1
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Hill TD, Basnet S, Lepird HH, Rightnowar BW, Moran SD. Anisotropic dynamics of an interfacial enzyme active site observed using tethered substrate analogs and ultrafast 2D IR spectroscopy. J Chem Phys 2023; 159:165101. [PMID: 37870142 PMCID: PMC10597647 DOI: 10.1063/5.0167991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 09/29/2023] [Indexed: 10/24/2023] Open
Abstract
Enzymes accelerate the rates of biomolecular reactions by many orders of magnitude compared to bulk solution, and it is widely understood that this catalytic effect arises from a combination of polar pre-organization and electrostatic transition state stabilization. A number of recent reports have also implicated ultrafast (femtosecond-picosecond) timescale motions in enzymatic activity. However, complications arising from spatially-distributed disorder, the occurrence of multiple substrate binding modes, and the influence of hydration dynamics on solvent-exposed active sites still confound many experimental studies. Here we use ultrafast two-dimensional infrared (2D IR) spectroscopy and covalently-tethered substrate analogs to examine dynamical properties of the promiscuous Pyrococcus horikoshii ene-reductase (PhENR) active site in two binding configurations mimicking proposed "inactive" and "reactive" Michaelis complexes. Spectral diffusion measurements of aryl-nitrile substrate analogs reveal an end-to-end tradeoff between fast (sub-ps) and slow (>5 ps) motions. Fermi resonant aryl-azide analogs that sense interactions of coupled oscillators are described. Lineshape and quantum beat analyses of these probes reveal characteristics that correlate with aryl-nitrile frequency fluctuation correlation functions parameters, demonstrating that this anisotropy is an intrinsic property of the water-exposed active site, where countervailing gradients of fast dynamics and disorder in the reactant ground state are maintained near the hydration interface. Our results suggest several plausible factors leading to state-selective rate enhancement and promiscuity in PhENR. This study also highlights a strategy to detect perturbations to vibrational modes outside the transparent window of the mid-IR spectrum, which may be extended to other macromolecular systems.
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Affiliation(s)
| | - Sunil Basnet
- School of Chemical and Biomolecular Sciences, Southern Illinois University Carbondale, 1245 Lincoln Drive MC 4409, Carbondale, Illinois 62901, USA
| | - Hannah H. Lepird
- School of Chemical and Biomolecular Sciences, Southern Illinois University Carbondale, 1245 Lincoln Drive MC 4409, Carbondale, Illinois 62901, USA
| | - Blaze W. Rightnowar
- School of Chemical and Biomolecular Sciences, Southern Illinois University Carbondale, 1245 Lincoln Drive MC 4409, Carbondale, Illinois 62901, USA
| | - Sean D. Moran
- School of Chemical and Biomolecular Sciences, Southern Illinois University Carbondale, 1245 Lincoln Drive MC 4409, Carbondale, Illinois 62901, USA
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2
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Bai M, Pratap R, Salarvand S, Lu Y. Correlation of temperature dependence of hydride kinetic isotope effects with donor-acceptor distances in two solvents of different polarities. Org Biomol Chem 2023; 21:5090-5097. [PMID: 37278324 PMCID: PMC10339711 DOI: 10.1039/d3ob00718a] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Recently observed nearly temperature (T)-independent kinetic isotope effects (KIEs) in wild-type enzymes and T-dependent KIEs in variants were used to suggest that H-tunneling in enzymes is assisted by the fast protein vibrations that help sample short donor-acceptor distances (DADs). This supports the recently proposed role of protein vibrations in DAD sampling catalysis. However, use of T-dependence of KIEs to suggest DAD sampling associated with protein vibrations is debated. We have formulated a hypothesis regarding the correlation and designed experiments in solution to investigate it. The hypothesis is, a more rigid system with shorter DADTRS's at the tunneling ready states (TRSs) gives rise to a weaker T-dependence of KIEs, i.e., a smaller ΔEa (= EaD - EaH). In a former work, the solvent effects of acetonitrile versus chloroform on the ΔEa of NADH/NAD+ model reactions were determined, and the DADPRC's of the productive reactant complexes (PRCs) were computed to substitute the DADTRS for the DADTRS-ΔEa correlation study. A smaller ΔEa was found in the more polar acetonitrile where the positively charged PRC is better solvated and has a shorter DADPRC, indirectly supporting the hypothesis. In this work, the TRS structures of different DADTRS's for the hydride tunneling reaction from 1,3-dimethyl-2-phenylimidazoline to 10-methylacridinium were computed. The N-CH3/CD3 secondary KIEs on both reactants were calculated and fitted to the observed values to find the DADTRS order in both solutions. It was found that the equilibrium DADTRS is shorter in acetonitrile than in chloroform. Results directly support the DADTRS-ΔEa correlation hypothesis as well as the explanation that links T-dependence of KIEs to DAD sampling catalysis in enzymes.
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Affiliation(s)
- Mingxuan Bai
- Department of Chemistry, Southern Illinois University Edwardsville, Edwardsville, Illinois 62026, USA.
| | - Rijal Pratap
- Department of Chemistry, Southern Illinois University Edwardsville, Edwardsville, Illinois 62026, USA.
| | - Sanaz Salarvand
- Department of Chemistry, Southern Illinois University Edwardsville, Edwardsville, Illinois 62026, USA.
| | - Yun Lu
- Department of Chemistry, Southern Illinois University Edwardsville, Edwardsville, Illinois 62026, USA.
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3
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Banik S, Sansi AK, Nandan S, Roy TK. On the Proton Shuttle Motion in Protonated Acetylene: An Electronic Structure Perspective. ChemistrySelect 2020. [DOI: 10.1002/slct.202002524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Subrata Banik
- Department of ChemistrySchool of Chemical and BiotechnologySASTRA Deemed University Thanjavur 613401 Tamilnadu India
| | - Ankit Kumar Sansi
- Department of Chemistry and Chemical SciencesCentral University of Jammu, Rahya-Suchani (Bagla) Jammu 180011 India
| | - Shiv Nandan
- Department of Chemistry and Chemical SciencesCentral University of Jammu, Rahya-Suchani (Bagla) Jammu 180011 India
| | - Tapta Kanchan Roy
- Department of Chemistry and Chemical SciencesCentral University of Jammu, Rahya-Suchani (Bagla) Jammu 180011 India
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4
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Kohen A. Kinetic Isotope Effects as Probes for Hydrogen Tunneling, Coupled Motion and Dynamics Contributions to Enzyme Catalysis. PROGRESS IN REACTION KINETICS AND MECHANISM 2019. [DOI: 10.3184/007967403103165486] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Since the early days of enzymology attempts have been made to deconvolute the various contributions of physical phenomena to enzyme catalysis. Here we present experimental and theoretical studies that examine the possible role of hydrogen tunneling, coupled motion, and enzyme dynamics in catalysis. In this review, we first introduce basic concepts of enzyme catalysis from a physical chemistry point of view. Then, we present several recent developments in the application of experimental tools that can probe tunneling, coupled motion, dynamic effects and other possible physical phenomena that may contribute to catalysis. These tools include kinetic isotope effects (KIEs), their temperature dependency and H/D/T mutual relations (the Swain–Schaad relationship). Several theories and models that assist in understanding those phenomena are also described. The possibility that these models invoke a direct role for the enzyme's dynamics (environmental fluctuations and rearrangements) is discussed. Finally, the need to compare the enzymatic reaction to the uncatalyzed one while investigating contributions to catalysis is emphasised.
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Affiliation(s)
- Amnon Kohen
- Department of Chemistry, University of Iowa, Iowa City, IA 52242, USA
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5
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Kulkarni Y, Liao Q, Petrović D, Krüger DM, Strodel B, Amyes TL, Richard JP, Kamerlin SCL. Enzyme Architecture: Modeling the Operation of a Hydrophobic Clamp in Catalysis by Triosephosphate Isomerase. J Am Chem Soc 2017; 139:10514-10525. [PMID: 28683550 PMCID: PMC5543394 DOI: 10.1021/jacs.7b05576] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Indexed: 12/22/2022]
Abstract
Triosephosphate isomerase (TIM) is a proficient catalyst of the reversible isomerization of dihydroxyacetone phosphate (DHAP) to d-glyceraldehyde phosphate (GAP), via general base catalysis by E165. Historically, this enzyme has been an extremely important model system for understanding the fundamentals of biological catalysis. TIM is activated through an energetically demanding conformational change, which helps position the side chains of two key hydrophobic residues (I170 and L230), over the carboxylate side chain of E165. This is critical both for creating a hydrophobic pocket for the catalytic base and for maintaining correct active site architecture. Truncation of these residues to alanine causes significant falloffs in TIM's catalytic activity, but experiments have failed to provide a full description of the action of this clamp in promoting substrate deprotonation. We perform here detailed empirical valence bond calculations of the TIM-catalyzed deprotonation of DHAP and GAP by both wild-type TIM and its I170A, L230A, and I170A/L230A mutants, obtaining exceptional quantitative agreement with experiment. Our calculations provide a linear free energy relationship, with slope 0.8, between the activation barriers and Gibbs free energies for these TIM-catalyzed reactions. We conclude that these clamping side chains minimize the Gibbs free energy for substrate deprotonation, and that the effects on reaction driving force are largely expressed at the transition state for proton transfer. Our combined analysis of previous experimental and current computational results allows us to provide an overview of the breakdown of ground-state and transition state effects in enzyme catalysis in unprecedented detail, providing a molecular description of the operation of a hydrophobic clamp in triosephosphate isomerase.
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Affiliation(s)
- Yashraj
S. Kulkarni
- Science
for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, Uppsala S-751 24, Sweden
| | - Qinghua Liao
- Science
for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, Uppsala S-751 24, Sweden
| | - Dušan Petrović
- Institute
of Complex Systems: Structural Biochemistry, Forschungszentrum Jülich, Jülich 52425, Germany
| | - Dennis M. Krüger
- Science
for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, Uppsala S-751 24, Sweden
| | - Birgit Strodel
- Institute
of Complex Systems: Structural Biochemistry, Forschungszentrum Jülich, Jülich 52425, Germany
- Institute
of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Universitätsstrasse 1, Düsseldorf 40225, Germany
| | - Tina L. Amyes
- Department
of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - John P. Richard
- Department
of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - Shina C. L. Kamerlin
- Science
for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, Uppsala S-751 24, Sweden
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6
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Lu X, Ovchinnikov V, Demapan D, Roston D, Cui Q. Regulation and Plasticity of Catalysis in Enzymes: Insights from Analysis of Mechanochemical Coupling in Myosin. Biochemistry 2017; 56:1482-1497. [PMID: 28225609 DOI: 10.1021/acs.biochem.7b00016] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The mechanism of ATP hydrolysis in the myosin motor domain is analyzed using a combination of DFTB3/CHARMM simulations and enhanced sampling techniques. The motor domain is modeled in the pre-powerstroke state, in the post-rigor state, and as a hybrid based on the post-rigor state with a closed nucleotide-binding pocket. The ATP hydrolysis activity is found to depend on the positioning of nearby water molecules, and a network of polar residues facilitates proton transfer and charge redistribution during hydrolysis. Comparison of the observed hydrolysis pathways and the corresponding free energy profiles leads to detailed models for the mechanism of ATP hydrolysis in the pre-powerstroke state and proposes factors that regulate the hydrolysis activity in different conformational states. In the pre-powerstroke state, the scissile Pγ-O3β bond breaks early in the reaction. Proton transfer from the lytic water to the γ-phosphate through active site residues is an important part of the kinetic bottleneck; several hydrolysis pathways that feature distinct proton transfer routes are found to have similar free energy barriers, suggesting a significant degree of plasticity in the hydrolysis mechanism. Comparison of hydrolysis in the pre-powerstroke state and the closed post-rigor model suggests that optimization of residues beyond the active site for electrostatic stabilization and preorganization is likely important to enzyme design.
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Affiliation(s)
- Xiya Lu
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Victor Ovchinnikov
- Department of Chemistry and Chemical Biology, Harvard University , 12 Oxford Street, Boston, Massachusetts 02138, United States
| | - Darren Demapan
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Daniel Roston
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Qiang Cui
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
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7
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Liu LL, Wang Y, Chen CP, Yu HX, Zhao LS, Wang XC. Tuning the electronic and magnetic properties of penta-graphene using a hydrogen atom: a theoretical study. RSC Adv 2017. [DOI: 10.1039/c7ra06956a] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Through changing the adsorption configuration of the hydrogen atom, we can remarkably increase the magnetic moment of penta-graphene by 137 times.
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Affiliation(s)
- Lin-Lin Liu
- Institute of Atomic and Molecular Physics
- Jilin University
- Changchun
- China
- Jilin Provincial Key Laboratory of Applied Atomic and Molecular Spectroscopy
| | - Ying Wang
- Institute of Atomic and Molecular Physics
- Jilin University
- Changchun
- China
- Jilin Provincial Key Laboratory of Applied Atomic and Molecular Spectroscopy
| | - Chun-Ping Chen
- Institute of Atomic and Molecular Physics
- Jilin University
- Changchun
- China
- Jilin Provincial Key Laboratory of Applied Atomic and Molecular Spectroscopy
| | - Hong-Xia Yu
- Institute of Atomic and Molecular Physics
- Jilin University
- Changchun
- China
- Jilin Provincial Key Laboratory of Applied Atomic and Molecular Spectroscopy
| | - Lu-Si Zhao
- Institute of Atomic and Molecular Physics
- Jilin University
- Changchun
- China
- Jilin Provincial Key Laboratory of Applied Atomic and Molecular Spectroscopy
| | - Xiao-Chun Wang
- Institute of Atomic and Molecular Physics
- Jilin University
- Changchun
- China
- Jilin Provincial Key Laboratory of Applied Atomic and Molecular Spectroscopy
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8
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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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9
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Wide-dynamic-range kinetic investigations of deep proton tunnelling in proteins. Nat Chem 2016; 8:874-80. [PMID: 27554414 DOI: 10.1038/nchem.2527] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 04/14/2016] [Indexed: 11/08/2022]
Abstract
Directional proton transport along 'wires' that feed biochemical reactions in proteins is poorly understood. Amino-acid residues with high pKa are seldom considered as active transport elements in such wires because of their large classical barrier for proton dissociation. Here, we use the light-triggered proton wire of the green fluorescent protein to study its ground-electronic-state proton-transport kinetics, revealing a large temperature-dependent kinetic isotope effect. We show that 'deep' proton tunnelling between hydrogen-bonded oxygen atoms with a typical donor-acceptor distance of 2.7-2.8 Å fully accounts for the rates at all temperatures, including the unexpectedly large value (2.5 × 10(9) s(-1)) found at room temperature. The rate-limiting step in green fluorescent protein is assigned to tunnelling of the ionization-resistant serine hydroxyl proton. This suggests how high-pKa residues within a proton wire can act as a 'tunnel diode' to kinetically trap protons and control the direction of proton flow.
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10
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Peters B. Transition-State Theory, Dynamics, and Narrow Time Scale Separation in the Rate-Promoting Vibrations Model of Enzyme Catalysis. J Chem Theory Comput 2015; 6:1447-54. [PMID: 26615681 DOI: 10.1021/ct100051a] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The power of transition-state theory (TST) for understanding enzymes is evidenced by its recent use in the design and synthesis of highly active de novo enzymes. However, dynamics can influence reaction kinetics, and some studies of rate-promoting vibrations even claim that dynamical theories instead of TST are needed to understand enzymatic reaction mechanisms. For the rate-promoting vibration (RPV) model of enzyme catalysis [Antoniou et al., J. Chem. Phys. 2004, 121, 6442], a reactive flux correlation function analysis shows that dynamical effects do slow the kinetics. However, the RPV model also shows extremely long-lived correlations because the RPV and the bath are not directly coupled. Additionally, earlier studies of the RPV model show a narrow time scale separation due to a small 5kT barrier. Thus earlier findings based on the RPV model may have little bearing on the properties of real enzymes. The intrinsic reaction coordinate (IRC) reveals that the RPV is an important component of the reaction coordinate at early and late stages of the pathway, but the RPV is not an important component of the reaction coordinate direction at the transition state. The unstable eigenmode from harmonic TST (which coincides with the IRC at the saddle point) gives a larger transmission coefficient than the coordinate used in the correlation functions of Antoniou et al. Thus while TST cannot predict the transmission coefficient, the RPV model suggests that TST can provide mechanistic insights on elementary steps in enzyme catalysis. Finally, we propose a method for using the transition-state ensemble as predicted from harmonic TST to distinguish promoting vibrations from other more mundane bath variables.
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Affiliation(s)
- Baron Peters
- Departments of Chemical Engineering and Chemistry and Biochemistry, University of California, Santa Barbara, California 93106
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11
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Tuñón I, Laage D, Hynes JT. Are there dynamical effects in enzyme catalysis? Some thoughts concerning the enzymatic chemical step. Arch Biochem Biophys 2015; 582:42-55. [PMID: 26087289 PMCID: PMC4560206 DOI: 10.1016/j.abb.2015.06.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 06/05/2015] [Accepted: 06/06/2015] [Indexed: 11/21/2022]
Abstract
We offer some thoughts on the much debated issue of dynamical effects in enzyme catalysis, and more specifically on their potential role in the acceleration of the chemical step. Since the term 'dynamics' has been used with different meanings, we find it useful to first return to the Transition State Theory rate constant, its assumptions and the choices it involves, and detail the various sources of deviations from it due to dynamics (or not). We suggest that much can be learned about the key current questions for enzyme catalysis from prior extensive studies of dynamical and other effects in the case of reactions in solution. We analyze dynamical effects both in the neighborhood of the transition state and far from it, together with the situation when quantum nuclear motion is central to the reaction, and we illustrate our discussion with various examples of enzymatic reactions.
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Affiliation(s)
- Iñaki Tuñón
- Departamento de Química Física, Universidad de Valencia, Spain.
| | - Damien Laage
- Ecole Normale Supérieure-PSL Research University, Chemistry Department, Sorbonne Universités-UPMC University Paris 06, CNRS UMR 8640 Pasteur, 24 rue Lhomond, 75005 Paris, France.
| | - James T Hynes
- Ecole Normale Supérieure-PSL Research University, Chemistry Department, Sorbonne Universités-UPMC University Paris 06, CNRS UMR 8640 Pasteur, 24 rue Lhomond, 75005 Paris, France; Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309-0215, USA.
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12
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Luk LYP, Ruiz-Pernía JJ, Adesina AS, Loveridge EJ, Tuñón I, Moliner V, Allemann RK. Chemical Ligation and Isotope Labeling to Locate Dynamic Effects during Catalysis by Dihydrofolate Reductase. Angew Chem Int Ed Engl 2015; 54:9016-20. [PMID: 26079622 PMCID: PMC4985705 DOI: 10.1002/anie.201503968] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Indexed: 11/21/2022]
Abstract
Chemical ligation has been used to alter motions in specific regions of dihydrofolate reductase from E. coli and to investigate the effects of localized motional changes on enzyme catalysis. Two isotopic hybrids were prepared; one with the mobile N-terminal segment containing heavy isotopes ((2) H, (13) C, (15) N) and the remainder of the protein with natural isotopic abundance, and the other one with only the C-terminal segment isotopically labeled. Kinetic investigations indicated that isotopic substitution of the N-terminal segment affected only a physical step of catalysis, whereas the enzyme chemistry was affected by protein motions from the C-terminal segment. QM/MM studies support the idea that dynamic effects on catalysis mostly originate from the C-terminal segment. The use of isotope hybrids provides insights into the microscopic mechanism of dynamic coupling, which is difficult to obtain with other studies, and helps define the dynamic networks of intramolecular interactions central to enzyme catalysis.
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Affiliation(s)
- Louis Y P Luk
- School of Chemistry, Cardiff University, Park Place, Cardiff, CF10 3AT (UK)
| | - J Javier Ruiz-Pernía
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castelló (Spain)
| | | | - E Joel Loveridge
- School of Chemistry, Cardiff University, Park Place, Cardiff, CF10 3AT (UK)
| | - Iñaki Tuñón
- Departament de Química Física, Universitat de València, 46100 Burjassot (Spain).
| | - Vincent Moliner
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castelló (Spain).
| | - Rudolf K Allemann
- School of Chemistry, Cardiff University, Park Place, Cardiff, CF10 3AT (UK).
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13
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Luk LYP, Ruiz-Pernía JJ, Adesina AS, Loveridge EJ, Tuñón I, Moliner V, Allemann RK. Chemical Ligation and Isotope Labeling to Locate Dynamic Effects during Catalysis by Dihydrofolate Reductase. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201503968] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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14
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Luk LYP, Ruiz-Pernía JJ, Dawson WM, Loveridge EJ, Tuñón I, Moliner V, Allemann RK. Protein isotope effects in dihydrofolate reductase from Geobacillus stearothermophilus show entropic-enthalpic compensatory effects on the rate constant. J Am Chem Soc 2014; 136:17317-23. [PMID: 25396728 DOI: 10.1021/ja5102536] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Catalysis by dihydrofolate reductase from the moderately thermophilic bacterium Geobacillus stearothermophilus (BsDHFR) was investigated by isotope substitution of the enzyme. The enzyme kinetic isotope effect for hydride transfer was close to unity at physiological temperatures but increased with decreasing temperatures to a value of 1.65 at 5 °C. This behavior is opposite to that observed for DHFR from Escherichia coli (EcDHFR), where the enzyme kinetic isotope effect increased slightly with increasing temperature. These experimental results were reproduced in the framework of variational transition-state theory that includes a dynamical recrossing coefficient that varies with the mass of the protein. Our simulations indicate that BsDHFR has greater flexibility than EcDHFR on the ps-ns time scale, which affects the coupling of the environmental motions of the protein to the chemical coordinate and consequently to the recrossing trajectories on the reaction barrier. The intensity of the dynamic coupling in DHFRs is influenced by compensatory temperature-dependent factors, namely the enthalpic barrier needed to achieve an ideal transition-state configuration with minimal nonproductive trajectories and the protein disorder that disrupts the electrostatic preorganization required to stabilize the transition state. Together with our previous studies of other DHFRs, the results presented here provide a general explanation why protein dynamic effects vary between enzymes. Our theoretical treatment demonstrates that these effects can be satisfactorily reproduced by including a transmission coefficient in the rate constant calculation, whose dependence on temperature is affected by the protein flexibility.
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Affiliation(s)
- Louis Y P Luk
- School of Chemistry and ∥Cardiff Catalysis Institute, School of Chemistry, Cardiff University , Park Place, Cardiff, CF10 3AT, United Kingdom
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15
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Yahashiri A, Rubach JK, Plapp BV. Effects of cavities at the nicotinamide binding site of liver alcohol dehydrogenase on structure, dynamics and catalysis. Biochemistry 2014; 53:881-94. [PMID: 24437493 PMCID: PMC3969020 DOI: 10.1021/bi401583f] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
![]()
A role
for protein dynamics in enzymatic catalysis of hydrogen
transfer has received substantial scientific support, but the connections
between protein structure and catalysis remain to be established.
Valine residues 203 and 207 are at the binding site for the nicotinamide
ring of the coenzyme in liver alcohol dehydrogenase and have been
suggested to facilitate catalysis with “protein-promoting vibrations”
(PPV). We find that the V207A substitution has small effects on steady-state
kinetic constants and the rate of hydrogen transfer; the introduced
cavity is empty and is tolerated with minimal effects on structure
(determined at 1.2 Å for the complex with NAD+ and
2,3,4,5,6-pentafluorobenzyl alcohol). Thus, no evidence is found to
support a role for Val-207 in the dynamics of catalysis. The protein
structures and ligand geometries (including donor–acceptor
distances) in the V203A enzyme complexed with NAD+ and
2,3,4,5,6-pentafluorobenzyl alcohol or 2,2,2-trifluoroethanol (determined
at 1.1 Å) are very similar to those for the wild-type enzyme,
except that the introduced cavity accommodates a new water molecule
that contacts the nicotinamide ring. The structures of the V203A enzyme
complexes suggest, in contrast to previous studies, that the diminished
tunneling and decreased rate of hydride transfer (16-fold, relative
to that of the wild-type enzyme) are not due to differences in ground-state
ligand geometries. The V203A substitution may alter the PPV and the
reorganization energy for hydrogen transfer, but the protein scaffold
and equilibrium thermal motions within the Michaelis complex may be
more significant for enzyme catalysis.
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Affiliation(s)
- Atsushi Yahashiri
- Department of Biochemistry, The University of Iowa , Iowa City, Iowa 52242-1109, United States
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17
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Fan Y, Cembran A, Ma S, Gao J. Connecting protein conformational dynamics with catalytic function as illustrated in dihydrofolate reductase. Biochemistry 2013; 52:2036-49. [PMID: 23297871 DOI: 10.1021/bi301559q] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Combined quantum mechanics/molecular mechanics molecular dynamics simulations reveal that the M20 loop conformational dynamics of dihydrofolate reductase (DHFR) is severely restricted at the transition state of the hydride transfer as a result of the M42W/G121V double mutation. Consequently, the double-mutant enzyme has a reduced entropy of activation, i.e., increased entropic barrier, and altered temperature dependence of kinetic isotope effects in comparison with those of wild-type DHFR. Interestingly, in both wild-type DHFR and the double mutant, the average donor-acceptor distances are essentially the same in the Michaelis complex state (~3.5 Å) and the transition state (2.7 Å). It was found that an additional hydrogen bond is formed to stabilize the M20 loop in the closed conformation in the M42W/G121V double mutant. The computational results reflect a similar aim designed to knock out precisely the dynamic flexibility of the M20 loop in a different double mutant, N23PP/S148A.
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Affiliation(s)
- Yao Fan
- Department of Chemistry, Digital Technology Center, and Supercomputing Institute, University of Minnesota , 207 Pleasant Street Southeast, Minneapolis, Minnesota 55455, United States
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18
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Abstract
This chapter discusses progress over the past 15 years in understanding the role of protein dynamics in enzymatically catalyzed chemical reactions. Research has shown that protein motion on all timescales from femtoseconds to milliseconds can contribute to function, and in particular in some enzymes there are sub-picosecond motions, on the same timescale as barrier passage, the couple directly to chemical transformation, and are thus part of the reaction coordinate. Approaches such as transition path sampling and committor analysis have greatly enhanced our understanding of these processes.
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Affiliation(s)
- Steven D Schwartz
- Department of Chemistry, University of Arizona, 1306 East University Blvd., Tucson, AZ, 85721, USA,
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19
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Mai BK, Park K, Duong MPT, Kim Y. Proton Transfer Dependence on Hydrogen-Bonding of Solvent to the Water Wire: A Theoretical Study. J Phys Chem B 2012; 117:307-15. [DOI: 10.1021/jp310724g] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Binh Khanh Mai
- Department
of Applied Chemistry, Kyung Hee University, 1 Seochun-Dong,
Giheung-Gu, Yongin-Si, Gyeonggi-Do, 446-701, Korea
| | - Kisoo Park
- Department
of Applied Chemistry, Kyung Hee University, 1 Seochun-Dong,
Giheung-Gu, Yongin-Si, Gyeonggi-Do, 446-701, Korea
| | - My Phu Thi Duong
- Department
of Applied Chemistry, Kyung Hee University, 1 Seochun-Dong,
Giheung-Gu, Yongin-Si, Gyeonggi-Do, 446-701, Korea
| | - Yongho Kim
- Department
of Applied Chemistry, Kyung Hee University, 1 Seochun-Dong,
Giheung-Gu, Yongin-Si, Gyeonggi-Do, 446-701, Korea
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20
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Alavi S, Taghikhani M. Proton exchange in acid–base complexes induced by reaction coordinates with heavy atom motions. Chem Phys 2012. [DOI: 10.1016/j.chemphys.2012.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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21
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Nachimuthu S, Gao J, Truhlar DG. A Benchmark Test Suite for Proton Transfer Energies and its Use to Test Electronic Structure Model Chemistries. Chem Phys 2012; 400:8-12. [PMID: 23230346 PMCID: PMC3516617 DOI: 10.1016/j.chemphys.2012.01.014] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We present benchmark calculations of nine selected points on potential energy surfaces describing proton transfer process in three model systems, H(5)O(2) (+), CH(3)OH…H(+)…OH(2), and CH(3)COOH…OH(2). The calculated relative energies of these geometries are compared to those calculated by various wave function and density functional methods, including the polarized molecular orbital (PMO) model recently developed in our research group and other semiempirical molecular orbital methods. We found that the SCC-DFTB and PMO methods (the latter available so far only for molecules consisting of only O and H and therefore only for the first of the three model systems) give results that are, on average, within 2 kcal/mol of the benchmark results. Other semiempirical molecular orbital methods have mean unsigned errors (MUEs) of 3 to 8 kcal/mol, local density functionals have MUEs in the range 0.7 to 3.7 kcal/mol, and hybrid density functionals have MUEs of only 0.3 to 1.0 kcal/mol, with the best density functional performance obtained by hybrid meta-GGAs, especially M06 and PW6B95.
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Affiliation(s)
- Santhanamoorthi Nachimuthu
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, MN 55455-0431
| | - Jiali Gao
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, MN 55455-0431
| | - Donald G Truhlar
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, MN 55455-0431
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22
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Karton A, O’Reilly RJ, Radom L. Assessment of Theoretical Procedures for Calculating Barrier Heights for a Diverse Set of Water-Catalyzed Proton-Transfer Reactions. J Phys Chem A 2012; 116:4211-21. [DOI: 10.1021/jp301499y] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Amir Karton
- School of
Chemistry and ARC Centre of Excellence for
Free Radical Chemistry and Biotechnology, University of Sydney, Sydney, NSW 2006, Australia
| | - Robert J. O’Reilly
- School of
Chemistry and ARC Centre of Excellence for
Free Radical Chemistry and Biotechnology, University of Sydney, Sydney, NSW 2006, Australia
| | - Leo Radom
- School of
Chemistry and ARC Centre of Excellence for
Free Radical Chemistry and Biotechnology, University of Sydney, Sydney, NSW 2006, Australia
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23
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24
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Antoniou D, Schwartz SD. Protein dynamics and enzymatic chemical barrier passage. J Phys Chem B 2011; 115:15147-58. [PMID: 22031954 DOI: 10.1021/jp207876k] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
After many decades of investigation, the manner in which enzymes increase the rate of chemical reactions, at times by a factor of 10(17) compared to the rate of the corresponding solution phase reaction, is still opaque. A topic of significant discussion in the literature of the past 5-10 years has been the importance of protein dynamics in this process. This Feature Article will discuss the authors' work on this still controversial topic with focus on both methodology and application to real systems. The end conclusion of this work has been that for specific enzymes under study protein dynamics on both rapid time scales of barrier crossing (termed promoting vibrations by the authors) and of conformational fluctuations are central to the function of biological catalysts. In another enzyme we will discuss, the results are far less clear. The manner of the coupling of chemistry to protein dynamics has deep implications for protein architecture, both natural and created, and recent results reinforce the complexity of the protein form that has evolved to support these functions.
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Affiliation(s)
- Dimitri Antoniou
- Departments of Biophysics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, USA
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25
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Kipp DR, Silva RG, Schramm VL. Mass-dependent bond vibrational dynamics influence catalysis by HIV-1 protease. J Am Chem Soc 2011; 133:19358-61. [PMID: 22059645 DOI: 10.1021/ja209391n] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Protein motions that occur on the microsecond to millisecond time scale have been linked to enzymatic rates observed for catalytic turnovers, but not to transition-state barrier crossing. It has been hypothesized that enzyme motions on the femtosecond time scale of bond vibrations play a role in transition state formation. Here, we perturb femtosecond motion by substituting all nonexchangeable carbon, nitrogen, and hydrogen atoms with (13)C, (15)N, and (2)H and observe the catalytic effects in HIV-1 protease. According to the Born-Oppenheimer approximation, isotopic substitution alters vibrational frequency with unchanged electrostatic properties. With the use of a fluorescent peptide to report on multiple steps in the reaction, we observe significantly reduced rates in the heavy enzyme relative to the light enzyme. A possible interpretation of our results is that there exists a dynamic link between mass-dependent bond vibrations of the enzyme and events in the reaction coordinate.
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Affiliation(s)
- D Randal Kipp
- Department of Biochemistry, Albert Einstein College of Medicine at Yeshiva University, 1300 Morris Park Avenue, Bronx, New York 10461, USA
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26
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Flakus HT, Hachuła B. Polarized IR Spectra of the Hydrogen Bond in Two Different Oxindole Polymorphs with Cyclic Dimers in Their Lattices. J Phys Chem A 2011; 115:12150-60. [DOI: 10.1021/jp206073v] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Henryk T. Flakus
- Institute of Chemistry, University of Silesia, 9 Szkolna Street, Pl-40 006 Katowice, Poland
| | - Barbara Hachuła
- Institute of Chemistry, University of Silesia, 9 Szkolna Street, Pl-40 006 Katowice, Poland
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27
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Kanaan N, Ferrer S, Martí S, Garcia-Viloca M, Kohen A, Moliner V. Temperature dependence of the kinetic isotope effects in thymidylate synthase. A theoretical study. J Am Chem Soc 2011; 133:6692-702. [PMID: 21476498 PMCID: PMC3098132 DOI: 10.1021/ja1114369] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
In recent years, the temperature dependence of primary kinetic isotope effects (KIE) has been used as indicator for the physical nature of enzyme-catalyzed H-transfer reactions. An interactive study where experimental data and calculations examine the same chemical transformation is a critical means to interpret more properly temperature dependence of KIEs. Here, the rate-limiting step of the thymidylate synthase-catalyzed reaction has been studied by means of hybrid quantum mechanics/molecular mechanics (QM/MM) simulations in the theoretical framework of the ensemble-averaged variational transition-state theory with multidimensional tunneling (EA-VTST/MT) combined with Grote-Hynes theory. The KIEs were calculated across the same temperature range examined experimentally, revealing a temperature independent behavior, in agreement with experimental findings. The calculations show that the H-transfer proceeds with ∼91% by tunneling in the case of protium and ∼80% when the transferred protium is replaced by tritium. Dynamic recrossing coefficients are almost invariant with temperature and in all cases far from unity, showing significant coupling between protein motions and the reaction coordinate. In particular, the relative movement of a conserved arginine (Arg166 in Escherichia coli ) promotes the departure of a conserved cysteine (Cys146 in E. coli ) from the dUMP by polarizing the thioether bond thus facilitating this bond breaking that takes place concomitantly with the hydride transfer. These promoting vibrations of the enzyme, which represent some of the dimensions of the real reaction coordinate, would limit the search through configurational space to efficiently find those decreasing both barrier height and width, thereby enhancing the probability of H-transfer by either tunneling (through barrier) or classical (over-the-barrier) mechanisms. In other words, the thermal fluctuations that are coupled to the reaction coordinate, together with transition-state geometries and tunneling, are the same in different bath temperatures (within the limited experimental range examined). All these terms contribute to the observed temperature independent KIEs in thymidylate synthase.
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Affiliation(s)
- Natalia Kanaan
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castellón, Spain
| | - Silvia Ferrer
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castellón, Spain
| | - Sergio Martí
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castellón, Spain
| | - Mireia Garcia-Viloca
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Amnon Kohen
- Department of Chemistry, University of Iowa, Iowa City, IA 52242, USA
| | - Vicent Moliner
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castellón, Spain
- Institute of Applied Radiation Chemistry, Technical University of Lodz, 90-924 Lodz, Poland
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28
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Saritha B, Durga Prasad M. An Electronic Structure Perspective of the Promoter Modes in Proton Transfer Reactions. J Phys Chem A 2011; 115:2802-10. [DOI: 10.1021/jp108579t] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- B. Saritha
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
| | - M. Durga Prasad
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
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29
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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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30
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Kamerlin SCL, Warshel A. At the dawn of the 21st century: Is dynamics the missing link for understanding enzyme catalysis? Proteins 2010; 78:1339-75. [PMID: 20099310 PMCID: PMC2841229 DOI: 10.1002/prot.22654] [Citation(s) in RCA: 345] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Enzymes play a key role in almost all biological processes, accelerating a variety of metabolic reactions as well as controlling energy transduction, the transcription, and translation of genetic information, and signaling. They possess the remarkable capacity to accelerate reactions by many orders of magnitude compared to their uncatalyzed counterparts, making feasible crucial processes that would otherwise not occur on biologically relevant timescales. Thus, there is broad interest in understanding the catalytic power of enzymes on a molecular level. Several proposals have been put forward to try to explain this phenomenon, and one that has rapidly gained momentum in recent years is the idea that enzyme dynamics somehow contributes to catalysis. This review examines the dynamical proposal in a critical way, considering basically all reasonable definitions, including (but not limited to) such proposed effects as "coupling between conformational and chemical motions," "landscape searches" and "entropy funnels." It is shown that none of these proposed effects have been experimentally demonstrated to contribute to catalysis, nor are they supported by consistent theoretical studies. On the other hand, it is clarified that careful simulation studies have excluded most (if not all) dynamical proposals. This review places significant emphasis on clarifying the role of logical definitions of different catalytic proposals, and on the need for a clear formulation in terms of the assumed potential surface and reaction coordinate. Finally, it is pointed out that electrostatic preorganization actually accounts for the observed catalytic effects of enzymes, through the corresponding changes in the activation free energies.
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Affiliation(s)
- Shina C. L. Kamerlin
- Department of Chemistry, University of Southern California, 3620 McClintock Ave., Los Angeles CA-90089, USA
| | - Arieh Warshel
- Department of Chemistry, University of Southern California, 3620 McClintock Ave., Los Angeles CA-90089, USA
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31
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Kamerlin SCL, Mavri J, Warshel A. Examining the case for the effect of barrier compression on tunneling, vibrationally enhanced catalysis, catalytic entropy and related issues. FEBS Lett 2010; 584:2759-66. [PMID: 20433839 DOI: 10.1016/j.febslet.2010.04.062] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2010] [Revised: 04/21/2010] [Accepted: 04/22/2010] [Indexed: 10/19/2022]
Abstract
The idea that tunneling is enhanced by the compression of the donor-acceptor distance has attracted significant interest. In particular, recent studies argued that this proposal is consistent with pressure effects on enzymatic reactions, and that the observed pressure effects support the idea of vibrationally enhanced catalysis. However, a careful analysis of the current works reveals serious inconsistencies in the evidence presented to support these hypotheses. Apparently, tunneling decreases upon compression, and external pressure does not lead to the applicable compression of the free energy surface. Additionally, pressure experiments do not provide actual evidence for vibrationally enhanced catalysis. Finally, the temperature dependence of the entropy change in hydride transfer reactions is shown to reflect simple electrostatic effects.
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32
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Hu H, Yang W. Elucidating solvent contributions to solution reactions with ab initio QM/MM methods. J Phys Chem B 2010; 114:2755-9. [PMID: 20121225 PMCID: PMC3747775 DOI: 10.1021/jp905886q] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Computer simulations of reaction processes in solution in general rely on the definition of a reaction coordinate and the determination of the thermodynamic changes of the system along the reaction coordinate. The reaction coordinate often is constituted of characteristic geometrical properties of the reactive solute species, while the contributions of solvent molecules are implicitly included in the thermodynamics of the solute degrees of freedoms. However, solvent dynamics can provide the driving force for the reaction process, and in such cases explicit description of the solvent contribution in the free energy of the reaction process becomes necessary. We report here a method that can be used to analyze the solvent contributions to the reaction activation free energies from the combined QM/MM minimum free-energy path simulations. The method was applied to the self-exchange S(N)2 reaction of CH(3)Cl + Cl(-), showing that the importance of solvent-solute interactions to the reaction process. The results were further discussed in the context of coupling between solvent and solute molecules in reaction processes.
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Affiliation(s)
- Hao Hu
- Department of Chemistry, University of Hong Kong, Hong Kong
- Department of Chemistry, Duke University, Durham, NC 27708, USA
| | - Weitao Yang
- Department of Chemistry, Duke University, Durham, NC 27708, USA
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33
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Hay S, Johannissen LO, Sutcliffe MJ, Scrutton NS. Barrier compression and its contribution to both classical and quantum mechanical aspects of enzyme catalysis. Biophys J 2010; 98:121-8. [PMID: 20085724 DOI: 10.1016/j.bpj.2009.09.045] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2009] [Revised: 09/23/2009] [Accepted: 09/24/2009] [Indexed: 12/01/2022] Open
Abstract
It is generally accepted that enzymes catalyze reactions by lowering the apparent activation energy by transition state stabilization or through destabilization of ground states. A more controversial proposal is that enzymes can also accelerate reactions through barrier compression-an idea that has emerged from studies of H-tunneling reactions in enzyme systems. The effects of barrier compression on classical (over-the-barrier) reactions, and the partitioning between tunneling and classical reaction paths, have largely been ignored. We performed theoretical and computational studies on the effects of barrier compression on the shape of potential energy surfaces/reaction barriers for model (malonaldehyde and methane/methyl radical anion) and enzymatic (aromatic amine dehydrogenase) proton transfer systems. In all cases, we find that barrier compression is associated with an approximately linear decrease in the activation energy. For partially nonadiabatic proton transfers, we show that barrier compression enhances, to similar extents, the rate of classical and proton tunneling reactions. Our analysis suggests that barrier compression-through fast promoting vibrations, or other means-could be a general mechanism for enhancing the rate of not only tunneling, but also classical, proton transfers in enzyme catalysis.
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Affiliation(s)
- Sam Hay
- Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, United Kingdom
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34
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Abstract
An expression for the external force driving a system of two coupled oscillators in the condensed phase was derived in the frame of the Debye theory of solids. The time dependence and amplitude of the force is determined by the size of the cell embedding the coupled oscillators and its Debye temperature (theta(D)). The dynamics of the driven system of oscillators were followed in the two regimes of (a) low theta(D) and cell diameter, as a model of liquid water, and (b) large theta(D) and cell diameter, as a model of the core of a protein. The response in potential energy of the reference oscillator was computed for all possible values of the internal parameters of the system under investigation. For protein cores, the region in the parameter space of high maximum potential energy of the reference oscillator is considerably extended with respect to the corresponding simulation for water.
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Affiliation(s)
- Carlo Canepa
- Dipartimento di Chimica Generale e Chimica Organica, Università di Torino Corso Massimo d'Azeglio 48, 10125 Torino, Italy.
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35
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Parks JM, Hu H, Rudolph J, Yang W. Mechanism of Cdc25B phosphatase with the small molecule substrate p-nitrophenyl phosphate from QM/MM-MFEP calculations. J Phys Chem B 2009; 113:5217-24. [PMID: 19301836 DOI: 10.1021/jp805137x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cdc25B is a dual-specificity phosphatase that catalyzes the dephosphorylation of the Cdk2/CycA protein complex. This enzyme is an important regulator of the human cell cycle and has been identified as a potential anticancer target. In general, protein tyrosine phosphatases are thought to bind the dianionic form of the phosphate and employ general acid catalysis via the Asp residue in the highly conserved WPD-loop. However, the Cdc25 phosphatases form a special subfamily based on their distinct differences from other protein tyrosine phosphatases. Although Cdc25B contains the (H/V)CX(5)R catalytic motif present in all other protein tyrosine phosphatases, it lacks an analogous catalytic acid residue. No crystallographic data currently exist for the complex of Cdc25B with Cdk2/CycA, so in addition to its natural protein substrate, experimental and theoretical studies are often carried out with small molecule substrates. In an effort to gain understanding of the dephosphorylation mechanism of Cdc25B with a commonly used small molecule substrate, we have performed simulations of the rate-limiting step of the reaction catalyzed by Cdc25B with the substrate p-nitrophenyl phosphate using the recently developed QM/MM Minimum Free Energy Path method (Hu et al. J. Chem. Phys. 2008, 034105). We have simulated the first step of the reaction with both the monoanionic and the dianionic forms of the substrate, and our calculations favor a mechanism involving the monoanionic form. Thus, Cdc25 may employ a unique dephosphorylation mechanism among protein tyrosine phosphatases, at least in the case of the small molecule substrate p-nitrophenyl phosphate.
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Affiliation(s)
- Jerry M Parks
- Department of Chemistry, Duke University, 124 Science Drive, 5301 French Science Center, Durham, North Carolina 27708-0346, USA
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36
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Fanfrlík J, Brynda J, Rezác J, Hobza P, Lepsík M. Interpretation of protein/ligand crystal structure using QM/MM calculations: case of HIV-1 protease/metallacarborane complex. J Phys Chem B 2009; 112:15094-102. [PMID: 18975888 DOI: 10.1021/jp803528w] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Deltahedral metallacarborane compounds have recently been discovered as potent, specific, stable, and nontoxic inhibitors of HIV-1 protease (PR), the major target for AIDS therapy. The 2.15 A-resolution X-ray structure has exhibited a nonsymmetrical binding of the parental compound [Co(3+)-(C2B9H11)2](-) (GB-18) into PR dimer and a symmetrical arrangement in the crystal of two PR dimer complexes into a tetramer. In order to explore structural and energetic details of the inhibitor binding, quantum mechanics coupled with molecular mechanics approach was utilized. Realizing the close positioning of anionic inhibitors in the active site cavity, the possibility of an exchange of structural water molecules Wat50 and Wat128 by Na+ counterions was studied. The energy profiles for the rotation of the GB-18 molecules along their longitudinal axes in complex with PR were calculated. The results show that two Na+ counterions are present in the active site cavity and provide energetically favorable and unfavorable positions for carbon atoms within the carborane cages. Eighty-one rotamer combinations of four molecules of GB-18 bound to PR out of 4 x 10(5) are predicted to be highly populated. These results lay ground for further calculations of interaction energies between GB-18 and amino acids of PR active site and will make it possible to interpret computationally the binding of similar metallacarborane molecules to PR as well as to resistant PR variants. Moreover, this computational tool will allow the design of new, more potent metallacarborane-based HIV-1 protease inhibitors.
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Affiliation(s)
- Jindrich Fanfrlík
- Gilead Sciences and IOCB Research Center Prague, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
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37
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Hsieh CC, Chen KY, Hsieh WT, Lai CH, Shen JY, Jiang CM, Duan HS, Chou PT. Cyano Analogues of 7-Azaindole: Probing Excited-State Charge-Coupled Proton Transfer Reactions in Protic Solvents. Chemphyschem 2008; 9:2221-9. [DOI: 10.1002/cphc.200800352] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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38
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Atomic detail of chemical transformation at the transition state of an enzymatic reaction. Proc Natl Acad Sci U S A 2008; 105:16543-8. [PMID: 18946041 DOI: 10.1073/pnas.0808413105] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Transition path sampling (TPS) has been applied to the chemical step of human purine nucleoside phosphorylase (PNP). The transition path ensemble provides insight into the detailed mechanistic dynamics and atomic motion involved in transition state passage. The reaction mechanism involves early loss of the ribosidic bond to form a transition state with substantial ribooxacarbenium ion character, followed by dynamic motion from the enzyme and a conformational change in the ribosyl group leading to migration of the anomeric carbon toward phosphate, to form the product ribose 1-phosphate. Calculations of the commitment probability along reactive paths demonstrated the presence of a broad energy barrier at the transition state. TPS identified (i) compression of the O4'...O5' vibrational motion, (ii) optimized leaving group interactions, and (iii) activation of the phosphate nucleophile as the reaction proceeds through the transition state region. Dynamic motions on the femtosecond timescale provide the simultaneous optimization of these effects and coincide with transition state formation.
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39
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Ruiz-Pernía JJ, Tuñón I, Moliner V, Hynes JT, Roca M. Dynamic Effects on Reaction Rates in a Michael Addition Catalyzed by Chalcone Isomerase. Beyond the Frozen Environment Approach. J Am Chem Soc 2008; 130:7477-88. [DOI: 10.1021/ja801156y] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- J. Javier Ruiz-Pernía
- Departamento de Química Física, Universidad de Valencia, 46100 Burjassot, Spain, Departamento de Química Física y Analítica, Universidad Jaume I, 12071 Castellón, Spain, Département de Chimie, UMR 8640 Pasteur, Ecole Normale Supérieure, 75005 Paris, France, Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215, and Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062
| | - Iñaki Tuñón
- Departamento de Química Física, Universidad de Valencia, 46100 Burjassot, Spain, Departamento de Química Física y Analítica, Universidad Jaume I, 12071 Castellón, Spain, Département de Chimie, UMR 8640 Pasteur, Ecole Normale Supérieure, 75005 Paris, France, Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215, and Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062
| | - Vicente Moliner
- Departamento de Química Física, Universidad de Valencia, 46100 Burjassot, Spain, Departamento de Química Física y Analítica, Universidad Jaume I, 12071 Castellón, Spain, Département de Chimie, UMR 8640 Pasteur, Ecole Normale Supérieure, 75005 Paris, France, Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215, and Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062
| | - James T. Hynes
- Departamento de Química Física, Universidad de Valencia, 46100 Burjassot, Spain, Departamento de Química Física y Analítica, Universidad Jaume I, 12071 Castellón, Spain, Département de Chimie, UMR 8640 Pasteur, Ecole Normale Supérieure, 75005 Paris, France, Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215, and Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062
| | - Maite Roca
- Departamento de Química Física, Universidad de Valencia, 46100 Burjassot, Spain, Departamento de Química Física y Analítica, Universidad Jaume I, 12071 Castellón, Spain, Département de Chimie, UMR 8640 Pasteur, Ecole Normale Supérieure, 75005 Paris, France, Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215, and Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062
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40
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Sakumichi N, Ando K. Semiquantal analysis of adiabatic hydrogen transfer rate. J Chem Phys 2008; 128:164516. [DOI: 10.1063/1.2903746] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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41
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Benkovic SJ, Hammes GG, Hammes-Schiffer S. Free-Energy Landscape of Enzyme Catalysis. Biochemistry 2008; 47:3317-21. [DOI: 10.1021/bi800049z] [Citation(s) in RCA: 223] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Stephen J. Benkovic
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, and Department of Biochemistry, Box 3711, Duke University, Durham, North Carolina 27710
| | - Gordon G. Hammes
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, and Department of Biochemistry, Box 3711, Duke University, Durham, North Carolina 27710
| | - Sharon Hammes-Schiffer
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, and Department of Biochemistry, Box 3711, Duke University, Durham, North Carolina 27710
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42
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Hu H, Yang W. Free energies of chemical reactions in solution and in enzymes with ab initio quantum mechanics/molecular mechanics methods. Annu Rev Phys Chem 2008; 59:573-601. [PMID: 18393679 PMCID: PMC3727228 DOI: 10.1146/annurev.physchem.59.032607.093618] [Citation(s) in RCA: 349] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Combined quantum mechanics/molecular mechanics (QM/MM) methods provide an accurate and efficient energetic description of complex chemical and biological systems, leading to significant advances in the understanding of chemical reactions in solution and in enzymes. Here we review progress in QM/MM methodology and applications, focusing on ab initio QM-based approaches. Ab initio QM/MM methods capitalize on the accuracy and reliability of the associated quantum-mechanical approaches, however, at a much higher computational cost compared with semiempirical quantum-mechanical approaches. Thus reaction-path and activation free-energy calculations based on ab initio QM/MM methods encounter unique challenges in simulation timescales and phase-space sampling. This review features recent developments overcoming these challenges and enabling accurate free-energy determination for reaction processes in solution and in enzymes, along with applications.
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Affiliation(s)
- Hao Hu
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA.
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43
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Castillo R, Roca M, Soriano A, Moliner V, Tuñón I. Using Grote−Hynes Theory To Quantify Dynamical Effects on the Reaction Rate of Enzymatic Processes. The Case of Methyltransferases. J Phys Chem B 2007; 112:529-34. [DOI: 10.1021/jp077660b] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Raquel Castillo
- Departamento de Química Física y Analítica, Universidad Jaume I, 12071 Castellón, Spain, Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062, and Departamento de Química Física, Universidad de Valencia, 46100 Burjassot, Spain
| | - Maite Roca
- Departamento de Química Física y Analítica, Universidad Jaume I, 12071 Castellón, Spain, Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062, and Departamento de Química Física, Universidad de Valencia, 46100 Burjassot, Spain
| | - Alejandro Soriano
- Departamento de Química Física y Analítica, Universidad Jaume I, 12071 Castellón, Spain, Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062, and Departamento de Química Física, Universidad de Valencia, 46100 Burjassot, Spain
| | - Vicente Moliner
- Departamento de Química Física y Analítica, Universidad Jaume I, 12071 Castellón, Spain, Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062, and Departamento de Química Física, Universidad de Valencia, 46100 Burjassot, Spain
| | - Iñaki Tuñón
- Departamento de Química Física y Analítica, Universidad Jaume I, 12071 Castellón, Spain, Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062, and Departamento de Química Física, Universidad de Valencia, 46100 Burjassot, Spain
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44
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Olsson MHM, Parson WW, Warshel A. Dynamical contributions to enzyme catalysis: critical tests of a popular hypothesis. Chem Rev 2007; 106:1737-56. [PMID: 16683752 DOI: 10.1021/cr040427e] [Citation(s) in RCA: 254] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mats H M Olsson
- Department of Chemistry, University of Southern California, 3620 McClintock Avenue, Los Angeles, California 90089-1062, USA.
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45
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Quaytman SL, Schwartz SD. Reaction coordinate of an enzymatic reaction revealed by transition path sampling. Proc Natl Acad Sci U S A 2007; 104:12253-8. [PMID: 17640885 PMCID: PMC1941458 DOI: 10.1073/pnas.0704304104] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The transition path sampling method previously applied in our group to the reaction catalyzed by lactate dehydrogenase was used to generate a transition path ensemble for this reaction. Based on analysis of the reactive trajectories generated, important residues behind the active site were implicated in a compressional motion that brought the donor-acceptor atoms of the hydride closer together. In addition, residues behind the active site were implicated in a relaxational motion, locking the substrate in product formation. Although this suggested that the compression-relaxation motions of these residues were important to catalysis, it remained unproven. In this work, we used committor distribution analysis to show that these motions are integral components of the reaction coordinate.
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Affiliation(s)
| | - Steven D. Schwartz
- Departments of *Biophysics and
- Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461
- To whom correspondence should be addressed. E-mail:
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46
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Gao J, Ma S, Major DT, Nam K, Pu J, Truhlar DG. Mechanisms and free energies of enzymatic reactions. Chem Rev 2006; 106:3188-209. [PMID: 16895324 PMCID: PMC4477011 DOI: 10.1021/cr050293k] [Citation(s) in RCA: 317] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jiali Gao
- Department of Chemistry and Supercomputing Institute, Digital Technology Center, University of Minnesota, Minneapolis, Minnesota 55455
| | - Shuhua Ma
- Department of Chemistry and Supercomputing Institute, Digital Technology Center, University of Minnesota, Minneapolis, Minnesota 55455
| | - Dan T. Major
- Department of Chemistry and Supercomputing Institute, Digital Technology Center, University of Minnesota, Minneapolis, Minnesota 55455
| | - Kwangho Nam
- Department of Chemistry and Supercomputing Institute, Digital Technology Center, University of Minnesota, Minneapolis, Minnesota 55455
| | - Jingzhi Pu
- Department of Chemistry and Supercomputing Institute, Digital Technology Center, University of Minnesota, Minneapolis, Minnesota 55455
| | - Donald G. Truhlar
- Department of Chemistry and Supercomputing Institute, Digital Technology Center, University of Minnesota, Minneapolis, Minnesota 55455
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47
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Pu J, Gao J, Truhlar DG. Multidimensional tunneling, recrossing, and the transmission coefficient for enzymatic reactions. Chem Rev 2006; 106:3140-69. [PMID: 16895322 PMCID: PMC4478620 DOI: 10.1021/cr050308e] [Citation(s) in RCA: 288] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jingzhi Pu
- Department of Chemistry and Supercomputer Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, Minnesota 55455-0431
| | - Jiali Gao
- Department of Chemistry and Supercomputer Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, Minnesota 55455-0431
| | - Donald G. Truhlar
- Department of Chemistry and Supercomputer Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, Minnesota 55455-0431
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48
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Antoniou D, Basner J, Núñez S, Schwartz SD. Effect of enzyme dynamics on catalytic activity. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2006. [DOI: 10.1016/s0065-3160(06)41006-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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49
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Meyer MP, Klinman JP. Modeling temperature dependent kinetic isotope effects for hydrogen transfer in a series of soybean lipoxygenase mutants: The effect of anharmonicity upon transfer distance. Chem Phys 2005; 319:283-296. [PMID: 21132078 PMCID: PMC2995544 DOI: 10.1016/j.chemphys.2005.05.017] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Soybean lipoxygenase-1 (SLO) catalyzes the oxidation of linoleic acid. The rate-limiting step in this transformation is the net abstraction of the pro-S hydrogen atom from the center of the 1,5-pentadienyl moiety in linoleic acid. The large deuterium kinetic isotope effect (KIE) for this step appears in the first order rate constant ((D)k(cat) = 81 ± 5 at T = 25 °C). Furthermore, the KIE and the rate for protium abstraction are weakly temperature dependent (E(A,D) - E(A,H) = 0.9 ± 0.2 kcal/mol and E(A,H) = 2.1 ± 0.2 kcal/mol, respectively). Mutations at a hydrophobic site about 13 Å from the active site Fe(III), Ile(553), induce a marked temperature dependence that varies roughly in accordance with the degree to which the residue is changed in bulk from the wild type Ile. While the temperature dependence for these mutants varies from the wild type enzyme, the magnitude of the KIE at 25 °C is on the same order of magnitude. A hydrogen tunneling model [Kuznetsov, A.M., Ulstrup, J. Can. J. Chem. 77 (1999) 1085-1096] is utilized to model the KIE temperature profiles for the wild type SLO and each Ile(553) mutant. Hydrogenic wavefunctions are modeled using harmonic oscillators and Morse oscillators in order to explore the effects of anharmonicity upon computed kinetic observables used to characterize this hydrogen transfer.
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Affiliation(s)
- Matthew P. Meyer
- Department of Chemistry and Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Judith P. Klinman
- Department of Chemistry and Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
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50
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Konuklar FAS, Aviyente V, Haliloğlu T. Coupling of structural fluctuations to deamidation reaction in triosephosphate isomerase by Gaussian network model. Proteins 2005; 62:715-27. [PMID: 16323206 DOI: 10.1002/prot.20668] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
We study the structural fluctuations of triosephosphate isomerase (TIM) by an elastic model, namely, the Gaussian network model (GNM), to identify a network of coupled motions in the allosteric communication between its deamidation and catalytic sites, and the promoting motions for the deamidation activity. For this, three TIM structures have been studied: one crystal structure and two model structures designed to describe different putative models for the deamidation reaction taking place at the subunit interface. The structural fluctuations have been mapped on the functional properties; then the differences in the fluctuations between the two models in relation to the deamidation reaction have been considered. The results demonstrate that the qualitative picture of the mean-square fluctuations and the correlations between the fluctuations are similar in both, but the differences may affect the observed barrier height of the deamidation reaction. The higher packing density at regions close to deamidation sites, reflected by the high-frequency fluctuating residues in the respective regions, the stronger positive correlation between the fluctuations of the deamidation sites, and enhanced positive correlation of the primary deamidation site with the extended vicinity of the catalytic region on the juxtaposed unit promote the probability of the deamidation reaction. The results in general emphasize the importance of structural fluctuations in enzyme reactions, as well as proposing the present methodology as a plausible approach for studies on the network of coupled promoting motions in protein functions.
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Affiliation(s)
- F A S Konuklar
- Istanbul Technical University, Informatics Institute, Ayazağa Campus, Istanbul, Turkey
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