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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Acceleration of catalysis in dihydrofolate reductase by transient, site-specific photothermal excitation. Proc Natl Acad Sci U S A 2021; 118:2014592118. [PMID: 33468677 DOI: 10.1073/pnas.2014592118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We have studied the role of protein dynamics in chemical catalysis in the enzyme dihydrofolate reductase (DHFR), using a pump-probe method that employs pulsed-laser photothermal heating of a gold nanoparticle (AuNP) to directly excite a local region of the protein structure and transient absorbance to probe the effect on enzyme activity. Enzyme activity is accelerated by pulsed-laser excitation when the AuNP is attached close to a network of coupled motions in DHFR (on the FG loop, containing residues 116-132, or on a nearby alpha helix). No rate acceleration is observed when the AuNP is attached away from the network (distal mutant and His-tagged mutant) with pulsed excitation, or for any attachment site with continuous wave excitation. We interpret these results within an energy landscape model in which transient, site-specific addition of energy to the enzyme speeds up the search for reactive conformations by activating motions that facilitate this search.
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3
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Ruiz-Pernía JJ, Tuñón I, Moliner V, Allemann RK. Why are some Enzymes Dimers? Flexibility and Catalysis in Thermotoga Maritima Dihydrofolate Reductase. ACS Catal 2019; 9:5902-5911. [PMID: 31289693 PMCID: PMC6614790 DOI: 10.1021/acscatal.9b01250] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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Dihydrofolate
reductase from Thermotoga maritima (TmDFHFR) is a
dimeric thermophilic enzyme that catalyzes the hydride
transfer from the cofactor NADPH to dihydrofolate less efficiently
than other DHFR enzymes, such as the mesophilic analogue Escherichia
coli DHFR (EcDHFR). Using QM/MM potentials, we show that
the reduced catalytic efficiency of TmDHFR is most likely due to differences
in the amino acid sequence that stabilize the M20 loop in an open
conformation, which prevents the formation of some interactions in
the transition state and increases the number of water molecules in
the active site. However, dimerization provides two advantages to
the thermophilic enzyme: it protects its structure against denaturation
by reducing thermal fluctuations and it provides a less negative activation
entropy, toning down the increase of the activation free energy with
temperature. Our molecular picture is confirmed by the analysis of
the temperature dependence of enzyme kinetic isotope effects in different
DHFR enzymes.
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Affiliation(s)
- J. Javier Ruiz-Pernía
- Departamento de Química Física, Universitat de Valencia, 46100 Burjassot, Valencia, Spain
| | - Iñaki Tuñón
- Departamento de Química Física, Universitat de Valencia, 46100 Burjassot, Valencia, Spain
| | - Vicent Moliner
- Departamento de Química Física y Analítica, Universitat Jaume I, 12071 Castellón, Spain
| | - Rudolf K. Allemann
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
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4
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Loveridge EJ, Hroch L, Hughes RL, Williams T, Davies RL, Angelastro A, Luk LYP, Maglia G, Allemann RK. Reduction of Folate by Dihydrofolate Reductase from Thermotoga maritima. Biochemistry 2017; 56:1879-1886. [PMID: 28319664 DOI: 10.1021/acs.biochem.6b01268] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mammalian dihydrofolate reductases (DHFRs) catalyze the reduction of folate more efficiently than the equivalent bacterial enzymes do, despite typically having similar efficiencies for the reduction of their natural substrate, dihydrofolate. In contrast, we show here that DHFR from the hyperthermophilic bacterium Thermotoga maritima can catalyze reduction of folate to tetrahydrofolate with an efficiency similar to that of reduction of dihydrofolate under saturating conditions. Nuclear magnetic resonance and mass spectrometry experiments showed no evidence of the production of free dihydrofolate during either the EcDHFR- or TmDHFR-catalyzed reductions of folate, suggesting that both enzymes perform the two reduction steps without release of the partially reduced substrate. Our results imply that the reaction proceeds more efficiently in TmDHFR than in EcDHFR because the more open active site of TmDHFR facilitates protonation of folate. Because T. maritima lives under extreme conditions where tetrahydrofolate is particularly prone to oxidation, this ability to salvage folate may impart an advantage to the bacterium by minimizing the squandering of a valuable cofactor.
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Affiliation(s)
- E Joel Loveridge
- School of Chemistry, Cardiff University , Main Building, Park Place, Cardiff CF10 3AT, U.K.,Department of Chemistry, Swansea University , Singleton Park, Swansea SA2 8PP, U.K
| | - Lukas Hroch
- School of Chemistry, Cardiff University , Main Building, Park Place, Cardiff CF10 3AT, U.K.,Department of Pharmaceutical Chemistry and Drug Control, Faculty of Pharmacy in Hradec Kralove, Charles University in Prague , Akademika Heyrovskeho 1203, 500 05 Hradec Kralove, Czech Republic
| | - Robert L Hughes
- School of Chemistry, Cardiff University , Main Building, Park Place, Cardiff CF10 3AT, U.K
| | - Thomas Williams
- School of Chemistry, Cardiff University , Main Building, Park Place, Cardiff CF10 3AT, U.K
| | - Rhidian L Davies
- School of Chemistry, Cardiff University , Main Building, Park Place, Cardiff CF10 3AT, U.K
| | - Antonio Angelastro
- School of Chemistry, Cardiff University , Main Building, Park Place, Cardiff CF10 3AT, U.K
| | - Louis Y P Luk
- School of Chemistry, Cardiff University , Main Building, Park Place, Cardiff CF10 3AT, U.K
| | - Giovanni Maglia
- School of Chemical Sciences, University of Birmingham , Edgbaston, Birmingham B15 2TT, U.K
| | - Rudolf K Allemann
- School of Chemistry, Cardiff University , Main Building, Park Place, Cardiff CF10 3AT, U.K.,School of Chemical Sciences, University of Birmingham , Edgbaston, Birmingham B15 2TT, U.K
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5
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Luk LYP, Loveridge EJ, Allemann RK. Protein motions and dynamic effects in enzyme catalysis. Phys Chem Chem Phys 2016; 17:30817-27. [PMID: 25854702 DOI: 10.1039/c5cp00794a] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The role of protein motions in promoting the chemical step of enzyme catalysed reactions remains a subject of considerable debate. Here, a unified view of the role of protein dynamics in dihydrofolate reductase catalysis is described. Recently the role of such motions has been investigated by characterising the biophysical properties of isotopically substituted enzymes through a combination of experimental and computational analyses. Together with previous work, these results suggest that dynamic coupling to the chemical coordinate is detrimental to catalysis and may have been selected against during DHFR evolution. The full catalytic power of Nature's catalysts appears to depend on finely tuning protein motions in each step of the catalytic cycle.
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Affiliation(s)
- Louis Y P Luk
- School of Chemistry, Cardiff University, Park Place, Cardiff, CF10 3AT, UK.
| | - E Joel Loveridge
- School of Chemistry, Cardiff University, Park Place, Cardiff, CF10 3AT, UK.
| | - Rudolf K Allemann
- School of Chemistry, Cardiff University, Park Place, Cardiff, CF10 3AT, UK.
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6
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Chen JL, Yang Y, Zhang LL, Liang H, Huber T, Su XC, Otting G. Analysis of the solution conformations of T4 lysozyme by paramagnetic NMR spectroscopy. Phys Chem Chem Phys 2016; 18:5850-9. [DOI: 10.1039/c5cp07196h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Paramagnetic data show that the average structure of T4-lysozyme in solution is more open than its crystal structure.
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Affiliation(s)
- Jia-Liang Chen
- State Key Laboratory of Elemento-organic Chemistry
- The Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)
- Nankai University
- Tianjin 300071
- China
| | - Yin Yang
- State Key Laboratory of Elemento-organic Chemistry
- The Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)
- Nankai University
- Tianjin 300071
- China
| | - Lin-Lin Zhang
- State Key Laboratory of Elemento-organic Chemistry
- The Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)
- Nankai University
- Tianjin 300071
- China
| | - Haobo Liang
- Research School of Chemistry
- Australian National University
- Canberra
- Australia
| | - Thomas Huber
- Research School of Chemistry
- Australian National University
- Canberra
- Australia
| | - Xun-Cheng Su
- State Key Laboratory of Elemento-organic Chemistry
- The Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)
- Nankai University
- Tianjin 300071
- China
| | - Gottfried Otting
- Research School of Chemistry
- Australian National University
- Canberra
- Australia
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7
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Abstract
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The active
site of an enzyme is surrounded by a fluctuating environment of protein
and solvent conformational states, and a realistic calculation of
chemical reaction rates and kinetic isotope effects of enzyme-catalyzed
reactions must take account of this environmental diversity. Ensemble-averaged
variational transition state theory with multidimensional tunneling
(EA-VTST/MT) was developed as a way to carry out such calculations.
This theory incorporates ensemble averaging, quantized vibrational
energies, energy, tunneling, and recrossing of transition state dividing
surfaces in a systematic way. It has been applied successfully to
a number of hydrogen-, proton-, and hydride-transfer reactions. The
theory also exposes the set of effects that should be considered in
reliable rate constants calculations. We first review the basic
theory and the steps in the calculation. A key role is played by the
generalized free energy of activation profile, which is obtained by
quantizing the classical potential of mean force as a function of
a reaction coordinate because the one-way flux through the transition
state dividing surface can be written in terms of the generalized
free energy of activation. A recrossing transmission coefficient accounts
for the difference between the one-way flux through the chosen transition
state dividing surface and the net flux, and a tunneling transmission
coefficient converts classical motion along the reaction coordinate
to quantum mechanical motion. The tunneling calculation is multidimensional,
accounting for the change in vibrational frequencies along the tunneling
path and shortening of the tunneling path with respect to the minimum
energy path (MEP), as promoted by reaction-path curvature. The generalized
free energy of activation and the transmission coefficients both involve
averaging over an ensemble of reaction paths and conformations, and
this includes the coupling of protein motions to the rearrangement
of chemical bonds in a statistical mechanically correct way. The standard
deviations of the transmissions coefficients provide information on
the diversity of the distribution of reaction paths, barriers, and
protein conformations along the members of an ensemble of reaction
paths passing through the transition state. We first illustrate
the theory by discussing the application to both wild-type and mutant Escherichia coli dihydrofolate reductase and hyperthermophilic Thermotoga maritima dihydrofolate reductase (DHFR); DHFR
is of special interest because the protein conformational changes
have been widely studied. Then we present shorter discussions of several
other applications of EA-VTST/MT to transfer of protons, hydrogen
atoms, and hydride ions and their deuterated analogs. Systems discussed
include hydride transfer in alcohol dehydrogenase, xylose isomerase,
and thymidylate synthase, proton transfer in methylamine dehydrogenase,
hydrogen atom transfer in methylmalonyl-CoA mutase, and nucleophilic
substitution in haloalkane dehalogenase and two-dimensional potentials
of mean force for potentially coupled proton and hydride transfer
in the β-oxidation of butyryl-coenzyme A catalyzed by short-chain
acyl-CoA dehydrogenase and in the pyruvate to lactate transformation
catalyzed by lactate dehydrogenase.
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Affiliation(s)
- Laura Masgrau
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain
| | - Donald G. Truhlar
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455-0431, United States
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8
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Reddish MJ, Peng HL, Deng H, Panwar KS, Callender R, Dyer RB. Direct evidence of catalytic heterogeneity in lactate dehydrogenase by temperature jump infrared spectroscopy. J Phys Chem B 2014; 118:10854-62. [PMID: 25149276 PMCID: PMC4167064 DOI: 10.1021/jp5050546] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Protein conformational heterogeneity and dynamics are known to play an important role in enzyme catalysis, but their influence has been difficult to observe directly. We have studied the effects of heterogeneity in the catalytic reaction of pig heart lactate dehydrogenase using isotope edited infrared spectroscopy, laser-induced temperature jump relaxation, and kinetic modeling. The isotope edited infrared spectrum reveals the presence of multiple reactive conformations of pyruvate bound to the enzyme, with three major reactive populations having substrate C2 carbonyl stretches at 1686, 1679, and 1674 cm(-1), respectively. The temperature jump relaxation measurements and kinetic modeling indicate that these substates form a heterogeneous branched reaction pathway, and each substate catalyzes the conversion of pyruvate to lactate with a different rate. Furthermore, the rate of hydride transfer is inversely correlated with the frequency of the C2 carbonyl stretch (the rate increases as the frequency decreases), consistent with the relationship between the frequency of this mode and the polarization of the bond, which determines its reactivity toward hydride transfer. The enzyme does not appear to be optimized to use the fastest pathway preferentially but rather accesses multiple pathways in a search process that often selects slower ones. These results provide further support for a dynamic view of enzyme catalysis where the role of the enzyme is not just to bring reactants together but also to guide the conformational search for chemically competent interactions.
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Affiliation(s)
- Michael J Reddish
- Department of Chemistry, Emory University , Atlanta, Georgia 30322, United States
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9
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Francis K, Kohen A. Protein motions and the activation of the CH bond catalyzed by dihydrofolate reductase. Curr Opin Chem Biol 2014; 21:19-24. [PMID: 24742825 PMCID: PMC4149937 DOI: 10.1016/j.cbpa.2014.03.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2014] [Revised: 03/03/2014] [Accepted: 03/05/2014] [Indexed: 11/28/2022]
Abstract
The role of protein motions in enzymatic CH→C transfer is an area of great contemporary debate. An effective tool in probing such a role is the temperature dependence of the intrinsic kinetic isotope effects for the enzyme-catalyzed reaction. The outcome of those experiments is interpreted within the context of phenomenological Marcus-like models of hydrogen tunneling. The current review focuses on recent studies of dihydrofolate reductase (DHFR) and how the role of protein motions in the catalyzed reaction has been demonstrated. The motions in DHFR are controlled by local effects of active site residues, global effects involving remote residues across the enzyme and appear to be preserved during the evolution of the enzyme from bacteria to human.
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Affiliation(s)
- Kevin Francis
- Department of Chemistry, The University of Iowa, Iowa City, IA 52242, United States
| | - Amnon Kohen
- Department of Chemistry, The University of Iowa, Iowa City, IA 52242, United States.
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10
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Behiry EM, Evans RM, Guo J, Loveridge EJ, Allemann RK. Loop interactions during catalysis by dihydrofolate reductase from Moritella profunda. Biochemistry 2014; 53:4769-74. [PMID: 25014120 DOI: 10.1021/bi500508z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Dihydrofolate reductase (DHFR) is often used as a model system to study the relation between protein dynamics and catalysis. We have studied a number of variants of the cold-adapted DHFR from Moritella profunda (MpDHFR), in which the catalytically important M20 and FG loops have been altered, and present a comparison with the corresponding variants of the well-studied DHFR from Escherichia coli (EcDHFR). Mutations in the M20 loop do not affect the actual chemical step of transfer of hydride from reduced nicotinamide adenine dinucleotide phosphate to the substrate 7,8-dihydrofolate in the catalytic cycle in either enzyme; they affect the steady state turnover rate in EcDHFR but not in MpDHFR. Mutations in the FG loop also have different effects on catalysis by the two DHFRs. Despite the two enzymes most likely sharing a common catalytic cycle at pH 7, motions of these loops, known to be important for progression through the catalytic cycle in EcDHFR, appear not to play a significant role in MpDHFR.
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Affiliation(s)
- Enas M Behiry
- School of Chemistry, Cardiff University , Park Place, Cardiff CF10 3AT, United Kingdom
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11
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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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12
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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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13
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Loveridge EJ, Tey LH, Behiry EM, Dawson WM, Evans RM, Whittaker SBM, Günther UL, Williams C, Crump MP, Allemann RK. The role of large-scale motions in catalysis by dihydrofolate reductase. J Am Chem Soc 2011; 133:20561-70. [PMID: 22060818 PMCID: PMC3590880 DOI: 10.1021/ja208844j] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Dihydrofolate reductase has long been used as a model system to study the coupling of protein motions to enzymatic hydride transfer. By studying environmental effects on hydride transfer in dihydrofolate reductase (DHFR) from the cold-adapted bacterium Moritella profunda (MpDHFR) and comparing the flexibility of this enzyme to that of DHFR from Escherichia coli (EcDHFR), we demonstrate that factors that affect large-scale (i.e., long-range, but not necessarily large amplitude) protein motions have no effect on the kinetic isotope effect on hydride transfer or its temperature dependence, although the rates of the catalyzed reaction are affected. Hydrogen/deuterium exchange studies by NMR-spectroscopy show that MpDHFR is a more flexible enzyme than EcDHFR. NMR experiments with EcDHFR in the presence of cosolvents suggest differences in the conformational ensemble of the enzyme. The fact that enzymes from different environmental niches and with different flexibilities display the same behavior of the kinetic isotope effect on hydride transfer strongly suggests that, while protein motions are important to generate the reaction ready conformation, an optimal conformation with the correct electrostatics and geometry for the reaction to occur, they do not influence the nature of the chemical step itself; large-scale motions do not couple directly to hydride transfer proper in DHFR.
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Affiliation(s)
- E Joel Loveridge
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, United Kingdom
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14
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Microsecond Subdomain Folding in Dihydrofolate Reductase. J Mol Biol 2011; 410:329-42. [DOI: 10.1016/j.jmb.2011.04.057] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Revised: 03/19/2011] [Accepted: 04/21/2011] [Indexed: 11/15/2022]
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15
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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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16
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Wang Z, Kohen A. Thymidylate synthase catalyzed H-transfers: two chapters in one tale. J Am Chem Soc 2010; 132:9820-5. [PMID: 20575541 DOI: 10.1021/ja103010b] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Examination of the nature of different bond activations along the same catalytic path is of general interest in chemistry and biology. In this report, we compare the physical nature of two sequential H-transfers in the same enzymatic reaction. Thymidylate synthase (TSase) catalyzes a complex reaction that involves many chemical transformations including two different C-H bond cleavages, a rate-limiting C-H-C hydride transfer and a non-rate-limiting C-H-O proton transfer. Although the large kinetic complexity imposes difficulties in studying the proton transfer catalyzed by TSase, we are able to experimentally extract the intrinsic kinetic isotope effects (KIEs) on both steps. In contrast with the hydride transfer, the intrinsic KIEs of the proton transfer are temperature dependent. The results are interpreted within the framework of the Marcus-like model. This interpretation suggests that TSase optimizes the donor-acceptor geometries for the slower and overall rate-limiting hydride transfer but not for the faster proton transfer.
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Affiliation(s)
- Zhen Wang
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, USA
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17
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Characterization of azido-NAD+ to assess its potential as a two-dimensional infrared probe of enzyme dynamics. Anal Biochem 2010; 407:241-6. [PMID: 20705046 DOI: 10.1016/j.ab.2010.08.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2010] [Accepted: 08/05/2010] [Indexed: 11/23/2022]
Abstract
Enzyme active-site dynamics at femtosecond to picosecond time scales are of great biochemical importance, but remain relatively unexplored due to the lack of appropriate analytical methods. Two-dimensional infrared (2D IR) spectroscopy is one of the few methods that can examine chemical biological motions at this time scale, but all the IR probes used so far were specific to a few unique enzymes. The lack of IR probes of broader specificity is a major limitation to further 2D IR studies of enzyme dynamics. Here we describe the synthesis of a general IR probe for nicotinamide-dependent enzymes. This azido analog of the ubiquitous cofactor nicotinamide adenine dinucleotide is found to be stable and bind to several dehydrogenases with dissociation constants similar to that for the native cofactor. The infrared absorption spectra of this probe bound to several enzymes indicate that it has significant potential as a 2D IR probe to investigate femtosecond dynamics of nicotinamide-dependent enzymes.
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Loveridge EJ, Allemann RK. The temperature dependence of the kinetic isotope effects of dihydrofolate reductase from Thermotoga maritima is influenced by intersubunit interactions. Biochemistry 2010; 49:5390-6. [PMID: 20515024 DOI: 10.1021/bi100761x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Dihydrofolate reductase from the hyperthermophile Thermotoga maritima (TmDHFR) is unique among structurally characterized chromosomal DHFRs in that it forms a stable homodimer. Dimerization is believed to play a key role in the high thermal stability of TmDHFR, which is reflected in a melting temperature in excess of 85 degrees C. The dimer interface of TmDHFR is composed of a hydrophobic core with charged residues around the periphery. In particular, Lys129 of each subunit forms three-membered salt bridges with Glu136 and Glu138 of the other subunit. To probe the role of these salt bridges in the dimerization and thermal stability of TmDHFR, we generated a series of variants (TmDHFR-K129E, TmDHFR-E136K, TmDHFR-E138K, and TmDHFR-E136K/E138K) in which these residues were exchanged for residues whose side chains bear the opposite charge. Our results indicate that these salt bridges are key for the high thermal stability of TmDHFR but are not a requirement for dimerization. Although the rate of dihydrofolate reduction by TmDHFR is not significantly affected by the loss of the K129-E136-E138 salt bridges, changes to the temperature dependence of the kinetic isotope effect on hydride transfer are observed. These changes are in agreement with the proposal that DHFR catalysis may be affected by changes to the conformational ensemble of the enzyme rather than only to the coupling of protein motions to the reaction coordinate.
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Affiliation(s)
- E Joel Loveridge
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, 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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