1
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Lisitsa AE, Sukovatyi LA, Bartsev SI, Deeva AA, Kratasyuk VA, Nemtseva EV. Mechanisms of Viscous Media Effects on Elementary Steps of Bacterial Bioluminescent Reaction. Int J Mol Sci 2021; 22:8827. [PMID: 34445534 PMCID: PMC8396235 DOI: 10.3390/ijms22168827] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 08/06/2021] [Accepted: 08/10/2021] [Indexed: 12/16/2022] Open
Abstract
Enzymes activity in a cell is determined by many factors, among which viscosity of the microenvironment plays a significant role. Various cosolvents can imitate intracellular conditions in vitro, allowing to reduce a combination of different regulatory effects. The aim of the study was to analyze the media viscosity effects on the rate constants of the separate stages of the bacterial bioluminescent reaction. Non-steady-state reaction kinetics in glycerol and sucrose solutions was measured by stopped-flow technique and analyzed with a mathematical model developed in accordance with the sequence of reaction stages. Molecular dynamics methods were applied to reveal the effects of cosolvents on luciferase structure. We observed both in glycerol and in sucrose media that the stages of luciferase binding with flavin and aldehyde, in contrast to oxygen, are diffusion-limited. Moreover, unlike glycerol, sucrose solutions enhanced the rate of an electronically excited intermediate formation. The MD simulations showed that, in comparison with sucrose, glycerol molecules could penetrate the active-site gorge, but sucrose solutions caused a conformational change of functionally important αGlu175 of luciferase. Therefore, both cosolvents induce diffusion limitation of substrates binding. However, in sucrose media, increasing enzyme catalytic constant neutralizes viscosity effects. The activating effect of sucrose can be attributed to its exclusion from the catalytic gorge of luciferase and promotion of the formation of the active site structure favorable for the catalysis.
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Affiliation(s)
- Albert E Lisitsa
- Biophysics Department, Siberian Federal University, Svobodny 79, 660041 Krasnoyarsk, Russia
| | - Lev A Sukovatyi
- Biophysics Department, Siberian Federal University, Svobodny 79, 660041 Krasnoyarsk, Russia
| | - Sergey I Bartsev
- Biophysics Department, Siberian Federal University, Svobodny 79, 660041 Krasnoyarsk, Russia
- The Institute of Biophysics SB RAS, Akademgorodok 50/50, 660036 Krasnoyarsk, Russia
| | - Anna A Deeva
- Biophysics Department, Siberian Federal University, Svobodny 79, 660041 Krasnoyarsk, Russia
| | - Valentina A Kratasyuk
- Biophysics Department, Siberian Federal University, Svobodny 79, 660041 Krasnoyarsk, Russia
- The Institute of Biophysics SB RAS, Akademgorodok 50/50, 660036 Krasnoyarsk, Russia
| | - Elena V Nemtseva
- Biophysics Department, Siberian Federal University, Svobodny 79, 660041 Krasnoyarsk, Russia
- The Institute of Biophysics SB RAS, Akademgorodok 50/50, 660036 Krasnoyarsk, Russia
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2
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Adesina AS, Luk LYP, Allemann RK. Cryo-kinetics Reveal Dynamic Effects on the Chemistry of Human Dihydrofolate Reductase. Chembiochem 2021; 22:2410-2414. [PMID: 33876533 PMCID: PMC8360168 DOI: 10.1002/cbic.202100017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 04/16/2021] [Indexed: 12/03/2022]
Abstract
Effects of isotopic substitution on the rate constants of human dihydrofolate reductase (HsDHFR), an important target for anti‐cancer drugs, have not previously been characterized due to its complex fast kinetics. Here, we report the results of cryo‐measurements of the kinetics of the HsDHFR catalyzed reaction and the effects of protein motion on catalysis. Isotopic enzyme labeling revealed an enzyme KIE (kHLE/kHHE) close to unity above 0 °C; however, the enzyme KIE was increased to 1.72±0.15 at −20 °C, indicating that the coupling of protein motions to the chemical step is minimized under optimal conditions but enhanced at non‐physiological temperatures. The presented cryogenic approach provides an opportunity to probe the kinetics of mammalian DHFRs, thereby laying the foundation for characterizing their transition state structure.
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Affiliation(s)
| | - Louis Y P Luk
- 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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3
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Abstract
We review the adaptations of enzyme activity to different temperatures. Psychrophilic (cold-adapted) enzymes show significantly different activation parameters (lower activation enthalpies and entropies) from their mesophilic counterparts. Furthermore, there is increasing evidence that the temperature dependence of many enzyme-catalyzed reactions is more complex than is widely believed. Many enzymes show curvature in plots of activity versus temperature that is not accounted for by denaturation or unfolding. This is explained by macromolecular rate theory: A negative activation heat capacity for the rate-limiting chemical step leads directly to predictions of temperature optima; both entropy and enthalpy are temperature dependent. Fluctuations in the transition state ensemble are reduced compared to the ground state. We show how investigations combining experiment with molecular simulation are revealing fundamental details of enzyme thermoadaptation that are relevant for understanding aspects of enzyme evolution. Simulations can calculate relevant thermodynamic properties (such as activation enthalpies, entropies, and heat capacities) and reveal the molecular mechanisms underlying experimentally observed behavior.
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Affiliation(s)
- Vickery L Arcus
- School of Science, University of Waikato, Hamilton 3240, New Zealand;
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom;
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4
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Chéron N, Naepels M, Pluhařová E, Laage D. Protein Preferential Solvation in Water:Glycerol Mixtures. J Phys Chem B 2020; 124:1424-1437. [PMID: 31999925 DOI: 10.1021/acs.jpcb.9b11190] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
For proteins in solvent mixtures, the relative abundances of each solvent in their solvation shell have a critical impact on their properties. Preferential solvation of a series of proteins in water-glycerol mixtures is studied here over a broad range of solvent compositions via classical molecular dynamics simulations. Our simulation results reveal that the differences between shell and bulk compositions exhibit dramatic changes with solvent composition, temperature, and protein nature. In contrast with the simple and widely used picture where glycerol is completely excluded from the protein interface, we show that for aqueous solutions with less than 50% glycerol in volume, protein solvation shells have approximately the same composition as the bulk solvent and proteins are in direct contact with glycerol. We further demonstrate that at high glycerol concentration, glycerol depletion from the solvation shell is due to an entropic factor arising from the reduced accessibility of bulky glycerol molecules in protein cavities. The resulting molecular picture is important to understand protein activity and cryopreservation in mixed aqueous solvents.
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Affiliation(s)
- Nicolas Chéron
- PASTEUR, Département de chimie , École Normale Supérieure, PSL University, Sorbonne Université, CNRS , 75005 Paris , France
| | - Margaux Naepels
- PASTEUR, Département de chimie , École Normale Supérieure, PSL University, Sorbonne Université, CNRS , 75005 Paris , France
| | - Eva Pluhařová
- PASTEUR, Département de chimie , École Normale Supérieure, PSL University, Sorbonne Université, CNRS , 75005 Paris , France
| | - Damien Laage
- PASTEUR, Département de chimie , École Normale Supérieure, PSL University, Sorbonne Université, CNRS , 75005 Paris , France
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5
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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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6
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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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7
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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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8
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Ruiz-Pernía JJ, Behiry E, Luk LYP, Loveridge EJ, Tuñón I, Moliner V, Allemann RK. Minimization of dynamic effects in the evolution of dihydrofolate reductase. Chem Sci 2016; 7:3248-3255. [PMID: 29997817 PMCID: PMC6006479 DOI: 10.1039/c5sc04209g] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 02/02/2016] [Indexed: 11/22/2022] Open
Abstract
Protein isotope labeling is a powerful technique to probe functionally important motions in enzyme catalysis and can be applied to investigate the conformational dynamics of proteins. Previous investigations have indicated that dynamic coupling is detrimental to catalysis by dihydrofolate reductase (DHFR) from the mesophile Escherichia coli (EcDHFR). Comparison of DHFRs from organisms adapted to survive at a wide range of temperatures suggests that dynamic coupling in DHFR catalysis has been minimized during evolution; it arises from reorganizational motions needed to facilitate charge transfer events. Contrary to the behaviour observed for the DHFR from the moderate thermophile Geobacillus stearothermophilus (BsDHFR), the chemical transformation catalyzed by the cold-adapted bacterium Moritella profunda (MpDHFR) is only weakly affected by protein isotope substitutions at low temperatures, but the isotopically substituted enzyme is a substantially inferior catalyst at higher, non-physiological temperatures. QM/MM studies revealed that this behaviour is caused by the enzyme's structural sensitivity to temperature changes, which enhances unfavorable dynamic coupling at higher temperatures by promoting additional recrossing trajectories on the transition state dividing surface. We postulate that these motions are minimized by fine-tuning DHFR flexibility through optimization of the free energy surface of the reaction, such that a nearly static reaction-ready configuration with optimal electrostatic properties is maintained under physiological conditions.
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Affiliation(s)
- J Javier Ruiz-Pernía
- Departament de Química Física i Analítica , Universitat Jaume I , 12071 Castelló , Spain .
| | - Enas Behiry
- School of Chemistry & Cardiff Catalysis Institute , Cardiff University , Park Place , Cardiff , CF10 3AT , UK .
| | - Louis Y P Luk
- School of Chemistry & Cardiff Catalysis Institute , Cardiff University , Park Place , Cardiff , CF10 3AT , UK .
| | - E Joel Loveridge
- School of Chemistry & Cardiff Catalysis Institute , Cardiff University , Park Place , Cardiff , CF10 3AT , UK .
| | - Iñaki Tuñón
- Departament de Química Física , Universitat de València , 46100 Burjassot , Spain .
| | - Vicent Moliner
- Departament de Química Física i Analítica , Universitat Jaume I , 12071 Castelló , Spain .
| | - Rudolf K Allemann
- School of Chemistry & Cardiff Catalysis Institute , Cardiff University , Park Place , Cardiff , CF10 3AT , UK .
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9
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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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10
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Sashi P, Bhuyan AK. Viscosity Dependence of Some Protein and Enzyme Reaction Rates: Seventy-Five Years after Kramers. Biochemistry 2015; 54:4453-61. [PMID: 26135219 DOI: 10.1021/acs.biochem.5b00315] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Kramers rate theory is a milestone in chemical reaction research, but concerns regarding the basic understanding of condensed phase reaction rates of large molecules in viscous milieu persist. Experimental studies of Kramers theory rely on scaling reaction rates with inverse solvent viscosity, which is often equated with the bulk friction coefficient based on simple hydrodynamic relations. Apart from the difficulty of abstraction of the prefactor details from experimental data, it is not clear why the linearity of rate versus inverse viscosity, k ∝ η(-1), deviates widely for many reactions studied. In most cases, the deviation simulates a power law k ∝ η(-n), where the exponent n assumes fractional values. In rate-viscosity studies presented here, results for two reactions, unfolding of cytochrome c and cysteine protease activity of human ribosomal protein S4, show an exceedingly overdamped rate over a wide viscosity range, registering n values up to 2.4. Although the origin of this extraordinary reaction friction is not known at present, the results indicate that the viscosity exponent need not be bound by the 0-1 limit as generally suggested. For the third reaction studied here, thermal dissociation of CO from nativelike cytochrome c, the rate-viscosity behavior can be explained using Grote-Hynes theory of time-dependent friction in conjunction with correlated motions intrinsic to the protein. Analysis of the glycerol viscosity-dependent rate for the CO dissociation reaction in the presence of urea as the second variable shows that the protein stabilizing effect of subdenaturing amounts of urea is not affected by the bulk viscosity. It appears that a myriad of factors as diverse as parameter uncertainty due to the difficulty of knowing the exact reaction friction and both mode and consequences of protein-solvent interaction work in a complex manner to convey as though Kramers rate equation is not absolute.
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Affiliation(s)
- Pulikallu Sashi
- School of Chemistry, University of Hyderabad, Hyderabad 500 046, India
| | - Abani K Bhuyan
- School of Chemistry, University of Hyderabad, Hyderabad 500 046, India
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11
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Luk LP, Loveridge EJ, Allemann RK. Different dynamical effects in mesophilic and hyperthermophilic dihydrofolate reductases. J Am Chem Soc 2014; 136:6862-5. [PMID: 24779446 PMCID: PMC4046772 DOI: 10.1021/ja502673h] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Indexed: 01/18/2023]
Abstract
The role of protein dynamics in the reaction catalyzed by dihydrofolate reductase from the hyperthermophile Thermotoga maritima (TmDHFR) has been examined by enzyme isotope substitution ((15)N, (13)C, (2)H). In contrast to all other enzyme reactions investigated previously, including DHFR from Escherichia coli (EcDHFR), for which isotopic substitution led to decreased reactivity, the rate constant for the hydride transfer step is not affected by isotopic substitution of TmDHFR. TmDHFR therefore appears to lack the coupling of protein motions to the reaction coordinate that have been identified for EcDHFR catalysis. Clearly, dynamical coupling is not a universal phenomenon that affects the efficiency of enzyme catalysis.
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Affiliation(s)
- Louis
Y. P. Luk
- School
of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
| | - E. Joel Loveridge
- School
of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
| | - Rudolf K. Allemann
- School
of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
- Cardiff
Catalysis Institute, School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
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12
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Guo J, Luk LYP, Loveridge EJ, Allemann RK. Thermal adaptation of dihydrofolate reductase from the moderate thermophile Geobacillus stearothermophilus. Biochemistry 2014; 53:2855-63. [PMID: 24730604 PMCID: PMC4065160 DOI: 10.1021/bi500238q] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The thermal melting temperature of dihydrofolate reductase from Geobacillus stearothermophilus (BsDHFR) is ~30 °C higher than that of its homologue from the psychrophile Moritella profunda. Additional proline residues in the loop regions of BsDHFR have been proposed to enhance the thermostability of BsDHFR, but site-directed mutagenesis studies reveal that these proline residues contribute only minimally. Instead, the high thermal stability of BsDHFR is partly due to removal of water-accessible thermolabile residues such as glutamine and methionine, which are prone to hydrolysis or oxidation at high temperatures. The extra thermostability of BsDHFR can be obtained by ligand binding, or in the presence of salts or cosolvents such as glycerol and sucrose. The sum of all these incremental factors allows BsDHFR to function efficiently in the natural habitat of G. stearothermophilus, which is characterized by temperatures that can reach 75 °C.
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Affiliation(s)
- Jiannan Guo
- School of Chemistry, Cardiff University , Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
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13
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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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14
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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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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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Nagel ZD, Klinman JP. Update 1 of: Tunneling and dynamics in enzymatic hydride transfer. Chem Rev 2010; 110:PR41-67. [PMID: 21141912 PMCID: PMC4067601 DOI: 10.1021/cr1001035] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Zachary D. Nagel
- Departments of Chemistry and of Molecular and Cell Biology and the
California Institute for Quantitative Biosciences, University of California,
Berkeley, California 94720
| | - Judith P. Klinman
- Departments of Chemistry and of Molecular and Cell Biology and the
California Institute for Quantitative Biosciences, University of California,
Berkeley, California 94720
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17
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Nashine VC, Hammes-Schiffer S, Benkovic SJ. Coupled motions in enzyme catalysis. Curr Opin Chem Biol 2010; 14:644-51. [PMID: 20729130 DOI: 10.1016/j.cbpa.2010.07.020] [Citation(s) in RCA: 137] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2010] [Revised: 07/14/2010] [Accepted: 07/24/2010] [Indexed: 10/19/2022]
Abstract
Recently, the hypothesis that protein motions are involved in enzymatic turnover has gained significant attention. We review cases where there is evidence that protein motions are rate-limiting in the overall catalytic cycle and examine experimental and theoretical evidence for how such motions enhance the probability of sampling the transition state configurations relative to the ground state. The impact of tunneling, the possible role of vibrational coupling and the value of conformational chemical landscapes are also scrutinized.
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Affiliation(s)
- Vishal C Nashine
- Department of Chemistry, The Pennsylvania State University, 414 Wartik Laboratory, University Park, PA 16802, USA
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18
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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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19
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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: 44] [Impact Index Per Article: 3.1] [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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20
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Loveridge EJ, Maglia G, Allemann RK. The role of arginine 28 in catalysis by dihydrofolate reductase from the hyperthermophile Thermotoga maritima. Chembiochem 2010; 10:2624-7. [PMID: 19816891 DOI: 10.1002/cbic.200900465] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- E Joel Loveridge
- School of Chemistry, Cardiff University, Park Place, Cardiff, CF10 3AT, UK
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21
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Heyes DJ, Sakuma M, Scrutton NS. Solvent-slaved protein motions accompany proton but not hydride tunneling in light-activated protochlorophyllide oxidoreductase. Angew Chem Int Ed Engl 2009; 48:3850-3. [PMID: 19373814 DOI: 10.1002/anie.200900086] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
H(+) but not H(-): The reduction reaction of protochlorophyllide catalyzed by protochlorophyllide oxidoreductase features solvent-slaved motions that control the proton- but not the hydride-tunneling mechanism. These motions imply a long-range dynamic network from the solvent to the enzyme active site that facilitate proton transfer (see picture, left). Motions for hydride transfer are more localized and are not slaved by the solvent (see picture, right).
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Affiliation(s)
- Derren J Heyes
- Manchester Interdisciplinary Biocentre, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
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22
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Loveridge EJ, Rodriguez RJ, Swanwick RS, Allemann RK. Effect of Dimerization on the Stability and Catalytic Activity of Dihydrofolate Reductase from the Hyperthermophile Thermotoga maritima. Biochemistry 2009; 48:5922-33. [DOI: 10.1021/bi900411a] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- E. Joel Loveridge
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT, United Kingdom
| | - Robert J. Rodriguez
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT, United Kingdom
| | - Richard S. Swanwick
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT, United Kingdom
| | - Rudolf K. Allemann
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT, United Kingdom
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23
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Heyes D, Sakuma M, Scrutton N. Solvent-Slaved Protein Motions Accompany Proton but Not Hydride Tunneling in Light-Activated Protochlorophyllide Oxidoreductase. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200900086] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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24
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Loveridge EJ, Behiry EM, Swanwick RS, Allemann RK. Different Reaction Mechanisms for Mesophilic and Thermophilic Dihydrofolate Reductases. J Am Chem Soc 2009; 131:6926-7. [DOI: 10.1021/ja901441k] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- E. Joel Loveridge
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT, U.K
| | - Enas M. Behiry
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT, U.K
| | - Richard S. Swanwick
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT, U.K
| | - Rudolf K. Allemann
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT, U.K
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25
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Abstract
Much work has gone into understanding the physical basis of the enormous catalytic power of enzymes over the last 50 years or so. Nevertheless, the detailed mechanism used by Nature's catalysts to speed chemical transformations remains elusive. DHFR (dihydrofolate reductase) has served as a paradigm to study the relationship between the structure, function and dynamics of enzymatic transformations. A complex reaction cascade, which involves rearrangements and movements of loops and domains of the enzyme, is used to orientate cofactor and substrate in a reactive configuration from which hydride is transferred by quantum mechanical tunnelling. In the present paper, we review results from experiments that probe the influence of protein dynamics on the chemical step of the reaction catalysed by TmDHFR (DHFR from Thermotoga maritima). This enzyme appears to have evolved an optimal structure that can maintain a catalytically competent conformation under extreme conditions.
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