of Life Sciences, and School of Chemical Engineering and Analytical Science, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Michael J. Sutcliffe
- Manchester Interdisciplinary Biocentre, Faculty of Life Sciences, and School of Chemical Engineering and Analytical Science, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Sam Hay
- Manchester Interdisciplinary Biocentre, Faculty of Life Sciences, and School of Chemical Engineering and Analytical Science, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Nigel S. Scrutton
- Manchester Interdisciplinary Biocentre, Faculty of Life Sciences, and School of Chemical Engineering and Analytical Science, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
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Loveridge EJ, Tey LH, Allemann RK. Solvent effects on catalysis by Escherichia coli dihydrofolate reductase. J Am Chem Soc 2010; 132:1137-43. [PMID: 20047317 DOI: 10.1021/ja909353c] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Hydride transfer catalyzed by dihydrofolate reductase (DHFR) has been described previously within an environmentally coupled model of hydrogen tunneling, where protein motions control binding of substrate and cofactor to generate a tunneling ready conformation and modulate the width of the activation barrier and hence the reaction rate. Changes to the composition of the reaction medium are known to perturb protein motions. We have measured kinetic parameters of the reaction catalyzed by DHFR from Escherichia coli in the presence of various cosolvents and cosolutes and show that the dielectric constant, but not the viscosity, of the reaction medium affects the rate of reaction. Neither the primary kinetic isotope effect on the reaction nor its temperature dependence were affected by changes to the bulk solvent properties. These results are in agreement with our previous report on the effect of solvent composition on catalysis by DHFR from the hyperthermophile Thermotoga maritima. However, the effect of solvent on the temperature dependence of the kinetic isotope effect on hydride transfer catalyzed by E. coli DHFR is difficult to explain within a model, in which long-range motions couple to the chemical step of the reaction, but may indicate the existence of a short-range promoting vibration or the presence of multiple nearly isoenergetic conformational substates of enzymes with similar but distinct catalytic properties.
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Affiliation(s)
- E Joel Loveridge
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, UK
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Hay S, Pudney CR, Sutcliffe MJ, Scrutton NS. Probing active site geometry using high pressure and secondary isotope effects in an enzyme-catalysed 'deep' H-tunnelling reaction. J PHYS ORG CHEM 2010; 23:696-701. [PMID: 20890464 DOI: 10.1002/poc.1653] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
We report the first study of the effects of hydrostatic pressure on α-2° KIEs for an enzyme-catalysed H-transfer reaction that occurs by 'deep' tunnelling. High pressure causes a significant decrease in the observed α-2° KIE on the pre-steady-state hydride transfer from NADH to FMN in the flavoprotein morphinone reductase. We have recently shown that high pressure causes a reduction in macroscopic reaction barrier width for this reaction. Using DFT vibrational analysis of a simple active site model, we posit that the decrease in α-2° KIE with pressure may arise due to a decrease in the vibrational coupling between the NADH primary (transferred) and secondary hydrogens in the 'tunnelling ready configuration', which more closely resembles the reactant state than the transition state.
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Affiliation(s)
- Sam Hay
- Manchester Interdisciplinary Biocentre and Faculty of Life Science, University of Manchester, 131 Princess Street, Manchester M1 7ND, UK
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25
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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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