1
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Jaglan R, Mandal D. The role of potential energy surface in quantum mechanical tunneling: A computational perspective. COMPUT THEOR CHEM 2020. [DOI: 10.1016/j.comptc.2020.112920] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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2
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Kannath S, Adamczyk P, Ferro-Costas D, Fernández-Ramos A, Major DT, Dybala-Defratyka A. Role of Microsolvation and Quantum Effects in the Accurate Prediction of Kinetic Isotope Effects: The Case of Hydrogen Atom Abstraction in Ethanol by Atomic Hydrogen in Aqueous Solution. J Chem Theory Comput 2020; 16:847-859. [PMID: 31904954 PMCID: PMC7588029 DOI: 10.1021/acs.jctc.9b00774] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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Hydrogen abstraction from ethanol
by atomic hydrogen in aqueous
solution is studied using two theoretical approaches: the multipath
variational transition state theory (MP-VTST) and a path-integral
formalism in combination with free-energy perturbation and umbrella
sampling (PI-FEP/UM). The performance of the models is compared to
experimental values of H kinetic isotope effects (KIE). Solvation
models used in this study ranged from purely implicit, via mixed–microsolvation
treated quantum mechanically via the density functional theory (DFT)
to fully explicit representation of the solvent, which was incorporated
using a combined quantum mechanical-molecular mechanical (QM/MM) potential.
The effects of the transition state conformation and the position
of microsolvating water molecules interacting with the solute on the
KIE are discussed. The KIEs are in good agreement with experiment
when MP-VTST is used together with a model that includes microsolvation
of the polar part of ethanol by five or six water molecules, emphasizing
the importance of explicit solvation in KIE calculations. Both, MP-VTST
and PI-FEP/UM enable detailed characterization of nuclear quantum
effects accompanying the hydrogen atom transfer reaction in aqueous
solution.
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Affiliation(s)
- Suraj Kannath
- Institute of Applied Radiation Chemistry, Faculty of Chemistry , Lodz University of Technology , Zeromskiego 116 , 90-924 Lodz , Poland
| | - Paweł Adamczyk
- Institute of Applied Radiation Chemistry, Faculty of Chemistry , Lodz University of Technology , Zeromskiego 116 , 90-924 Lodz , Poland
| | - David Ferro-Costas
- LAQV@REQUIMTE, Department of Chemistry & Biochemistry, Faculty of Sciences , University of Porto , Rua do Campo Alegre , 4169-007 Porto , Portugal.,Center for Research in Biological Chemistry and Molecular Materials (CIQUS) , Universidade de Santiago de Compostela , 15782 Santiago de Compostela , Spain
| | - Antonio Fernández-Ramos
- Center for Research in Biological Chemistry and Molecular Materials (CIQUS) , Universidade de Santiago de Compostela , 15782 Santiago de Compostela , Spain
| | - Dan Thomas Major
- Department of Chemistry and Institute for Nanotechnology & Advanced Materials , Bar-Ilan University , Ramat-Gan 52900 , Israel
| | - Agnieszka Dybala-Defratyka
- Institute of Applied Radiation Chemistry, Faculty of Chemistry , Lodz University of Technology , Zeromskiego 116 , 90-924 Lodz , Poland
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3
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Gao LG, Zhang RM, Xu X, Truhlar DG. Quantum Effects on H2 Diffusion in Zeolite RHO: Inverse Kinetic Isotope Effect for Sieving. J Am Chem Soc 2019; 141:13635-13642. [DOI: 10.1021/jacs.9b06506] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lu Gem Gao
- Center for Combustion Energy, Department of Energy and Power Engineering, and Key Laboratory for Thermal Science and Power Engineering of Ministry of Education, Tsinghua University, Beijing 100084, China
- Department of Chemistry, Chemical Theory Center, and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
| | - Rui Ming Zhang
- Center for Combustion Energy, Department of Energy and Power Engineering, and Key Laboratory for Thermal Science and Power Engineering of Ministry of Education, Tsinghua University, Beijing 100084, China
| | - Xuefei Xu
- Center for Combustion Energy, Department of Energy and Power Engineering, and Key Laboratory for Thermal Science and Power Engineering of Ministry of Education, Tsinghua University, Beijing 100084, China
| | - Donald G. Truhlar
- Department of Chemistry, Chemical Theory Center, and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
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4
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Mazarei E, Hosein Mousavipour S. Theoretical Study on the Dynamics and Kinetics of the Reaction of CH 2OH with OH. J Phys Chem A 2018; 122:9761-9777. [PMID: 30508487 DOI: 10.1021/acs.jpca.8b09621] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The stochastic one-dimensional chemical master equation (CME) simulation method was used to investigate the dynamics of the reaction of CH2OH with OH. A multiwell multichannel potential energy surface (PES) was constructed at the CCSD(T)/Aug-cc-pVTZ//CBS-QB3 and QCISD(T)/Aug-cc-pVTZ//CBS-QB3 levels of theory. The constructed PES consisted of three chemically activated intermediates and two van der Waals complexes. The fractional population analysis unraveled the role of the energized intermediates and van der Waals complexes in the early stages of this complex reaction. The CME calculations provided the phenomenological rate constants through analysis of the eigenvalues and eigenvectors of collision matrices while Leonard-Jones potential was used to model the collisions. The CME results indicated that CH2O and H2O were the major products, in accordance with the literature. Also, the findings declared the temperature and pressure independence of the reaction over a wide range of temperature (250 to 2400 K) and pressure (0.1 to 7 atm). Furthermore, the efficiency of tunneling on the hydrogen transfer isomerization reaction of trans-HCOH to CH2O was confirmed over the temperature range of 250 to 3000 K. The rate constants for different reaction channels are reported.
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Affiliation(s)
- Elham Mazarei
- Department of Chemistry, College of Science , Shiraz University , Shiraz , Iran
| | - S Hosein Mousavipour
- Department of Chemistry, College of Science , Shiraz University , Shiraz , Iran.,Department of Chemistry, Faculty of Science , Sultan Qaboos University , Muscat , Sultanate of Oman
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5
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Wick CR, Smith DM. Modeling the Reactions Catalyzed by Coenzyme B 12 Dependent Enzymes: Accuracy and Cost-Quality Balance. J Phys Chem A 2018; 122:1747-1755. [PMID: 29389127 DOI: 10.1021/acs.jpca.7b11798] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The reactions catalyzed by coenzyme B12 dependent enzymes are formally initiated by the homolytic cleavage of a carbon-cobalt bond and a subsequent or concerted H-atom-transfer reaction. A reasonable model chemistry for describing those reactions should, therefore, account for an accurate description of both reactions. The inherent limitation due to the necessary system size renders the coenzyme B12 system a suitable candidate for DFT or hybrid QM/MM methods; however, the accurate description of both homolytic Co-C cleavage and H-atom-transfer reactions within this framework is challenging and can lead to controversial results with varying accuracy. We present an assessment study of 16 common density functionals applied to prototypical model systems for both reactions. H-abstraction reactions were modeled on the basis of four reference reactions designed to resemble a broad range of coenzyme B12 reactions. The Co-C cleavage reaction is treated by an ONIOM(QM/MM) setup that is in excellent agreement with solution-phase experimental data and is as accurate as full DFT calculations on the complete model system. We find that the meta-GGAs TPSS-D3 and M06L-D3 and the meta-hybrid M06-D3 give the best overall performance with MUEs for both types of reactions below 10 kJ mol-1. Our recommended model chemistry allows for a fast and accurate description of coenzyme B12 chemistry that is readily applicable to study the reactions in an enzymatic framework.
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Affiliation(s)
- Christian R Wick
- Division of Physical Chemistry, Group for Computational Life Sciences, Ruđer Bošković Institute , Bijenička cesta 54, 10000 Zagreb, Croatia
| | - David M Smith
- Division of Physical Chemistry, Group for Computational Life Sciences, Ruđer Bošković Institute , Bijenička cesta 54, 10000 Zagreb, Croatia.,Center for Computational Chemistry, FAU Erlangen-Nürnberg , Nägelsbachstrasse 25, 91052 Erlangen, Germany
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6
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Li X, Liao T, Chung LW. Computational Prediction of Excited-State Carbon Tunneling in the Two Steps of Triplet Zimmerman Di-π-Methane Rearrangement. J Am Chem Soc 2017; 139:16438-16441. [PMID: 29037035 DOI: 10.1021/jacs.7b07539] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The photoinduced Zimmerman di-π-methane (DPM) rearrangement of polycyclic molecules to form synthetically useful cyclopropane derivatives was found experimentally to proceed in a triplet excited state. We have applied state-of-the-art quantum mechanical methods, including M06-2X, DLPNO-CCSD(T) and variational transition-state theory with multidimensional tunneling corrections, to an investigation of the reaction rates of the two steps in the triplet DPM rearrangement of dibenzobarrelene, benzobarrelene and barrelene. This study predicts a high probability of carbon tunneling in regions around the two consecutive transition states at 200-300 K, and an enhancement in the rates by 104-276/35-67% with carbon tunneling at 200/300 K. The Arrhenius plots of the rate constants were found to be curved at low temperatures. Moreover, the computed 12C/13C kinetic isotope effects were affected significantly by carbon tunneling and temperature. Our predictions of electronically excited-state carbon tunneling and two consecutive carbon tunneling are unprecedented. Heavy-atom tunneling in some photoinduced reactions with reactive intermediates and narrow barriers can be potentially observed at relatively low temperature in experiments.
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Affiliation(s)
- Xin Li
- Department of Chemistry, South University of Science and Technology of China , Shenzhen 518055, China
| | - Tao Liao
- Department of Chemistry, South University of Science and Technology of China , Shenzhen 518055, China
| | - Lung Wa Chung
- Department of Chemistry, South University of Science and Technology of China , Shenzhen 518055, China
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7
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Abstract
Enzyme isotope effects, or the kinetic effects of "heavy" enzymes, refer to the effect of isotopically labeled protein residues on the enzyme's activity or physical properties. These effects are increasingly employed in the examination of the possible contributions of protein dynamics to enzyme catalysis. One hypothesis assumed that isotopic substitution of all 12C, 14N, and nonexchangeable 1H by 13C, 15N, and 2H, would slow down protein picosecond to femtosecond dynamics without any effect on the system's electrostatics following the Born-Oppenheimer approximation. It was suggested that reduced reaction rates reported for several "heavy" enzymes accords with that hypothesis. However, numerous deviations from the predictions of that hypothesis were also reported. Current studies also attempt to test the role of individual residues by site-specific labeling or by labeling a pattern of residues on activity. It appears that in several systems the protein's fast dynamics are indeed reduced in "heavy" enzymes in a way that reduces the probability of barrier crossing of its chemical step. Other observations, however, indicated that slower protein dynamics are electrostatically altered in isotopically labeled enzymes. Interestingly, these effects appear to be system dependent, thus it might be premature to suggest a general role of "heavy" enzymes' effect on catalysis.
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8
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Hu S, Soudackov AV, Hammes-Schiffer S, Klinman JP. Enhanced Rigidification within a Double Mutant of Soybean Lipoxygenase Provides Experimental Support for Vibronically Nonadiabatic Proton-Coupled Electron Transfer Models. ACS Catal 2017; 7:3569-3574. [PMID: 29250456 PMCID: PMC5724529 DOI: 10.1021/acscatal.7b00688] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 04/07/2017] [Indexed: 01/20/2023]
Abstract
Soybean lipoxygenase (SLO) is a prototype for nonadiabatic hydrogen tunneling reactions and, as such, has served as the subject of numerous theoretical studies. In this work, we report a nearly temperature-independent kinetic isotope effect (KIE) with an average KIE value of 661 ± 27 for a double mutant (DM) of SLO at six temperatures. The data are well-reproduced within a vibronically nonadiabatic proton-coupled electron transfer model in which the active site has become rigidified compared to wild-type enzyme and single-site mutants. A combined temperature-pressure perturbation further shows that temperature-dependent global motions within DM-SLO are more resistant to perturbation by elevated pressure. These findings provide strong experimental support for the model of hydrogen tunneling in SLO, where optimization of both local protein and ligand motions and distal conformational rearrangements is a prerequisite for effective proton vibrational wave function overlap between the substrate and the active-site iron cofactor.
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Affiliation(s)
- Shenshen Hu
- Department of Chemistry, Department of Molecular and Cell Biology, and California Institute
for Quantitative Biosciences, University
of California, Berkeley, California 94720, United States
| | - Alexander V. Soudackov
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Sharon Hammes-Schiffer
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Judith P. Klinman
- Department of Chemistry, Department of Molecular and Cell Biology, and California Institute
for Quantitative Biosciences, University
of California, Berkeley, California 94720, United States
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9
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Bao JL, Truhlar DG. Variational transition state theory: theoretical framework and recent developments. Chem Soc Rev 2017; 46:7548-7596. [DOI: 10.1039/c7cs00602k] [Citation(s) in RCA: 207] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
This article reviews the fundamentals of variational transition state theory (VTST), its recent theoretical development, and some modern applications.
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Affiliation(s)
- Junwei Lucas Bao
- Department of Chemistry
- Chemical Theory Center, and Minnesota Supercomputing Institute
- University of Minnesota
- Minneapolis
- USA
| | - Donald G. Truhlar
- Department of Chemistry
- Chemical Theory Center, and Minnesota Supercomputing Institute
- University of Minnesota
- Minneapolis
- USA
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10
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González-Lafont À, Lluch JM. Kinetic isotope effects in chemical and biochemical reactions: physical basis and theoretical methods of calculation. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2016. [DOI: 10.1002/wcms.1268] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Àngels González-Lafont
- Institut de Biotecnologia i de Biomedicina and Departament de Química; Universitat Autònoma de Barcelona; Bellaterra, Barcelona Spain
| | - José M. Lluch
- Institut de Biotecnologia i de Biomedicina and Departament de Química; Universitat Autònoma de Barcelona; Bellaterra, Barcelona Spain
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11
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Karmakar S, Datta A. Role of Heavy Atom Tunneling in Myers–Saito Cyclization of Cyclic Enyne-Cumulene Systems. J Phys Chem B 2016; 120:945-50. [DOI: 10.1021/acs.jpcb.5b12465] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sharmistha Karmakar
- Department of Spectroscopy, Indian Association for the Cultivation of Science, 2A and 2B Raja S. C. Mullick Road,
Jadavpur − 700032, Kolkata, West Bengal, India
| | - Ayan Datta
- Department of Spectroscopy, Indian Association for the Cultivation of Science, 2A and 2B Raja S. C. Mullick Road,
Jadavpur − 700032, Kolkata, West Bengal, India
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12
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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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13
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Truhlar DG. Transition state theory for enzyme kinetics. Arch Biochem Biophys 2015; 582:10-7. [PMID: 26008760 PMCID: PMC4555010 DOI: 10.1016/j.abb.2015.05.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 05/15/2015] [Accepted: 05/18/2015] [Indexed: 11/18/2022]
Abstract
This article is an essay that discusses the concepts underlying the application of modern transition state theory to reactions in enzymes. Issues covered include the potential of mean force, the quantization of vibrations, the free energy of activation, and transmission coefficients to account for nonequilibrium effect, recrossing, and tunneling.
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Affiliation(s)
- Donald G Truhlar
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN 55455, United States.
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14
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Vardi-Kilshtain A, Nitoker N, Major DT. Nuclear quantum effects and kinetic isotope effects in enzyme reactions. Arch Biochem Biophys 2015; 582:18-27. [DOI: 10.1016/j.abb.2015.03.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 03/02/2015] [Accepted: 03/03/2015] [Indexed: 11/28/2022]
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15
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Kwon YH, Mai BK, Lee YM, Dhuri SN, Mandal D, Cho KB, Kim Y, Shaik S, Nam W. Determination of Spin Inversion Probability, H-Tunneling Correction, and Regioselectivity in the Two-State Reactivity of Nonheme Iron(IV)-Oxo Complexes. J Phys Chem Lett 2015; 6:1472-1476. [PMID: 26263154 DOI: 10.1021/acs.jpclett.5b00527] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We show by experiments that nonheme Fe(IV)O species react with cyclohexene to yield selective hydrogen atom transfer (HAT) reactions with virtually no C═C epoxidation. Straightforward DFT calculations reveal, however, that C═C epoxidation on the S = 2 state possesses a low-energy barrier and should contribute substantially to the oxidation of cyclohexene by the nonheme Fe(IV)O species. By modeling the selectivity of this two-site reactivity, we show that an interplay of tunneling and spin inversion probability (SIP) reverses the apparent barriers and prefers exclusive S = 1 HAT over mixed HAT and C═C epoxidation on S = 2. The model enables us to derive a SIP value by combining experimental and theoretical results.
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Affiliation(s)
- Yoon Hye Kwon
- †Department of Chemistry and Nano Science, Ewha Womans University, Seoul 120-750, Korea
| | - Binh Khanh Mai
- ‡Department of Applied Chemistry and Institute of Natural Sciences, Kyung Hee University, Gyeonggi-do 446-701, Korea
| | - Yong-Min Lee
- †Department of Chemistry and Nano Science, Ewha Womans University, Seoul 120-750, Korea
| | - Sunder N Dhuri
- †Department of Chemistry and Nano Science, Ewha Womans University, Seoul 120-750, Korea
- ¶Department of Chemistry, Goa University, Goa 403 206, India
| | - Debasish Mandal
- §Institute of Chemistry and the Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - Kyung-Bin Cho
- †Department of Chemistry and Nano Science, Ewha Womans University, Seoul 120-750, Korea
| | - Yongho Kim
- ‡Department of Applied Chemistry and Institute of Natural Sciences, Kyung Hee University, Gyeonggi-do 446-701, Korea
| | - Sason Shaik
- §Institute of Chemistry and the Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - Wonwoo Nam
- †Department of Chemistry and Nano Science, Ewha Womans University, Seoul 120-750, Korea
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16
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The entropic contributions in vitamin B12 enzymes still reflect the electrostatic paradigm. Proc Natl Acad Sci U S A 2015; 112:4328-33. [PMID: 25805820 DOI: 10.1073/pnas.1503828112] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The catalytic power of enzymes containing coenzyme B12 has been, in some respects, the "last bastion" for the strain hypothesis. Our previous study of this system established by a careful sampling that the major part of the catalytic effect is due to the electrostatic interaction between the ribose of the ado group and the protein and that the strain contribution is very small. This finding has not been sufficiently appreciated due to misunderstandings of the power of the empirical valence bond (EVB) calculations and the need of sufficient sampling. Furthermore, some interesting new experiments point toward entropic effects as the source of the catalytic power, casting doubt on the validity of the electrostatic idea, at least, in the case of B12 enzymes. Here, we focus on the observation of the entropic effects and on analyzing their origin. We clarify that our EVB approach evaluates free energies rather than enthalpies and demonstrate by using the restraint release (RR) approach that the observed entropic contribution to the activation barrier is of electrostatic origin. Our study illustrates the power of the RR approach by evaluating the entropic contributions to catalysis and provides further support to our paradigm for the origin of the catalytic power of B12 enzymes. Overall, our study provides major support to our electrostatic preorganization idea and also highlights the basic requirements from ab initio quantum mechanics/molecular mechanics calculations of activation free energies of enzymatic reactions.
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17
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Abstract
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The active
site of an enzyme is surrounded by a fluctuating environment of protein
and solvent conformational states, and a realistic calculation of
chemical reaction rates and kinetic isotope effects of enzyme-catalyzed
reactions must take account of this environmental diversity. Ensemble-averaged
variational transition state theory with multidimensional tunneling
(EA-VTST/MT) was developed as a way to carry out such calculations.
This theory incorporates ensemble averaging, quantized vibrational
energies, energy, tunneling, and recrossing of transition state dividing
surfaces in a systematic way. It has been applied successfully to
a number of hydrogen-, proton-, and hydride-transfer reactions. The
theory also exposes the set of effects that should be considered in
reliable rate constants calculations. We first review the basic
theory and the steps in the calculation. A key role is played by the
generalized free energy of activation profile, which is obtained by
quantizing the classical potential of mean force as a function of
a reaction coordinate because the one-way flux through the transition
state dividing surface can be written in terms of the generalized
free energy of activation. A recrossing transmission coefficient accounts
for the difference between the one-way flux through the chosen transition
state dividing surface and the net flux, and a tunneling transmission
coefficient converts classical motion along the reaction coordinate
to quantum mechanical motion. The tunneling calculation is multidimensional,
accounting for the change in vibrational frequencies along the tunneling
path and shortening of the tunneling path with respect to the minimum
energy path (MEP), as promoted by reaction-path curvature. The generalized
free energy of activation and the transmission coefficients both involve
averaging over an ensemble of reaction paths and conformations, and
this includes the coupling of protein motions to the rearrangement
of chemical bonds in a statistical mechanically correct way. The standard
deviations of the transmissions coefficients provide information on
the diversity of the distribution of reaction paths, barriers, and
protein conformations along the members of an ensemble of reaction
paths passing through the transition state. We first illustrate
the theory by discussing the application to both wild-type and mutant Escherichia coli dihydrofolate reductase and hyperthermophilic Thermotoga maritima dihydrofolate reductase (DHFR); DHFR
is of special interest because the protein conformational changes
have been widely studied. Then we present shorter discussions of several
other applications of EA-VTST/MT to transfer of protons, hydrogen
atoms, and hydride ions and their deuterated analogs. Systems discussed
include hydride transfer in alcohol dehydrogenase, xylose isomerase,
and thymidylate synthase, proton transfer in methylamine dehydrogenase,
hydrogen atom transfer in methylmalonyl-CoA mutase, and nucleophilic
substitution in haloalkane dehalogenase and two-dimensional potentials
of mean force for potentially coupled proton and hydride transfer
in the β-oxidation of butyryl-coenzyme A catalyzed by short-chain
acyl-CoA dehydrogenase and in the pyruvate to lactate transformation
catalyzed by lactate dehydrogenase.
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Affiliation(s)
- Laura Masgrau
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain
| | - Donald G. Truhlar
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455-0431, United States
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18
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Menon BRK, Menon N, Fisher K, Rigby SEJ, Leys D, Scrutton NS. Glutamate 338 is an electrostatic facilitator of C-Co bond breakage in a dynamic/electrostatic model of catalysis by ornithine aminomutase. FEBS J 2015; 282:1242-55. [PMID: 25627283 PMCID: PMC4413051 DOI: 10.1111/febs.13215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 01/16/2015] [Accepted: 01/23/2015] [Indexed: 01/04/2023]
Abstract
How cobalamin-dependent enzymes promote C–Co homolysis to initiate radical catalysis has been debated extensively. For the pyridoxal 5′-phosphate and cobalamin-dependent enzymes lysine 5,6-aminomutase and ornithine 4,5-aminomutase (OAM), large-scale re-orientation of the cobalamin-binding domain linked to C–Co bond breakage has been proposed. In these models, substrate binding triggers dynamic sampling of the B12-binding Rossmann domain to achieve a catalytically competent ‘closed’ conformational state. In ‘closed’ conformations of OAM, Glu338 is thought to facilitate C–Co bond breakage by close association with the cobalamin adenosyl group. We investigated this using stopped-flow continuous-wave photolysis, viscosity dependence kinetic measurements, and electron paramagnetic resonance spectroscopy of a series of Glu338 variants. We found that substrate-induced C–Co bond homolysis is compromised in Glu388 variant forms of OAM, although photolysis of the C–Co bond is not affected by the identity of residue 338. Electrostatic interactions of Glu338 with the 5′-deoxyadenosyl group of B12 potentiate C–Co bond homolysis in ‘closed’ conformations only; these conformations are unlocked by substrate binding. Our studies extend earlier models that identified a requirement for large-scale motion of the cobalamin domain. Our findings indicate that large-scale motion is required to pre-organize the active site by enabling transient formation of ‘closed’ conformations of OAM. In ‘closed’ conformations, Glu338 interacts with the 5′-deoxyadenosyl group of cobalamin. This interaction is required to potentiate C–Co homolysis, and is a crucial component of the approximately 1012 rate enhancement achieved by cobalamin-dependent enzymes for C–Co bond homolysis.
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Affiliation(s)
- Binuraj R K Menon
- Biotechnology and Biological Sciences Research Council/Engineering and Physical Sciences Research Council Centre for Synthetic Biology of Fine and Speciality Chemicals, Manchester Institute of Biotechnology, Faculty of Life Sciences, The University of Manchester, UK
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19
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Mandal D, Ramanan R, Usharani D, Janardanan D, Wang B, Shaik S. How does tunneling contribute to counterintuitive H-abstraction reactivity of nonheme Fe(IV)O oxidants with alkanes? J Am Chem Soc 2015; 137:722-33. [PMID: 25513834 DOI: 10.1021/ja509465w] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
This article addresses the intriguing hydrogen-abstraction (H-abstraction) and oxygen-transfer (O-transfer) reactivity of a series of nonheme [Fe(IV)(O)(TMC)(Lax)](z+) complexes, with a tetramethyl cyclam ligand and a variable axial ligand (Lax), toward three substrates: 1,4-cyclohexadiene, 9,10-dihydroanthracene, and triphenyl phosphine. Experimentally, O-transfer-reactivity follows the relative electrophilicity of the complexes, whereas the corresponding H-abstraction-reactivity generally increases as the axial ligand becomes a better electron donor, hence exhibiting an antielectrophilic trend. Our theoretical results show that the antielectrophilic trend in H-abstraction is affected by tunneling contributions. Room-temperature tunneling increases with increase of the electron donation power of the axial-ligand, and this reverses the natural electrophilic trend, as revealed through calculations without tunneling, and leads to the observed antielectrophilic trend. By contrast, O-transfer-reactivity, not being subject to tunneling, retains an electrophilic-dependent reactivity trend, as revealed experimentally and computationally. Tunneling-corrected kinetic-isotope effect (KIE) calculations matched the experimental KIE values only if all of the H-abstraction reactions proceeded on the quintet state (S = 2) surface. As such, the present results corroborate the initially predicted two-state reactivity (TSR) scenario for these reactions. The increase of tunneling with the electron-releasing power of the axial ligand, and the reversal of the "natural" reactivity pattern, support the "tunneling control" hypothesis (Schreiner et al., ref 19). Should these predictions be corroborated, the entire field of C-H bond activation in bioinorganic chemistry would lay open to reinvestigation.
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Affiliation(s)
- Debasish Mandal
- Institute of Chemistry and the Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem , 91904 Jerusalem, Israel
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20
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Trakhtenberg LI. Tunneling transfer of atomic particles in chemical and biological reactions: The role of intermolecular vibrations and media reorganization. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2014. [DOI: 10.1134/s003602441411020x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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21
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Brunk E, Kellett W, Richards NGJ, Rothlisberger U. A mechanochemical switch to control radical intermediates. Biochemistry 2014; 53:3830-8. [PMID: 24846280 PMCID: PMC4067147 DOI: 10.1021/bi500050k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 05/17/2014] [Indexed: 12/24/2022]
Abstract
B₁₂-dependent enzymes employ radical species with exceptional prowess to catalyze some of the most chemically challenging, thermodynamically unfavorable reactions. However, dealing with highly reactive intermediates is an extremely demanding task, requiring sophisticated control strategies to prevent unwanted side reactions. Using hybrid quantum mechanical/molecular mechanical simulations, we follow the full catalytic cycle of an AdoB₁₂-dependent enzyme and present the details of a mechanism that utilizes a highly effective mechanochemical switch. When the switch is "off", the 5'-deoxyadenosyl radical moiety is stabilized by releasing the internal strain of an enzyme-imposed conformation. Turning the switch "on," the enzyme environment becomes the driving force to impose a distinct conformation of the 5'-deoxyadenosyl radical to avoid deleterious radical transfer. This mechanochemical switch illustrates the elaborate way in which enzymes attain selectivity of extremely chemically challenging reactions.
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Affiliation(s)
- Elizabeth Brunk
- Laboratory
of Computational Chemistry and Biochemistry, EPFL, Lausanne, Switzerland 1015
| | - Whitney
F. Kellett
- Indiana
University-Purdue University, Indianapolis, Indiana 46202, United States
| | - Nigel G. J. Richards
- Indiana
University-Purdue University, Indianapolis, Indiana 46202, United States
| | - Ursula Rothlisberger
- Laboratory
of Computational Chemistry and Biochemistry, EPFL, Lausanne, Switzerland 1015
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22
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Karmakar S, Datta A. Role of Quantum Mechanical Tunneling on the γ-Effect of Silicon on Carbenes in 3-Trimethylsilylcyclobutylidene. J Phys Chem B 2014; 118:2553-8. [DOI: 10.1021/jp4116029] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sharmistha Karmakar
- Department of Spectroscopy, Indian Association for the Cultivation of Science, 2A and 2B Raja S. C. Mullick Road, Jadavpur - 700032, Kolkata, West Bengal, India
| | - Ayan Datta
- Department of Spectroscopy, Indian Association for the Cultivation of Science, 2A and 2B Raja S. C. Mullick Road, Jadavpur - 700032, Kolkata, West Bengal, India
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23
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Román-Meléndez GD, von Glehn P, Harvey JN, Mulholland AJ, Marsh ENG. Role of active site residues in promoting cobalt-carbon bond homolysis in adenosylcobalamin-dependent mutases revealed through experiment and computation. Biochemistry 2014; 53:169-77. [PMID: 24341954 PMCID: PMC3928028 DOI: 10.1021/bi4012644] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Adenosylcobalamin (AdoCbl) serves as a source of reactive free radicals that are generated by homolytic scission of the coenzyme's cobalt-carbon bond. AdoCbl-dependent enzymes accelerate AdoCbl homolysis by ∼10(12)-fold, but the mechanism by which this is accomplished remains unclear. We have combined experimental and computational approaches to gain molecular-level insight into this process for glutamate mutase. Two residues, glutamate 330 and lysine 326, form hydrogen bonds with the adenosyl group of the coenzyme. A series of mutations that impair the enzyme's ability to catalyze coenzyme homolysis and tritium exchange with the substrate by 2-4 orders of magnitude were introduced at these positions. These mutations, together with the wild-type enzyme, were also characterized in silico by molecular dynamics simulations of the enzyme-AdoCbl-substrate complex with AdoCbl modeled in the associated (Co-C bond formed) or dissociated [adenosyl radical with cob(II)alamin] state. The simulations reveal that the number of hydrogen bonds between the adenosyl group and the protein side chains increases in the homolytically dissociated state, with respect to the associated state, for both the wild-type and mutant enzymes. The mutations also cause a progressive increase in the mean distance between the 5'-carbon of the adenosyl radical and the abstractable hydrogen of the substrate. Interestingly, the distance between the 5'-carbon and substrate hydrogen, determined computationally, was found to inversely correlate with the log k for tritium exchange (r = 0.93) determined experimentally. Taken together, these results point to a dual role for these residues: they both stabilize the homolytic state through electrostatic interactions between the protein and the dissociated coenzyme and correctly position the adenosyl radical to facilitate the abstraction of hydrogen from the substrate.
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Affiliation(s)
| | - Patrick von Glehn
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, UK
| | - Jeremy N. Harvey
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, UK
| | - Adrian J. Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, UK
| | - E. Neil G. Marsh
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
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24
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Klippenstein SJ, Pande VS, Truhlar DG. Chemical Kinetics and Mechanisms of Complex Systems: A Perspective on Recent Theoretical Advances. J Am Chem Soc 2014; 136:528-46. [DOI: 10.1021/ja408723a] [Citation(s) in RCA: 187] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Stephen J. Klippenstein
- Chemical
Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Vijay S. Pande
- Department
of Chemistry and Structural Biology, Stanford University, Stanford, California 94305, United States
| | - Donald G. Truhlar
- Department
of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
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25
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Zheng J, Xu X, Meana-Pañeda R, Truhlar DG. Army ants tunneling for classical simulations. Chem Sci 2014. [DOI: 10.1039/c3sc53290a] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We present an algorithm, called army ants tunneling, for adding tunneling to classical trajectories by means of quantal rare event sampling.
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Affiliation(s)
- Jingjing Zheng
- Department of Chemistry
- Chemical Theory Center, and Supercomputing Institute
- University of Minnesota
- Minneapolis, USA
| | - Xuefei Xu
- Department of Chemistry
- Chemical Theory Center, and Supercomputing Institute
- University of Minnesota
- Minneapolis, USA
| | - Rubén Meana-Pañeda
- Department of Chemistry
- Chemical Theory Center, and Supercomputing Institute
- University of Minnesota
- Minneapolis, USA
| | - Donald G. Truhlar
- Department of Chemistry
- Chemical Theory Center, and Supercomputing Institute
- University of Minnesota
- Minneapolis, USA
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26
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Wiebe H, Prachnau M, Weinberg N. Hydrogen transfer reactions in viscous media — Potential and free energy surfaces in solvent–solute coordinates and their kinetic implications. CAN J CHEM 2013. [DOI: 10.1139/cjc-2012-0554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Two-dimensional potential energy and free energy surfaces are obtained using quantum mechanical and molecular dynamics calculations for four hydrogen transfer reactions in n-hexane solvent: the methyl–methane, n-propyl–n-propane, n-pentyl–n-pentane, and t-butyl–isobutane systems. The resultant surfaces have similar landscapes despite the fact the equilibrated solvent cavities for these systems are notably different in size and shape. The kinetic implications of these landscapes are discussed. The Arrhenius and tunneling kinetics of hydrogen transfer in nonpolar hydrocarbon solute–solvent systems are not expected to show any significant viscosity dependence.
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Affiliation(s)
- Heather Wiebe
- Department of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Melissa Prachnau
- Department of Chemistry, University of the Fraser Valley, Abbotsford, BC V2S 7M8, Canada
| | - Noham Weinberg
- Department of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
- Department of Chemistry, University of the Fraser Valley, Abbotsford, BC V2S 7M8, Canada
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27
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28
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Buckel W, Friedrich P, Golding BT. Wasserstoffbrücken führen das kurzlebige 5′-Desoxyadenosylradikal zum Tatort. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201205299] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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29
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Buckel W, Friedrich P, Golding BT. Hydrogen bonds guide the short-lived 5'-deoxyadenosyl radical to the place of action. Angew Chem Int Ed Engl 2012; 51:9974-6. [PMID: 22945861 DOI: 10.1002/anie.201205299] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Indexed: 11/08/2022]
Affiliation(s)
- Wolfgang Buckel
- Laboratorium für Mikrobiologie, Fachbereich Biologie, Philipps-Universität, 35032 Marburg, Germany.
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30
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Jose D, Datta A. Tunneling Governs Intramolecular Proton Transfer in Thiotropolone at Room Temperature. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201203355] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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31
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Jose D, Datta A. Tunneling Governs Intramolecular Proton Transfer in Thiotropolone at Room Temperature. Angew Chem Int Ed Engl 2012; 51:9389-92. [DOI: 10.1002/anie.201203355] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Revised: 07/26/2012] [Indexed: 11/11/2022]
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32
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Adenosylcobalamin enzymes: theory and experiment begin to converge. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1824:1154-64. [PMID: 22516318 DOI: 10.1016/j.bbapap.2012.03.012] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Revised: 02/04/2012] [Accepted: 03/27/2012] [Indexed: 11/21/2022]
Abstract
Adenosylcobalamin (coenzyme B(12)) serves as the cofactor for a group of enzymes that catalyze unusual rearrangement or elimination reactions. The role of the cofactor as the initiator of reactive free radicals needed for these reactions is well established. Less clear is how these enzymes activate the coenzyme towards homolysis and control the radicals once generated. The availability of high resolution X-ray structures combined with detailed kinetic and spectroscopic analyses have allowed several adenosylcobalamin enzymes to be computationally modeled in some detail. Computer simulations have generally obtained good agreement with experimental data and provided valuable insight into the mechanisms of these unusual reactions. Importantly, atomistic modeling of the enzymes has allowed the role of specific interactions between protein, substrate and coenzyme to be explored, leading to mechanistic predictions that can now be tested experimentally. This article is part of a Special Issue entitled: Radical SAM enzymes and Radical Enzymology.
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33
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Glowacki DR, Harvey JN, Mulholland AJ. Taking Ockham's razor to enzyme dynamics and catalysis. Nat Chem 2012; 4:169-76. [PMID: 22354430 DOI: 10.1038/nchem.1244] [Citation(s) in RCA: 181] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The role of protein dynamics in enzyme catalysis is a matter of intense current debate. Enzyme-catalysed reactions that involve significant quantum tunnelling can give rise to experimental kinetic isotope effects with complex temperature dependences, and it has been suggested that standard statistical rate theories, such as transition-state theory, are inadequate for their explanation. Here we introduce aspects of transition-state theory relevant to the study of enzyme reactivity, taking cues from chemical kinetics and dynamics studies of small molecules in the gas phase and in solution--where breakdowns of statistical theories have received significant attention and their origins are relatively better understood. We discuss recent theoretical approaches to understanding enzyme activity and then show how experimental observations for a number of enzymes may be reproduced using a transition-state-theory framework with physically reasonable parameters. Essential to this simple model is the inclusion of multiple conformations with different reactivity.
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Affiliation(s)
- David R Glowacki
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK.
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34
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Pang J, Li X, Morokuma K, Scrutton NS, Sutcliffe MJ. Large-Scale Domain Conformational Change Is Coupled to the Activation of the Co–C Bond in the B12-Dependent Enzyme Ornithine 4,5-Aminomutase: A Computational Study. J Am Chem Soc 2012; 134:2367-77. [DOI: 10.1021/ja210417k] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
| | - Xin Li
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
| | - Keiji Morokuma
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
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35
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Bucher D, Sandala GM, Durbeej B, Radom L, Smith DM. The Elusive 5′-Deoxyadenosyl Radical in Coenzyme-B12-Mediated Reactions. J Am Chem Soc 2012; 134:1591-9. [DOI: 10.1021/ja207809b] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Denis Bucher
- School of Chemistry and ARC Centre of Excellence
for Free Radical Chemistry
and Biotechnology, University of Sydney, Sydney, NSW 2006, Australia
| | - Gregory M. Sandala
- School of Chemistry and ARC Centre of Excellence
for Free Radical Chemistry
and Biotechnology, University of Sydney, Sydney, NSW 2006, Australia
- Division of Organic
Chemistry and Biochemistry, Ruđer Bošković Institute, 10002 Zagreb, Croatia
| | - Bo Durbeej
- Division of Computational
Physics, IFM Theory and Modelling, Linköping University, SE-581 83 Linköping, Sweden
| | - Leo Radom
- School of Chemistry and ARC Centre of Excellence
for Free Radical Chemistry
and Biotechnology, University of Sydney, Sydney, NSW 2006, Australia
| | - David M. Smith
- Division of Organic
Chemistry and Biochemistry, Ruđer Bošković Institute, 10002 Zagreb, Croatia
- Computer-Chemie-Centrum, University of Erlangen-Nürnberg, 91052 Erlangen, Germany
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36
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Dutta S, Rock W, Cook RJ, Kohen A, Cheatum CM. Two-dimensional infrared spectroscopy of azido-nicotinamide adenine dinucleotide in water. J Chem Phys 2011; 135:055106. [PMID: 21823737 PMCID: PMC3162616 DOI: 10.1063/1.3623418] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2011] [Accepted: 07/12/2011] [Indexed: 11/14/2022] Open
Abstract
Mid-IR active analogs of enzyme cofactors have the potential to be important spectroscopic reporters of enzyme active site dynamics. Azido-nicotinamide adenine dinucleotide (NAD(+)), which has been recently synthesized in our laboratory, is a mid-IR active analog of NAD(+), a ubiquitous redox cofactor in biology. In this study, we measure the frequency-frequency time correlation function for the antisymmetric stretching vibration of the azido group of azido-NAD(+) in water. Our results are consistent with previous studies of pseudohalides in water. We conclude that azido-NAD(+) is sensitive to local environmental fluctuations, which, in water, are dominated by hydrogen-bond dynamics of the water molecules around the probe. Our results demonstrate the potential of azido-NAD(+) as a vibrational probe and illustrate the potential of substituted NAD(+)-analogs as reporters of local structural dynamics that could be used for studies of protein dynamics in NAD-dependent enzymes.
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Affiliation(s)
- Samrat Dutta
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, USA
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37
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Rommel JB, Kästner J. The fragmentation-recombination mechanism of the enzyme glutamate mutase studied by QM/MM simulations. J Am Chem Soc 2011; 133:10195-203. [PMID: 21612278 DOI: 10.1021/ja202312d] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The radical mechanism of the conversion of glutamate to methylaspartate catalyzed by glutamate mutase is studied with quantum mechanical/molecular mechanical (QM/MM) simulations based on density functional theory (DFT/MM). The hydrogen transfer between the substrate and the cofactor is found to be rate limiting with a barrier of 101.1 kJ mol(-1). A careful comparison to the uncatalyzed reaction in water is performed. The protein influences the reaction predominantly electrostatically and to a lesser degree sterically. Our calculations shed light on the atomistic details of the reaction mechanism. The well-known arginine claw and Glu 171 ( Clostridium cochlearium notation) are found to have the strongest influence on the reaction. However, a catalytic role of Glu 214, Lys 322, Gln 147, Glu 330, Lys 326, and Met 294 is found as well. The arginine claw keeps the intermediates in place and is probably responsible for the enantioselectivity. Glu 171 temporarily accepts a proton from the glutamyl radical intermediate and donates it back at the end of the reaction. We relate our results to experimental data when available. Our simulations lead to further understanding of how glutamate mutase catalyzes the carbon skeleton rearrangement of glutamate.
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Affiliation(s)
- Judith B Rommel
- Computational Biochemistry Group, Institute of Theoretical Chemistry, University of Stuttgart, Stuttgart, Germany
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38
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Fleming DG, Arseneau DJ, Sukhorukov O, Brewer JH, Mielke SL, Schatz GC, Garrett BC, Peterson KA, Truhlar DG. Kinetic Isotope Effects for the Reactions of Muonic Helium and Muonium with H
2. Science 2011; 331:448-50. [DOI: 10.1126/science.1199421] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Donald G. Fleming
- TRIUMF and Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z1
| | - Donald J. Arseneau
- TRIUMF and Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z1
| | - Oleksandr Sukhorukov
- TRIUMF and Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z1
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - Jess H. Brewer
- Department of Physics, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z1
| | - Steven L. Mielke
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455–0431, USA
| | - George C. Schatz
- Department of Chemistry, Northwestern University, Evanston, IL 60208–3113, USA
| | - Bruce C. Garrett
- Chemical and Material Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Kirk A. Peterson
- Department of Chemistry, Washington State University, Pullman, WA 99164–4630, USA
| | - Donald G. Truhlar
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455–0431, USA
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39
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Meana-Pañeda R, Truhlar DG, Fernández-Ramos A. Direct Dynamics Implementation of the Least-Action Tunneling Transmission Coefficient. Application to the CH4/CD3H/CD4 + CF3 Abstraction Reactions. J Chem Theory Comput 2010; 6:3015-25. [PMID: 26616766 DOI: 10.1021/ct100285a] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present two new direct dynamics algorithms for calculating transmission coefficients of polyatomic chemical reactions by the multidimensional least-action tunneling approximation. The new algorithms are called the interpolated least-action tunneling method based on one-dimensional interpolation (ILAT1D) and the double interpolated least-action tunneling (DILAT) method. The DILAT algorithm, which uses a one-dimensional spline under tension to interpolate both of the effective potentials along the nonadiabatic portions of tunneling paths and the imaginary action integrals as functions of tunneling energies, was designed for the calculation of multidimensional LAT transmission coefficients for very large polyatomic systems. The performance of this algorithm has been tested for the CH4/CD3H/CD4 + CF3 hydrogen abstraction reactions with encouraging results, i.e., when the fitting is performed using 13 points, the algorithm is about 30 times faster than the full calculation with deviations that are smaller than 5%. This makes direct dynamics least-action tunneling calculations practical for larger systems, higher levels of electron correlation, and/or larger basis sets.
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Affiliation(s)
- Rubén Meana-Pañeda
- Department of Physical Chemistry and Center for Research in Biological Chemistry and Molecular Materials, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain and Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431
| | - Donald G Truhlar
- Department of Physical Chemistry and Center for Research in Biological Chemistry and Molecular Materials, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain and Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431
| | - Antonio Fernández-Ramos
- Department of Physical Chemistry and Center for Research in Biological Chemistry and Molecular Materials, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain and Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431
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40
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Swiderek K, Paneth P. Importance of the lactate dehydrogenase quaternary structure in theoretical calculations. J Phys Chem B 2010; 114:3393-7. [PMID: 20155895 DOI: 10.1021/jp100026z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Using the example of lactate dehydrogenase, we show that enzyme quaternary structure has an important influence on the structure of the active site and that models that comprise all amino acids in the vicinity of an active site, but are missing this structural information, can lead to incorrect results. We also show that binding isotope effects are very sensitive to the geometric parameters, and thus one should be very cautious when interpreting results obtained with models that are too coarse. In terms of the type of hydrogen bonds, our results indicate that binding isotope effects are pronounced only when a hydrogen bond exhibits some covalent character.
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Affiliation(s)
- Katarzyna Swiderek
- Institute of Applied Radiation Chemistry, Technical University of Lodz, ulica Zeromskiego 116, 90-924 Lodz, Poland
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41
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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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42
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Ouchi A, Nagaoka SI, Mukai K. Tunneling Effect in Regeneration Reaction of Vitamin E by Ubiquinol. J Phys Chem B 2010; 114:6601-7. [DOI: 10.1021/jp910856m] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Aya Ouchi
- Department of Chemistry, Faculty of Science, Ehime University, Matsuyama 790-8577, Japan
| | - Shin-ichi Nagaoka
- Department of Chemistry, Faculty of Science, Ehime University, Matsuyama 790-8577, Japan
| | - Kazuo Mukai
- Department of Chemistry, Faculty of Science, Ehime University, Matsuyama 790-8577, Japan
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Yoon M, Song H, Håkansson K, Marsh ENG. Hydrogen tunneling in adenosylcobalamin-dependent glutamate mutase: evidence from intrinsic kinetic isotope effects measured by intramolecular competition. Biochemistry 2010; 49:3168-73. [PMID: 20225826 DOI: 10.1021/bi1001695] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hydrogen atom transfer reactions between the substrate and coenzyme are key mechanistic features of all adenosylcobalamin-dependent enzymes. For one of these enzymes, glutamate mutase, we have investigated whether hydrogen tunneling makes a significant contribution to the mechanism by examining the temperature dependence of the deuterium kinetic isotope effect associated with the transfer of a hydrogen atom from methylaspartate to the coenzyme. To do this, we designed a novel intramolecular competition experiment that allowed us to measure the intrinsic kinetic isotope effect, even though hydrogen transfer may not be rate-determining. From the Arrhenius plot of the kinetic isotope effect, the ratio of the pre-exponential factors (A(H)/A(D)) was 0.17 +/- 0.04 and the isotope effect on the activation energy [DeltaE(a(D-H))] was 1.94 +/- 0.13 kcal/mol. The results imply that a significant degree of hydrogen tunneling occurs in glutamate mutase, even though the intrinsic kinetic isotope effects are well within the semiclassical limit and are much smaller than those measured for other AdoCbl enzymes and model reactions for which hydrogen tunneling has been implicated.
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Affiliation(s)
- Miri Yoon
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, USA
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44
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Truhlar DG. Tunneling in enzymatic and nonenzymatic hydrogen transfer reactions. J PHYS ORG CHEM 2010. [DOI: 10.1002/poc.1676] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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45
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Marsh ENG, Patterson DP, Li L. Adenosyl radical: reagent and catalyst in enzyme reactions. Chembiochem 2010; 11:604-21. [PMID: 20191656 PMCID: PMC3011887 DOI: 10.1002/cbic.200900777] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2009] [Indexed: 12/17/2022]
Abstract
Adenosine is undoubtedly an ancient biological molecule that is a component of many enzyme cofactors: ATP, FADH, NAD(P)H, and coenzyme A, to name but a few, and, of course, of RNA. Here we present an overview of the role of adenosine in its most reactive form: as an organic radical formed either by homolytic cleavage of adenosylcobalamin (coenzyme B(12), AdoCbl) or by single-electron reduction of S-adenosylmethionine (AdoMet) complexed to an iron-sulfur cluster. Although many of the enzymes we discuss are newly discovered, adenosine's role as a radical cofactor most likely arose very early in evolution, before the advent of photosynthesis and the production of molecular oxygen, which rapidly inactivates many radical enzymes. AdoCbl-dependent enzymes appear to be confined to a rather narrow repertoire of rearrangement reactions involving 1,2-hydrogen atom migrations; nevertheless, mechanistic insights gained from studying these enzymes have proved extremely valuable in understanding how enzymes generate and control highly reactive free radical intermediates. In contrast, there has been a recent explosion in the number of radical-AdoMet enzymes discovered that catalyze a remarkably wide range of chemically challenging reactions; here there is much still to learn about their mechanisms. Although all the radical-AdoMet enzymes so far characterized come from anaerobically growing microbes and are very oxygen sensitive, there is tantalizing evidence that some of these enzymes might be active in aerobic organisms including humans.
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Affiliation(s)
- E. Neil G. Marsh
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Dustin P. Patterson
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Lei Li
- Department of Chemistry and Chemical Biology, Indiana University – Purdue University Indianapolis, Indianapolis, IN 46202, USA
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Kamerlin SCL, Warshel A. An Analysis of All the Relevant Facts and Arguments Indicates that Enzyme Catalysis Does Not Involve Large Contributions from Nuclear Tunneling. J PHYS ORG CHEM 2010; 23:677-684. [PMID: 21494414 DOI: 10.1002/poc.1620] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Shina C L Kamerlin
- Department of Chemistry, University of Southern California, 3620 McClintock Ave., Los Angeles CA-90089, USA
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Durbeej B, Sandala GM, Bucher D, Smith DM, Radom L. On the importance of ribose orientation in the substrate activation of the coenzyme B12-dependent mutases. Chemistry 2009; 15:8578-8585. [PMID: 19630017 DOI: 10.1002/chem.200901002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The degree to which the corrin ring portion of coenzyme B(12) can facilitate the H-atom-abstraction step in the glutamate mutase (GM)-catalyzed reaction of (S)-glutamate has been investigated with density functional theory. The crystal structure of GM identifies two possible orientations of the ribose portion of coenzyme B(12). In one orientation (A), the OH groups of the ribose extend away from the corrin ring, whereas in the other orientation (B) the OH groups, especially that involving O3', are instead directed towards the corrin ring. Our calculations identify a sizable stabilization amounting to about 30 kJ mol(-1) in the transition structure (TS) complex corresponding to orientation B (TS(B)CorIm). In the TS complex where the ribose instead is positioned in orientation A, no such effect is manifested. The observed stabilization in TS(B)CorIm appears to be the result of favorable interactions involving O3' and the corrin ring, including a C-HO hydrogen bond. We find that the degree of stabilization is not particularly sensitive to the Co-C distance. Our calculations show that any potential stabilization afforded to the H-atom-abstraction step by coenzyme B(12) is sensitive to the orientation of the ribose moiety.
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Affiliation(s)
- Bo Durbeej
- 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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Li X, Chung LW, Paneth P, Morokuma K. DFT and ONIOM(DFT:MM) studies on Co-C bond cleavage and hydrogen transfer in B12-dependent methylmalonyl-CoA mutase. Stepwise or concerted mechanism? J Am Chem Soc 2009; 131:5115-25. [PMID: 19309090 DOI: 10.1021/ja807677z] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The considerable protein effect on the homolytic Co-C bond cleavage to form the 5'-deoxyadenosyl (Ado) radical and cob(II)alamin and the subsequent hydrogen transfer from the methylmalonyl-CoA substrate to the Ado radical in the methylmalonyl-CoA mutase (MMCM) have been extensively studied by DFT and ONIOM(DFT/MM) methods. Several quantum models have been used to systematically study the protein effect. The calculations have shown that the Co-C bond dissociation energy is very much reduced in the protein, compared to that in the gas phase. The large protein effect can be decomposed into the cage effect, the effect of coenzyme geometrical distortion, and the protein MM effect. The largest contributor is the MM effect, which mainly consists of the interaction of the QM part of the coenzyme with the MM part of the coenzyme and the surrounding residues. In particular, Glu370 plays an important role in the Co-C bond cleavage process. These effects tremendously enhance the stability of the Co-C bond cleavage state in the protein. The initial Co-C bond cleavage and the subsequent hydrogen transfer were found to occur in a stepwise manner in the protein, although the concerted pathway for the Co-C bond cleavage coupled with the hydrogen transfer is more favored in the gas phase. The assumed concerted transition state in the protein has more deformation of the coenzyme and the substrate and has less interaction with the protein than the stepwise route. Key factors and residues in promoting the enzymatic reaction rate have been discussed in detail.
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Affiliation(s)
- Xin Li
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
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49
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A possible mechanism for evading temperature quantum decoherence in living matter by feshbach resonance. Int J Mol Sci 2009; 10:2084-106. [PMID: 19564941 PMCID: PMC2695269 DOI: 10.3390/ijms10052084] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2009] [Revised: 04/29/2009] [Accepted: 05/11/2009] [Indexed: 12/02/2022] Open
Abstract
A new possible scenario for the origin of the molecular collective behaviour associated with the emergence of living matter is presented. We propose that the transition from a non-living to a living cell could be mapped to a quantum transition to a coherent entanglement of condensates, like in a multigap BCS superconductor. Here the decoherence-evading qualities at high temperature are based on the Feshbach resonance that has been recently proposed as the driving mechanism for high Tc superconductors. Finally we discuss how the proximity to a particular critical point is relevant to the emergence of coherence in the living cell.
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Insights into the mechanisms of adenosylcobalamin (coenzyme B12)-dependent enzymes from rapid chemical quench experiments. Biochem Soc Trans 2009; 37:336-42. [PMID: 19290858 DOI: 10.1042/bst0370336] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Glutamate mutase is one of a group of adenosylcobalamin-dependent enzymes that use free radicals to catalyse unusual and chemically difficult rearrangements involving 1,2-migrations of hydrogen atoms. A key mechanistic feature of these enzymes is the transfer of the migrating hydrogen atom between substrate, coenzyme and product. The present review summarizes recent experiments from my laboratory that have used rapid chemical quench techniques to identify intermediates in the reaction and probe the mechanism of hydrogen transfer through a variety of pre-steady-state kinetic isotope effect measurements.
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