1
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Wu YJ, Takahashi K, Lin JJM. Kinetics of the Simplest Criegee Intermediate Reaction with Water Vapor: Revisit and Isotope Effect. J Phys Chem A 2023; 127:8059-8072. [PMID: 37734061 DOI: 10.1021/acs.jpca.3c03418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/23/2023]
Abstract
The kinetics of the simplest Criegee intermediate (CH2OO) reaction with water vapor was revisited. By improving the signal-to-noise ratio and the precision of water concentration, we found that the kinetics of CH2OO involves not only two water molecules but also one and three water molecules. Our experimental results suggest that the decay of CH2OO can be described as d[CH2OO]/dt = -kobs[CH2OO]; kobs = k0 + k1[water] + k2[water]2 + k3[water]3; k1 = (4.22 ± 0.48) × 10-16 cm3 s-1, k2 = (10.66 ± 0.83) × 10-33 cm6 s-1, k3 = (1.48 ± 0.17) × 10-50 cm9 s-1 at 298 K and 300 Torr with the respective Arrhenius activation energies of Ea1 = 1.8 ± 1.1 kcal mol-1, Ea2 = -11.1 ± 2.1 kcal mol-1, Ea3 = -17.4 ± 3.9 kcal mol-1. The contribution of the k3[water]3 term becomes less significant at higher temperatures around 345 K, but it is not ignorable at 298 K and lower temperatures. By quantifying the concentrations of H2O and D2O with a Coriolis-type direct mass flow sensor, the kinetic isotope effect (KIE) was investigated at 298 K and 300 Torr and KIE(k1) = k1(H2O)/k1(D2O) = 1.30 ± 0.32; similarly, KIE(k2) = 2.25 ± 0.44 and KIE(k3) = 0.99 ± 0.13. These mild KIE values are consistent with theoretical calculations based on the variational transition state theory, confirming that the title reaction has a broad and low barrier, and the reaction coordinate involves not only the motion of a hydrogen atom but also that of an oxygen atom. Comparing the results recorded under 300 Torr (N2 buffer gas) with those under 600 Torr, a weak pressure effect of k3 was found. From quantum chemistry calculations, we found that the CH2OO + 3H2O reaction is dominated by the reaction pathways involving a ring structure consisting of two water molecules, which facilitate the hydrogen atom transfer, while the third water molecule is hydrogen-bonded outside the ring. Furthermore, analysis based on dipole capture rates showed that the CH2OO(H2O) + (H2O)2 and CH2OO(H2O)2 + H2O pathways will dominate in the three water reaction.
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Affiliation(s)
- Yen-Ju Wu
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106923, Taiwan
- Department of Chemistry, National Taiwan University, Taipei 106923, Taiwan
| | - Kaito Takahashi
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106923, Taiwan
| | - Jim Jr-Min Lin
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106923, Taiwan
- Department of Chemistry, National Taiwan University, Taipei 106923, Taiwan
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2
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Shayesteh Zadeh A, Khan SA, Vandervelden C, Peters B. Site-Averaged Ab Initio Kinetics: Importance Learning for Multistep Reactions on Amorphous Supports. J Chem Theory Comput 2023; 19:2873-2886. [PMID: 37093705 DOI: 10.1021/acs.jctc.3c00160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Single-atom centers on amorphous supports include catalysts for polymerization, partial oxidation, metathesis, hydrogenolysis, and more. The disordered environment makes each site different, and the kinetics exponentially magnifies these differences to make ab initio site-averaged kinetics calculations extremely difficult. This work extends the importance learning algorithm for efficient and precise site-averaged kinetics estimates to ab initio calculations and multistep reaction mechanisms. Specifically, we calculate site-averaged proton transfer relaxation rates on an ensemble of cluster models representing Brønsted acid sites on silica-alumina. We include direct and water-assisted proton transfer pathways and simultaneously estimate the water adsorption and activation enthalpies for forward and backward proton transfers. We use density functional theory (DFT) to obtain a site-averaged rate, somewhat like a turnover frequency, for the proton transfer relaxation rate. Finally, we show that importance learning can provide orders-of-magnitude acceleration over standard sampling methods for site-averaged rate calculations in cases where the rate is dominated by a few highly active sites.
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Affiliation(s)
- Armin Shayesteh Zadeh
- Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Salman A Khan
- Delaware Energy Institute (DEI), University of Delaware, Newark, Delaware 19711, United States
| | | | - Baron Peters
- Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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3
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Chen BW. Equilibrium and kinetic isotope effects in heterogeneous catalysis: A density functional theory perspective. CATAL COMMUN 2023. [DOI: 10.1016/j.catcom.2023.106654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023] Open
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4
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Adesina AS, Luk LYP, Allemann RK. Cryo-kinetics Reveal Dynamic Effects on the Chemistry of Human Dihydrofolate Reductase. Chembiochem 2021; 22:2410-2414. [PMID: 33876533 PMCID: PMC8360168 DOI: 10.1002/cbic.202100017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 04/16/2021] [Indexed: 12/03/2022]
Abstract
Effects of isotopic substitution on the rate constants of human dihydrofolate reductase (HsDHFR), an important target for anti-cancer drugs, have not previously been characterized due to its complex fast kinetics. Here, we report the results of cryo-measurements of the kinetics of the HsDHFR catalyzed reaction and the effects of protein motion on catalysis. Isotopic enzyme labeling revealed an enzyme KIE (kHLE /kHHE ) close to unity above 0 °C; however, the enzyme KIE was increased to 1.72±0.15 at -20 °C, indicating that the coupling of protein motions to the chemical step is minimized under optimal conditions but enhanced at non-physiological temperatures. The presented cryogenic approach provides an opportunity to probe the kinetics of mammalian DHFRs, thereby laying the foundation for characterizing their transition state structure.
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Affiliation(s)
| | - Louis Y. P. Luk
- School of ChemistryCardiff UniversityPark PlaceCardiffCF10 3ATUK
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5
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6
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Offenbacher AR, Sharma A, Doan PE, Klinman JP, Hoffman BM. The Soybean Lipoxygenase-Substrate Complex: Correlation between the Properties of Tunneling-Ready States and ENDOR-Detected Structures of Ground States. Biochemistry 2020; 59:901-910. [PMID: 32022556 PMCID: PMC7188194 DOI: 10.1021/acs.biochem.9b00861] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Hydrogen tunneling in enzymatic C-H activation requires a dynamical sampling among ground-state enzyme-substrate (E-S) conformations, which transiently generates a tunneling-ready state (TRS). The TRS is characterized by a hydrogen donor-acceptor distance (DAD) of 2.7 Å, ∼0.5 Å shorter than the dominant DAD of optimized ground states. Recently, a high-resolution, 13C electron-nuclear double-resonance (ENDOR) approach was developed to characterize the ground-state structure of the complex of the linoleic acid (LA) substrate with soybean lipoxygenase (SLO). The resulting enzyme-substrate model revealed two ground-state conformers with different distances between the target C11 of LA and the catalytically active cofactor [Fe(III)-OH]: the active conformer "a", with a van der Waals DAD of 3.1 Å between C11 and metal-bound hydroxide, and an inactive conformer "b", with a distance that is almost 1 Å longer. Herein, the structure of the E-S complex is examined for a series of six variants in which subtle structural modifications of SLO have been introduced either at a hydrophobic side chain near the bound substrate or at a remote residue within a protein network whose flexibility influences hydrogen transfer. A remarkable correlation is found between the ENDOR-derived population of the active ground-state conformer a and the kinetically derived differential enthalpic barrier for D versus H transfer, ΔEa, with the latter increasing as the fraction of conformer a decreases. As proposed, ΔEa provides a "ruler" for the DAD within the TRS. ENDOR measurements further corroborate the previous identification of a dynamical network coupling the buried active site of SLO to the surface. This study shows that subtle imperfections within the initial ground-state structures of E-S complexes are accompanied by compromised geometries at the TRS.
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Affiliation(s)
- Adam R. Offenbacher
- Department of Chemistry, East Carolina University, Greenville, North Carolina 27858
- Department of Chemistry and California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720
| | - Ajay Sharma
- Department of Chemistry, Northwestern University, Evanston, Illinois 602084
| | - Peter E. Doan
- Department of Chemistry, Northwestern University, Evanston, Illinois 602084
| | - Judith P. Klinman
- Department of Chemistry and California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720
| | - Brian M. Hoffman
- Department of Chemistry, Northwestern University, Evanston, Illinois 602084
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7
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Kostenko A, Ray K, Iavarone AT, Offenbacher AR. Kinetic Characterization of the C-H Activation Step for the Lipoxygenase from the Pathogenic Fungus Magnaporthe oryzae: Impact of N-Linked Glycosylation. Biochemistry 2019; 58:3193-3203. [PMID: 31264852 DOI: 10.1021/acs.biochem.9b00467] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Lipoxygenases from pathogenic fungi belong to the lipoxygenase family of enzymes, which catalyze C-H activation of polyunsaturated fatty acids to form a diverse set of cell-signaling hydroperoxides. While the lipoxygenase catalytic domains are structurally and functionally similar, these fungal enzymes are decorated with N-linked glycans. The impact of N-linked glycans on the structure and function of these enzymes remains largely unknown. One exemplary system is MoLOX, a lipoxygenase from the fungus Magnaporthe oryzae, that is emerging as an important target for the devastating rice blast disease. Herein, we demonstrate that hydrogen transfer, associated with C-H cleavage of the substrate linoleic acid by MoLOX, is rate-determining and occurs by a hydrogen tunneling mechanism. Using the differential enthalpic barrier for hydrogen and deuterium transfer, ΔEa, as a kinetic reporter of tunneling efficiency, a disproportionate increase in the activation energy for deuterium transfer is observed upon treatment of MoLOX with a peptide:N-glycosidase that cleaves N-linked carbohydrates from the protein. This increased ΔEa is consistent with an impairment of substrate positioning in the enzyme-substrate complex for both the tunneling ready state and the ground state. These results provide new insight into the functional consequences of N-linked glycosylation on lipoxygenase C-H activation and have important implications for MoLOX inhibitor design.
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Affiliation(s)
- Anastasiia Kostenko
- Department of Chemistry , East Carolina University , Greenville , North Carolina 27858 , United States
| | - Katherine Ray
- Department of Biology , East Carolina University , Greenville , North Carolina 27858 , United States
| | - Anthony T Iavarone
- California Institute for Quantitative Biosciences (QB3) , University of California , Berkeley , California 94720 , United States
| | - Adam R Offenbacher
- Department of Chemistry , East Carolina University , Greenville , North Carolina 27858 , United States
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8
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Ruiz-Pernía JJ, Tuñón I, Moliner V, Allemann RK. Why are some Enzymes Dimers? Flexibility and Catalysis in Thermotoga Maritima Dihydrofolate Reductase. ACS Catal 2019; 9:5902-5911. [PMID: 31289693 PMCID: PMC6614790 DOI: 10.1021/acscatal.9b01250] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Dihydrofolate
reductase from Thermotoga maritima (TmDFHFR) is a
dimeric thermophilic enzyme that catalyzes the hydride
transfer from the cofactor NADPH to dihydrofolate less efficiently
than other DHFR enzymes, such as the mesophilic analogue Escherichia
coli DHFR (EcDHFR). Using QM/MM potentials, we show that
the reduced catalytic efficiency of TmDHFR is most likely due to differences
in the amino acid sequence that stabilize the M20 loop in an open
conformation, which prevents the formation of some interactions in
the transition state and increases the number of water molecules in
the active site. However, dimerization provides two advantages to
the thermophilic enzyme: it protects its structure against denaturation
by reducing thermal fluctuations and it provides a less negative activation
entropy, toning down the increase of the activation free energy with
temperature. Our molecular picture is confirmed by the analysis of
the temperature dependence of enzyme kinetic isotope effects in different
DHFR enzymes.
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Affiliation(s)
- J. Javier Ruiz-Pernía
- Departamento de Química Física, Universitat de Valencia, 46100 Burjassot, Valencia, Spain
| | - Iñaki Tuñón
- Departamento de Química Física, Universitat de Valencia, 46100 Burjassot, Valencia, Spain
| | - Vicent Moliner
- Departamento de Química Física y Analítica, Universitat Jaume I, 12071 Castellón, Spain
| | - Rudolf K. Allemann
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
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9
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Li X, York DM, Meyer MP. Quantum Suppression of Intramolecular Deuterium Kinetic Isotope Effects in a Pericyclic Hydrogen Transfer Reaction. J Phys Chem A 2019; 123:3647-3654. [PMID: 30855141 DOI: 10.1021/acs.jpca.9b00172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
It is generally accepted that hydrogen tunneling enhances both primary and secondary H/D kinetic isotope effects (KIEs) over what would be expected under the assumptions of classical barrier transition. Previous studies have exclusively shown that the effects of tunneling upon primary H/D KIEs have been much larger than those observed for secondary H/D KIEs. Here we present a series of experimental H/D KIE results associated with the Chugaev elimination of methyl xanthate derived from β-phenylethanol over the temperature range of 180 to 290 °C. Intramolecular H/D KIEs computed according to classical transition state theory (TST) are markedly overestimated relative to experimentally measured values. Experimental intermolecular H/D KIEs and direct dynamic calculations based on canonical variational transition state theory (CVT) with small-curvature tunneling correction (SCT) reveal that this result is largely the consequence of extraordinary tunneling enhancement of the secondary H/D KIE. This unexpected behavior is examined in the context of other similar hydrogen transfer reactions.
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Affiliation(s)
- Xiao Li
- Laboratory for Biomolecular Simulation Research, Center for Integrative Proteomics Research, and Department of Chemistry and Chemical Biology , Rutgers University , Piscataway , New Jersey 08854-8087 , United States
| | - Darrin M York
- Laboratory for Biomolecular Simulation Research, Center for Integrative Proteomics Research, and Department of Chemistry and Chemical Biology , Rutgers University , Piscataway , New Jersey 08854-8087 , United States
| | - Matthew P Meyer
- Department of Chemistry and Chemical Biology , University of California , Merced , California 95343 , United States
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10
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Löhle A, Kästner J. Calculation of Reaction Rate Constants in the Canonical and Microcanonical Ensemble. J Chem Theory Comput 2018; 14:5489-5498. [DOI: 10.1021/acs.jctc.8b00565] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Andreas Löhle
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart,Germany
| | - Johannes Kästner
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart,Germany
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11
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d'Agostino S, Fornasari L, Grepioni F, Braga D, Rossi F, Chierotti MR, Gobetto R. Precessional Motion in Crystalline Solid Solutions of Ionic Rotors. Chemistry 2018; 24:15059-15066. [PMID: 30011358 DOI: 10.1002/chem.201803071] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Indexed: 11/09/2022]
Abstract
The order-disorder phase transition associated with the uprise of reorientational motion in (DABCOH2)2+ , in the supramolecular salts of general formula [1⋅(DABCOH2 )]X2 (where 1=12-crown-4, DABCO=1,4-diazabicyclo[2.2.2]octane, and X=Cl- or Br- ), has been investigated by variable temperature X-ray diffraction on single crystals and powder samples, as well as by DSC and solid-state NMR spectroscopy (SSNMR). The two compounds undergo a reversible phase change at 292 and 290 K, respectively. The two crystalline materials form solid solutions [1⋅(DABCOH2 )]Cl2x Br2(1-x) in the whole composition range (0 < x<1), with a decrease in the temperature of transition to a minimum of ca 280 K, corresponding to x=0.5. Activation energy values for the dynamic processes, evaluated by variable-temperature 13 C magic-angle spinning (MAS) SSNMR and line-shape analysis are ca. 50 kJ mol-1 in all cases. Combined diffraction and spectroscopic evidence has allowed the detection of a novel dynamic process for the (DABCOH2 )2+ dications, based on a room temperature precessional motion that is frozen out below the disorder-order transition; to the best of the authors' knowledge this phenomenon has never been observed before.
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Affiliation(s)
- Simone d'Agostino
- Dipartimento di Chimica G. Ciamician, Università di Bologna, Via Selmi, 2, 40126, Bologna, Italy
| | - Luca Fornasari
- Dipartimento di Chimica G. Ciamician, Università di Bologna, Via Selmi, 2, 40126, Bologna, Italy
| | - Fabrizia Grepioni
- Dipartimento di Chimica G. Ciamician, Università di Bologna, Via Selmi, 2, 40126, Bologna, Italy
| | - Dario Braga
- Dipartimento di Chimica G. Ciamician, Università di Bologna, Via Selmi, 2, 40126, Bologna, Italy
| | - Federica Rossi
- Department of Chemistry and NIS Centre, University of Torino, Via Giuria 7, 10125, Torino, Italy
| | - Michele R Chierotti
- Department of Chemistry and NIS Centre, University of Torino, Via Giuria 7, 10125, Torino, Italy
| | - Roberto Gobetto
- Department of Chemistry and NIS Centre, University of Torino, Via Giuria 7, 10125, Torino, Italy
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12
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Wang Y, Olankitwanit A, Rajca S, Rajca A. Intramolecular Hydrogen Atom Transfer in Aminyl Radical at Room Temperature with Large Kinetic Isotope Effect. J Am Chem Soc 2017; 139:7144-7147. [PMID: 28514849 PMCID: PMC5528148 DOI: 10.1021/jacs.7b02692] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We report a large kinetic isotope effect at 298 K, kH/kD ≈ 150, associated with an intramolecular 1,5-hydrogen atom transfer (1,5-HAT) in the decay of a PEGylated carbazyl (aminyl) radical in solution. The experimental observations surprisingly combine the hallmarks of tunneling, including large KIEs and unusual activation parameters, with linear Arrhenius and Eyring plots over an exceptionally wide temperature range of 116 K.
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Affiliation(s)
- Ying Wang
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304
| | - Arnon Olankitwanit
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304
| | - Suchada Rajca
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304
| | - Andrzej Rajca
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304
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13
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Shinya S, Ghinet MG, Brzezinski R, Furuita K, Kojima C, Shah S, Kovrigin EL, Fukamizo T. NMR line shape analysis of a multi-state ligand binding mechanism in chitosanase. JOURNAL OF BIOMOLECULAR NMR 2017; 67:309-319. [PMID: 28393280 DOI: 10.1007/s10858-017-0109-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 04/02/2017] [Indexed: 06/07/2023]
Abstract
Chitosan interaction with chitosanase was examined through analysis of spectral line shapes in the NMR HSQC titration experiments. We established that the substrate, chitosan hexamer, binds to the enzyme through the three-state induced-fit mechanism with fast formation of the encounter complex followed by slow isomerization of the bound-state into the final conformation. Mapping of the chemical shift perturbations in two sequential steps of the mechanism highlighted involvement of the substrate-binding subsites and the hinge region in the binding reaction. Equilibrium parameters of the three-state model agreed with the overall thermodynamic dissociation constant determined by ITC. This study presented the first kinetic evidence of the induced-fit mechanism in the glycoside hydrolases.
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Affiliation(s)
- Shoko Shinya
- Department of Advanced Bioscience, Kindai University, 3327-204 Nakamachi, Nara, 631-8505, Japan
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Mariana G Ghinet
- Département de Biologie, Faculté des Sciences, Université de Sherbrooke, 2500, boul. de l'Université, Sherbrooke, QC, J1K 2R1, Canada
- Département de Pharmacologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, J1H 5N4, Canada
| | - Ryszard Brzezinski
- Département de Biologie, Faculté des Sciences, Université de Sherbrooke, 2500, boul. de l'Université, Sherbrooke, QC, J1K 2R1, Canada
| | - Kyoko Furuita
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Chojiro Kojima
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Sneha Shah
- Department of Chemistry, Marquette University, Milwaukee, WI, 53201, USA
| | - Evgenii L Kovrigin
- Department of Chemistry, Marquette University, Milwaukee, WI, 53201, USA.
| | - Tamo Fukamizo
- Department of Advanced Bioscience, Kindai University, 3327-204 Nakamachi, Nara, 631-8505, Japan.
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14
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Meisner J, Markmeyer MN, Bohner MU, Kästner J. Comparison of classical reaction paths and tunneling paths studied with the semiclassical instanton theory. Phys Chem Chem Phys 2017; 19:23085-23094. [DOI: 10.1039/c7cp03722h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Comparison of classical reaction paths and semiclassical instanton paths for a proton transfer reaction mechanism.
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Affiliation(s)
- Jan Meisner
- Institute for Theoretical Chemistry
- University of Stuttgart
- Pfaffenwaldring 55
- Stuttgart
- Germany
| | - Max N. Markmeyer
- Institute for Theoretical Chemistry
- University of Stuttgart
- Pfaffenwaldring 55
- Stuttgart
- Germany
| | - Matthias U. Bohner
- Institute for Theoretical Chemistry
- University of Stuttgart
- Pfaffenwaldring 55
- Stuttgart
- Germany
| | - Johannes Kästner
- Institute for Theoretical Chemistry
- University of Stuttgart
- Pfaffenwaldring 55
- Stuttgart
- Germany
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15
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16
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Meisner J, Kästner J. Atom Tunneling in Chemistry. Angew Chem Int Ed Engl 2016; 55:5400-13. [DOI: 10.1002/anie.201511028] [Citation(s) in RCA: 140] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 01/08/2016] [Indexed: 01/01/2023]
Affiliation(s)
- Jan Meisner
- Institut für Theoretische Chemie Universität Stuttgart Pfaffenwaldring 55 70569 Stuttgart Germany
| | - Johannes Kästner
- Institut für Theoretische Chemie Universität Stuttgart Pfaffenwaldring 55 70569 Stuttgart Germany
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17
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Affiliation(s)
- Jan Meisner
- Institut für Theoretische Chemie Universität Stuttgart Pfaffenwaldring 55 70569 Stuttgart Deutschland
| | - Johannes Kästner
- Institut für Theoretische Chemie Universität Stuttgart Pfaffenwaldring 55 70569 Stuttgart Deutschland
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18
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Roginskii VA. Kinetic isotope effect in the oxidation of unsaturated fatty acids. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY B 2015. [DOI: 10.1134/s1990793115030094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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19
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Johannissen LO, Hay S, Scrutton NS. Nuclear quantum tunnelling in enzymatic reactions – an enzymologist's perspective. Phys Chem Chem Phys 2015; 17:30775-82. [DOI: 10.1039/c5cp00614g] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The roles of nuclear quantum tunnelling and dynamics in enzyme reactions are discussed in this perspective on H-transfer reactions.
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Affiliation(s)
- Linus O. Johannissen
- SYNBIOCHEM
- Manchester Institute of Biotechnology
- Faculty of Life Sciences
- The University of Manchester
- Manchester M1 7DN
| | - Sam Hay
- SYNBIOCHEM
- Manchester Institute of Biotechnology
- Faculty of Life Sciences
- The University of Manchester
- Manchester M1 7DN
| | - Nigel S. Scrutton
- SYNBIOCHEM
- Manchester Institute of Biotechnology
- Faculty of Life Sciences
- The University of Manchester
- Manchester M1 7DN
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20
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Staniforth M, Young JD, Cole DR, Karsili TNV, Ashfold MNR, Stavros VG. Ultrafast Excited-State Dynamics of 2,4-Dimethylpyrrole. J Phys Chem A 2014; 118:10909-18. [DOI: 10.1021/jp508919s] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Michael Staniforth
- Department
of Chemistry, University of Warwick, Library Road, Coventry, CV4 7AL, U.K
| | - Jamie D. Young
- Department
of Chemistry, University of Warwick, Library Road, Coventry, CV4 7AL, U.K
| | - Daniel R. Cole
- Department
of Chemistry, University of Warwick, Library Road, Coventry, CV4 7AL, U.K
| | - Tolga N. V. Karsili
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol, BS8 1TS, U.K
| | | | - Vasilios G. Stavros
- Department
of Chemistry, University of Warwick, Library Road, Coventry, CV4 7AL, U.K
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21
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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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22
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Francis K, Kohen A. Standards for the reporting of kinetic isotope effects in enzymology. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.pisc.2014.02.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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23
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Francis K, Stojković V, Kohen A. Preservation of protein dynamics in dihydrofolate reductase evolution. J Biol Chem 2013; 288:35961-8. [PMID: 24158440 PMCID: PMC3861645 DOI: 10.1074/jbc.m113.507632] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 10/09/2013] [Indexed: 11/06/2022] Open
Abstract
The hydride transfer reaction catalyzed by dihydrofolate reductase (DHFR) is a model for examining how protein dynamics contribute to enzymatic function. The relationship between functional motions and enzyme evolution has attracted significant attention. Recent studies on N23PP Escherichia coli DHFR (ecDHFR) mutant, designed to resemble parts of the human enzyme, indicated a reduced single turnover rate. NMR relaxation dispersion experiments with that enzyme showed rigidification of millisecond Met-20 loop motions (Bhabha, G., Lee, J., Ekiert, D. C., Gam, J., Wilson, I. A., Dyson, H. J., Benkovic, S. J., and Wright, P. E. (2011) Science 332, 234-238). A more recent study of this mutant, however, indicated that fast motions along the reaction coordinate are actually more dispersed than for wild-type ecDHFR (WT). Furthermore, a double mutant (N23PP/G51PEKN) that better mimics the human enzyme seems to restore both the single turnover rates and narrow distribution of fast dynamics (Liu, C. T., Hanoian, P., French, T. H., Hammes-Schiffer, S., and Benkovic, S. J. (2013) Proc. Natl. Acad. Sci. U.S.A. 110, 10159-11064). Here, we measured intrinsic kinetic isotope effects for both N23PP and N23PP/G51PEKN double mutant DHFRs over a temperature range. The findings indicate that although the C-H→C transfer and dynamics along the reaction coordinate are impaired in the altered N23PP mutant, both seem to be restored in the N23PP/G51PEKN double mutant. This indicates that the evolution of G51PEKN, although remote from the Met-20 loop, alleviated the loop rigidification that would have been caused by N23PP, enabling WT-like H-tunneling. The correlation between the calculated dynamics, the nature of C-H→C transfer, and a phylogenetic analysis of DHFR sequences are consistent with evolutionary preservation of the protein dynamics to enable H-tunneling from well reorganized active sites.
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Affiliation(s)
- Kevin Francis
- From the Department of Chemistry, The University of Iowa, Iowa City, Iowa 52242
| | - Vanja Stojković
- From the Department of Chemistry, The University of Iowa, Iowa City, Iowa 52242
| | - Amnon Kohen
- From the Department of Chemistry, The University of Iowa, Iowa City, Iowa 52242
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24
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Fang H, Kim Y. Excited-State Tautomerization of 7-Azaindole in Nonpolar Solution: A Theoretical Study Based on Liquid-Phase Potential Surfaces of Mean Force. J Chem Theory Comput 2013; 9:3557-66. [DOI: 10.1021/ct3010694] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hua Fang
- Department of Applied Chemistry, Kyung Hee University, 1 Seochun-Dong,
Giheung-Gu, Yongin-Si, Gyeonggi-Do, 446-701, Republic of Korea
| | - Yongho Kim
- Department of Applied Chemistry, Kyung Hee University, 1 Seochun-Dong,
Giheung-Gu, Yongin-Si, Gyeonggi-Do, 446-701, Republic of Korea
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25
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Liuni P, Olkhov-Mitsel E, Orellana A, Wilson DJ. Measuring kinetic isotope effects in enzyme reactions using time-resolved electrospray mass spectrometry. Anal Chem 2013; 85:3758-64. [PMID: 23461634 DOI: 10.1021/ac400191t] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Kinetic isotope effect (KIE) measurements are a powerful tool for studying enzyme mechanisms; they can provide insights into microscopic catalytic processes and even structural constraints for transition states. However, KIEs have not come into widespread use in enzymology, due in large part to the requirement for prohibitively cumbersome experimental procedures and daunting analytical frameworks. In this work, we introduce time-resolved electrospray ionization mass spectrometry (TRESI-MS) as a straightforward, precise, and inexpensive method for measuring KIEs. Neither radioisotopes nor large amounts of material are needed and kinetic measurements for isotopically "labeled" and "unlabeled" species are acquired simultaneously in a single "competitive" assay. The approach is demonstrated first using a relatively large isotope effect associated with yeast alcohol dehydrogenase (YADH) catalyzed oxidation of ethanol. The measured macroscopic KIE of 2.19 ± 0.05 is consistent with comparable measurements in the literature but cannot be interpreted in a way that provides insights into isotope effects in individual microscopic steps. To demonstrate the ability of TRESI-MS to directly measure intrinsic KIEs and to characterize the precision of the technique, we measure a much smaller (12)C/(13)C KIE associated specifically with presteady state acylation of chymotrypsin during hydrolysis of an ester substrate.
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Affiliation(s)
- Peter Liuni
- Department of Chemistry, York University, Toronto, ON, Canada
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26
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Pudney CR, Lane RSK, Fielding AJ, Magennis SW, Hay S, Scrutton NS. Enzymatic single-molecule kinetic isotope effects. J Am Chem Soc 2013; 135:3855-64. [PMID: 23402437 DOI: 10.1021/ja309286r] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Ensemble-based measurements of kinetic isotope effects (KIEs) have advanced physical understanding of enzyme-catalyzed reactions, but controversies remain. KIEs are used as reporters of rate-limiting H-transfer steps, quantum mechanical tunnelling, dynamics and multiple reactive states. Single molecule (SM) enzymatic KIEs could provide new information on the physical basis of enzyme catalysis. Here, single pair fluorescence energy transfer (spFRET) was used to measure SM enzymatic KIEs on the H-transfer catalyzed by the enzyme pentaerythritol tetranitrate reductase. We evaluated a range of methods for extracting the SM KIE from single molecule spFRET time traces. The SM KIE enabled separation of contributions from nonenzymatic protein and fluorophore processes and H-transfer reactions. Our work demonstrates SM KIE analysis as a new method for deconvolving reaction chemistry from intrinsic dynamics.
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Affiliation(s)
- Christopher R Pudney
- Manchester Institute of Biotechnology and Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
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27
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28
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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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29
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Hammann B, Razzaghi M, Kashefolgheta S, Lu Y. Imbalanced tunneling ready states in alcohol dehydrogenase model reactions: rehybridization lags behind H-tunneling. Chem Commun (Camb) 2012; 48:11337-9. [DOI: 10.1039/c2cc36110h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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30
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Brala CJ, Pilepić V, Sajenko I, Karković A, Uršić S. Ions Can Move a Proton-Coupled Electron-Transfer Reaction into Tunneling Regime. Helv Chim Acta 2011. [DOI: 10.1002/hlca.201100035] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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31
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Karković A, Brala CJ, Pilepić V, Uršić S. Solvent-induced hydrogen tunnelling in ascorbate proton-coupled electron transfers. Tetrahedron Lett 2011. [DOI: 10.1016/j.tetlet.2011.01.142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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32
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33
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Lim H, Park SY, Jang DJ. Excited-State Double Proton Transfer Dynamics of Model DNA Base Pairs: 7-Hydroxyquinoline Dimers. J Phys Chem A 2010; 114:11432-5. [DOI: 10.1021/jp106301q] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Hyeongtaek Lim
- School of Chemistry, Seoul National University, NS60, Seoul 151-747, Korea
| | - Sun-Young Park
- School of Chemistry, Seoul National University, NS60, Seoul 151-747, Korea
| | - Du-Jeon Jang
- School of Chemistry, Seoul National University, NS60, Seoul 151-747, Korea
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34
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Characterizing the dynamics of functionally relevant complexes of formate dehydrogenase. Proc Natl Acad Sci U S A 2010; 107:17974-9. [PMID: 20876138 DOI: 10.1073/pnas.0912190107] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The potential for femtosecond to picosecond time-scale motions to influence the rate of the intrinsic chemical step in enzyme-catalyzed reactions is a source of significant controversy. Among the central challenges in resolving this controversy is the difficulty of experimentally characterizing thermally activated motions at this time scale in functionally relevant enzyme complexes. We report a series of measurements to address this problem using two-dimensional infrared spectroscopy to characterize the time scales of active-site motions in complexes of formate dehydrogenase with the transition-state-analog inhibitor azide (N(3)(-)). We observe that the frequency-frequency time correlation functions (FFCF) for the ternary complexes with NAD(+) and NADH decay completely with slow time constants of 3.2 ps and 4.6 ps, respectively. This result suggests that in the vicinity of the transition state, the active-site enzyme structure samples a narrow and relatively rigid conformational distribution indicating that the transition-state structure is well organized for the reaction. In contrast, for the binary complex, we observe a significant static contribution to the FFCF similar to what is seen in other enzymes, indicating the presence of the slow motions that occur on time scales longer than our measurement window.
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35
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Characterization of azido-NAD+ to assess its potential as a two-dimensional infrared probe of enzyme dynamics. Anal Biochem 2010; 407:241-6. [PMID: 20705046 DOI: 10.1016/j.ab.2010.08.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2010] [Accepted: 08/05/2010] [Indexed: 11/23/2022]
Abstract
Enzyme active-site dynamics at femtosecond to picosecond time scales are of great biochemical importance, but remain relatively unexplored due to the lack of appropriate analytical methods. Two-dimensional infrared (2D IR) spectroscopy is one of the few methods that can examine chemical biological motions at this time scale, but all the IR probes used so far were specific to a few unique enzymes. The lack of IR probes of broader specificity is a major limitation to further 2D IR studies of enzyme dynamics. Here we describe the synthesis of a general IR probe for nicotinamide-dependent enzymes. This azido analog of the ubiquitous cofactor nicotinamide adenine dinucleotide is found to be stable and bind to several dehydrogenases with dissociation constants similar to that for the native cofactor. The infrared absorption spectra of this probe bound to several enzymes indicate that it has significant potential as a 2D IR probe to investigate femtosecond dynamics of nicotinamide-dependent enzymes.
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36
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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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37
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Hill SE, Bandaria JN, Fox M, Vanderah E, Kohen A, Cheatum CM. Exploring the molecular origins of protein dynamics in the active site of human carbonic anhydrase II. J Phys Chem B 2009; 113:11505-10. [PMID: 19637848 PMCID: PMC2736349 DOI: 10.1021/jp901321m] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We present three-pulse vibrational echo measurements of azide ion bound to the active site Zn of human carbonic anhydrase II (HCA II) and of two separate active-site mutants Thr199 --> Ala (T199A) and Leu198 --> Phe (L198F). Because structural motions of the protein active site influence the frequency of bound ligands, the differences in the time scales of the frequency-frequency correlation functions (FFCFs) obtained from global fits to each set of data allow us to make inferences about the time scales of the active site dynamics of HCA II. Surprisingly, the deletion of a potential electrostatic interaction in results in very little change in the FFCF, but the insertion of the bulky phenylalanine ring in causes much faster dynamics. We conclude that the fast, sub-picosecond time scale in the correlation function is attributable to hydrogen bond dynamics, and the slow, apparently static contribution is due to the conformational flexibility of Zn-bound azide in the active site.
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Affiliation(s)
- Sarah E Hill
- Department of Chemistry and Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, USA.
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38
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Stojković V, Kohen A. Enzymatic H Transfers: Quantum Tunneling and Coupled Motion from Kinetic Isotope Effect Studies. Isr J Chem 2009. [DOI: 10.1560/ijc.49.2.163] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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39
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Abstract
Much work has gone into understanding the physical basis of the enormous catalytic power of enzymes over the last 50 years or so. Nevertheless, the detailed mechanism used by Nature's catalysts to speed chemical transformations remains elusive. DHFR (dihydrofolate reductase) has served as a paradigm to study the relationship between the structure, function and dynamics of enzymatic transformations. A complex reaction cascade, which involves rearrangements and movements of loops and domains of the enzyme, is used to orientate cofactor and substrate in a reactive configuration from which hydride is transferred by quantum mechanical tunnelling. In the present paper, we review results from experiments that probe the influence of protein dynamics on the chemical step of the reaction catalysed by TmDHFR (DHFR from Thermotoga maritima). This enzyme appears to have evolved an optimal structure that can maintain a catalytically competent conformation under extreme conditions.
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40
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Dance I. The chemical mechanism of nitrogenase: hydrogen tunneling and further aspects of the intramolecular mechanism for hydrogenation of eta(2)-N(2) on FeMo-co to NH(3). Dalton Trans 2008:5992-8. [PMID: 19082055 DOI: 10.1039/b806103c] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The preceding paper (Dalton Trans., 2008, DOI: 10.1039/b806100a) describes the logical development of a chemical mechanism for the catalysis of hydrogenation of N(2) to 2NH(3) that occurs at the Fe(7)MoS(9)N(c)(homocitrate) cofactor (FeMo-co) of the enzyme nitrogenase. The mechanism uses a single replenishable path for serial supply of protons which become H atoms on FeMo-co, migrating to become S-H and Fe-H donors to N(2) and to the intermediates that follow. This chemical catalysis at FeMo-co is distinctly intramolecular: transition states and reaction profiles for the preferred 21 step pathway were presented. This paper describes a number of alternative intermediates and pathways that were considered in developing the mechanism. These results reveal further relevant principles of the reactivity of hydrogenated FeMo-co, and the reasons why these pathways are less likely to be part of the mechanism. The intramolecular character of the mechanism, and the relatively small distances over which H atoms transfer, lead to expectations of extensive quantum mechanical hydrogen tunneling as part of the catalytic rate enhancement. This possibility is supported by comparisons of reaction profiles with those for enzyme reactions for which tunneling is established.
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Affiliation(s)
- Ian Dance
- School of Chemistry, University of New South Wales, Sydney 2052, Australia.
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41
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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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42
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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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43
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Tejero I, González-Lafont A, Lluch JM. A PM3/d specific reaction parameterization for iron atom in the hydrogen abstraction catalyzed by soybean lipoxygenase-1. J Comput Chem 2007; 28:997-1005. [PMID: 17274015 DOI: 10.1002/jcc.20609] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
This paper reports a specific reaction parameter (SRP) PM3/d model for iron that can reproduce the DFT/MM results of the hydrogen abstraction reaction from the C11 position of linoleic acid by the Soybean lipoxygenase-1 enzyme. A suite of nonlinear optimization methods is outlined for semiempirical parameter development based on integrated evolutionary (genetic) and direction set minimization algorithms. The PM3/d-SRP Fe parameters are derived along three consecutive steps. The final parameterization step includes the effect of the whole enzyme in order to get a better quantum mechanical/molecular mechanical description.
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Affiliation(s)
- Ismael Tejero
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
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44
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Parkin G. Applications of deuterium isotope effects for probing aspects of reactions involving oxidative addition and reductive elimination of H–H and C–H bonds. J Labelled Comp Radiopharm 2007. [DOI: 10.1002/jlcr.1435] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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45
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Fitzpatrick PF. Insights into the mechanisms of flavoprotein oxidases from kinetic isotope effects. J Labelled Comp Radiopharm 2007; 50:1016-1025. [PMID: 19890477 DOI: 10.1002/jlcr.1400] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Deuterium, solvent, and (15)N kinetic isotope effects have been used to probe the mechanisms by which flavoproteins oxidize carbon-oxygen and carbon-nitrogen bonds in amines, hydroxy acids, and alcohols. For the amine oxidases d-amino acid oxidase, N-methyltryptophan oxidase, and tryptophan monooxygenase, d-serine, sarcosine, and alanine are slow substrates for which CH bond cleavage is fully rate limiting. Inverse isotope effects for each of 0.992-0.996 are consistent with a common mechanism involving hydride transfer from the uncharged amine. Computational analyses of possible mechanisms support this conclusion. Deuterium and solvent isotope effects with wild-type and mutant variants of the lactate dehydrogenase flavocytochrome b(2) show that OH and CH bond cleavage are not concerted, but become so in the Y254F enzyme. This is consistent with a highly asynchronous reaction in which OH bond cleavage precedes hydride transfer. The results of Hammett analyses and solvent and deuterium isotope effects support a similar mechanism for alcohol oxidase.
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Affiliation(s)
- Paul F Fitzpatrick
- Departments of Biochemistry and Biophysics and of Chemistry, Texas A&M University, College Station, TX 77843-2128, USA
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46
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Tejero I, Garcia-Viloca M, Gonzalez-Lafont A, Lluch JM, York DM. Enzyme dynamics and tunneling enhanced by compression in the hydrogen abstraction catalyzed by soybean lipoxygenase-1. J Phys Chem B 2006; 110:24708-19. [PMID: 17134234 DOI: 10.1021/jp066263i] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A fully microscopical simulation of the rate-limiting hydrogen abstraction catalyzed by soybean lipoxygenase-1 (SLO-1) has been carried out. This enzyme exhibits the largest, and weakly temperature dependent, experimental H/D kinetic isotope effect (KIE) reported for a biological system. The theoretical model used here includes the complete enzyme with a solvation shell of water molecules, the Fe(III)-OH- cofactor, and the linoleic acid substrate. We have used a hybrid QM(PM3/d-SRP)/MM method to describe the potential energy surface of the whole system, and the ensemble-averaged variational transition-state theory with multidimensional tunneling (EA-VTST/MT) to calculate the rate constant and the primary KIE. The computational results show that the compression of the wild-type active site enzyme results in the huge contribution of tunneling (99%) to the rate of the hydrogen abstraction. Importantly, the active site becomes more flexible in the Ile553Ala mutant reactant complex simulation (for which a markedly temperature dependent KIE has been experimentally determined), thus justifying the proposed key role of the gating promoting mode in the reaction catalyzed by SLO-1. Finally, the results indicate that the calculated KIE for the wild-type enzyme has an important dependence on the barrier width.
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Affiliation(s)
- Ismael Tejero
- Departament de Química and Institut de Biotecnologia i de Biomedicina, Universitat Autonoma de Barcelona, 08193, Bellaterra (Barcelona), Spain
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47
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Wang L, Goodey NM, Benkovic SJ, Kohen A. The role of enzyme dynamics and tunnelling in catalysing hydride transfer: studies of distal mutants of dihydrofolate reductase. Philos Trans R Soc Lond B Biol Sci 2006; 361:1307-15. [PMID: 16873118 PMCID: PMC1647312 DOI: 10.1098/rstb.2006.1871] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Residues M42 and G121 of Escherichia coli dihydrofolate reductase (ecDHFR) are on opposite sides of the catalytic centre (15 and 19 A away from it, respectively). Theoretical studies have suggested that these distal residues might be part of a dynamics network coupled to the reaction catalysed at the active site. The ecDHFR mutant G121V has been extensively studied and appeared to have a significant effect on rate, but only a mild effect on the nature of H-transfer. The present work examines the effect of M42W on the physical nature of the catalysed hydride transfer step. Intrinsic kinetic isotope effects (KIEs), their temperature dependence and activation parameters were studied. The findings presented here are in accordance with the environmentally coupled hydrogen tunnelling. In contrast to the wild-type (WT), fluctuations of the donor-acceptor distance were required, leading to a significant temperature dependence of KIEs and deflated intercepts. A comparison of M42W and G121V to the WT enzyme revealed that the reduced rates, the inflated primary KIEs and their temperature dependences resulted from an imperfect potential surface pre-arrangement relative to the WT enzyme. Apparently, the coupling of the enzyme's dynamics to the reaction coordinate was altered by the mutation, supporting the models in which dynamics of the whole protein is coupled to its catalysed chemistry.
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Affiliation(s)
- Lin Wang
- Department of Chemistry, University of IowaIowa City, IA 52242, USA
| | - Nina M Goodey
- Department of Chemistry, The Pennsylvania State UniversityUniversity Park, PA 16802, USA
| | - Stephen J Benkovic
- Department of Chemistry, The Pennsylvania State UniversityUniversity Park, PA 16802, USA
| | - Amnon Kohen
- Department of Chemistry, University of IowaIowa City, IA 52242, USA
- Author for correspondence ()
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48
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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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49
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Pang J, Pu J, Gao J, Truhlar DG, Allemann RK. Hydride Transfer Reaction Catalyzed by Hyperthermophilic Dihydrofolate Reductase Is Dominated by Quantum Mechanical Tunneling and Is Promoted by Both Inter- and Intramonomeric Correlated Motions. J Am Chem Soc 2006; 128:8015-23. [PMID: 16771517 DOI: 10.1021/ja061585l] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Simulations of hydride and deuteride transfer catalyzed by dihydrofolate reductase from the hyperthermophile Thermotoga maritima (TmDHFR) are presented. TmDHFR was modeled with its active homodimeric quaternary structure, where each monomer has three subdomains. The potential energy function was a combined quantum mechanical and molecular mechanical potential (69 atoms were treated quantum mechanically, and 35 287, by molecular mechanics). The calculations of the rate constants by ensemble-averaged variational transition state theory with multidimensional tunneling predicted that hydride and deuteride transfer at 278 K proceeded with 81 and 80% by tunneling. These percentages decreased to 50 and 49% at 338 K. The kinetic isotope effect was dominated by contributions of bound vibrations and decreased from 3.0 to 2.2 over the temperature range. The calculated rates for hydride and deuteride transfer catalyzed by the hypothetical monomer were smaller by approximately 2 orders of magnitude. At 298 K tunneling contributed 73 and 66% to hydride and deuteride transfer in the monomer. The decreased catalytic efficiency of the monomer was therefore not the result of a decrease of the tunneling contribution but an increase in the quasi-classical activation free energy. The catalytic effect was associated in the dimer with correlated motions between domains as well as within and between subunits. The intrasubunit correlated motions were decreased in the monomer when compared to both native dimeric TmDHFR and monomeric E. coli enzyme. TmDHFR and its E. coli homologue involve similar patterns of correlated interactions that affect the free energy barrier of hydride transfer despite only 27% sequence identity and different quaternary structures.
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Affiliation(s)
- Jiayun Pang
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT, UK
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50
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Roca M, Moliner V, Tuñón I, Hynes JT. Coupling between Protein and Reaction Dynamics in Enzymatic Processes: Application of Grote−Hynes Theory to Catechol O-Methyltransferase. J Am Chem Soc 2006; 128:6186-93. [PMID: 16669689 DOI: 10.1021/ja058826u] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The generalized Langevin equation (GLE)-based Grote-Hynes (GH) theory is used to calculate the transmission coefficients, kappa, for the methyl transfer from S-adenosylmethionine to catecholate both in aqueous solution and in the catechol O-methyltransferase active site. Values of kappa, which measures the deviation of the rate constants from the Transition State Theory (TST) predictions, are obtained by means of rare event molecular dynamics simulations. The results are 0.62 +/- 0.04 and 0.83 +/- 0.03 for the aqueous and enzymatic environments, respectively, while the Grote-Hynes predictions are 0.58 +/- 0.09 and 0.89 +/- 0.03, respectively. The Kramers theory estimates are much smaller, about 0.01 and 0.1, respectively. Thus, the enzymatic transmission coefficient is closer to TST predictions than the value obtained in solution. In addition, our results show that the enzymatic coefficient is also closer to its nonadiabatic (or frozen environment) limit than is the solution coefficient. These findings can be understood considering that, during the passage over the barrier top, there is a smaller coupling between the reactive system and the environment in the enzyme than in solution, as well as a smaller reorganization suffered by the enzyme. Analysis of the transition state friction kernel leads to the identification of some key vibrational modes governing the coupling between the two different environments and the reacting solute in the transition state region and insights on their relevance for the reaction dynamics' influence on the transmission coefficient.
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Affiliation(s)
- Maite Roca
- Departament de Ciències Experimentals, Universitat Jaume I, 12071 Castellón, Spain
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