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Miller SP, Gonçalves S, Matias PM, Dean AM. Evolution of a transition state: role of Lys100 in the active site of isocitrate dehydrogenase. Chembiochem 2014; 15:1145-53. [PMID: 24797066 DOI: 10.1002/cbic.201400040] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Indexed: 11/09/2022]
Abstract
An active site lysine essential to catalysis in isocitrate dehydrogenase (IDH) is absent from related enzymes. As all family members catalyze the same oxidative β-decarboxylation at the (2R)-malate core common to their substrates, it seems odd that an amino acid essential to one is not found in all. Ordinarily, hydride transfer to a nicotinamide C4 neutralizes the positive charge at N1 directly. In IDH, the negatively charged C4-carboxylate of isocitrate stabilizes the ground state positive charge on the adjacent nicotinamide N1, opposing hydride transfer. The critical lysine is poised to stabilize-and perhaps even protonate-an oxyanion formed on the nicotinamide 3-carboxamide, thereby enabling the hydride to be transferred while the positive charge at N1 is maintained. IDH might catalyze the same overall reaction as other family members, but dehydrogenation proceeds through a distinct, though related, transition state. Partial activation of lysine mutants by K(+) and NH4 (+) represents a throwback to the primordial state of the first promiscuous substrate family member.
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Affiliation(s)
- Stephen P Miller
- Biotechnology Institute, The University of Minnesota, 1479 Gortner Avenue, St. Paul, MN 55108 (USA)
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2
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Doron D, Major DT, Kohen A, Thiel W, Wu X. Hybrid Quantum and Classical Simulations of the Dihydrofolate Reductase Catalyzed Hydride Transfer Reaction on an Accurate Semi-Empirical Potential Energy Surface. J Chem Theory Comput 2011; 7:3420-37. [PMID: 26598171 DOI: 10.1021/ct2004808] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Dihydrofolate reductase (DHFR) catalyzes the reduction of 7,8-dihydrofolate by nicotinamide adenine dinucleotide phosphate hydride (NADPH) to form 5,6,7,8-tetrahydrofolate and oxidized nicotinamide. DHFR is a small, flexible, monomeric protein with no metals or SS bonds and serves as one of the enzymes commonly used to examine basic aspects in enzymology. In the current work, we present extensive benchmark calculations for several model reactions in the gas phase that are relevant to the DHFR catalyzed hydride transfer. To this end, we employ G4MP2 and CBS-QB3 ab initio calculations as well as numerous density functional theory methods. Using these results, we develop two specific reaction parameter (SRP) Hamiltonians based on the semiempirical AM1 method. The first generation SRP Hamiltonian does not account for dispersion, while the second generation SRP accounts for dispersion implicitly via the AM1 core-repulsion functions. These SRP semiempirical Hamiltonians are subsequently used in hybrid quantum mechanics/molecular mechanics simulations of the DHFR catalyzed reaction. Finally, kinetic isotope effects are computed using a mass-perturbation-based path-integral approach.
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Affiliation(s)
- Dvir Doron
- Department of Chemistry, The Lise Meitner-Minerva Center of Computational Quantum Chemistry, Bar-Ilan University , Ramat-Gan 52900, Israel
| | - Dan Thomas Major
- Department of Chemistry, The Lise Meitner-Minerva Center of Computational Quantum Chemistry, Bar-Ilan University , Ramat-Gan 52900, Israel
| | - Amnon Kohen
- Department of Chemistry, University of Iowa , Iowa City, Iowa 52242, United States
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Xin Wu
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
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3
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Castillo R, Oliva M, Martí S, Moliner V. A theoretical study of the catalytic mechanism of formate dehydrogenase. J Phys Chem B 2008; 112:10012-22. [PMID: 18646819 DOI: 10.1021/jp8025896] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A theoretical study of the hydride transfer between formate anion and nicotinamide adenine dinucleotide (NAD(+)) catalyzed by the enzyme formate dehydrogenase (FDH) has been carried out by a combination of two hybrid quantum mechanics/molecular mechanics techniques: statistical simulation methods and internal energy minimizations. Free energy profiles, obtained for the reaction in the enzyme active site and in solution, allow obtaining a comparative analysis of the behavior of both condensed media. Moreover, calculations of the reaction in aqueous media can be used to probe the dramatic differences between reactants state in the enzyme active site and in solution. The results suggest that the enzyme compresses the substrate and the cofactor into a conformation close to the transition structure by means of favorable interactions with the amino acid residues of the active site, thus facilitating the relative orientation of donor and acceptor atoms to favor the hydride transfer. Moreover, a permanent field created by the protein reduces the work required to reach the transition state (TS) with a concomitant polarization of the cofactor that would favor the hydride transfer. In contrast, in water the TS is destabilized with respect to the reactant species because the polarity of the solute diminishes as the reaction proceeds, and consequently the reaction field, which is created as a response to the change in the solute polarity, is also decreased. Therefore protein structure is responsible of both effects; substrate preorganization and TS stabilization thus diminishing the activation barrier. Because of the electrostatic features of the catalyzed reaction, both media preferentially stabilize the ground-state, thus explaining the small rate constant enhancement of this enzyme, but FDH does so to a much lower extent than aqueous solution. Finally, a good agreement between experimental and theoretical kinetic isotope effects is found, thus giving some credit to our results.
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Affiliation(s)
- R Castillo
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castelló, Spain
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4
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Sergi A, Watney JB, Wong KF, Hammes-Schiffer S. Freezing a Single Distal Motion in Dihydrofolate Reductase. J Phys Chem B 2006; 110:2435-41. [PMID: 16471835 DOI: 10.1021/jp056939u] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Constraining a single motion between distal residues separated by approximately 28 A in hybrid quantum/classical molecular dynamics simulations is found to increase the free energy barrier for hydride transfer in dihydrofolate reductase by approximately 3 kcal/mol. Our analysis indicates that a single distal constraint alters equilibrium motions throughout the enzyme on a wide range of time scales. This alteration of the conformational sampling of the entire system is sufficient to significantly increase the free energy barrier and decrease the rate of hydride transfer. Despite the changes in conformational sampling introduced by the constraint, the system assumes a similar transition state conformation with a donor-acceptor distance of approximately 2.72 A to enable the hydride transfer reaction. The modified thermal sampling leads to a substantial increase in the average donor-acceptor distance for the reactant state, however, thereby decreasing the probability of sampling the transition state conformations with the shorter distances required for hydride transfer. These simulations indicate that fast thermal fluctuations of the enzyme, substrate, and cofactor lead to conformational sampling of configurations that facilitate hydride transfer. The fast thermal motions are in equilibrium as the reaction progresses along the collective reaction coordinate, and the overall average equilibrium conformational changes occur on the slower time scale measured experimentally. Recent single molecule experiments suggest that at least some of these thermally averaged equilibrium conformational changes occur on the millisecond time scale of the hydride transfer reaction. Thus, introducing a constraint that modifies the conformational sampling of an enzyme could significantly impact its catalytic activity.
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Affiliation(s)
- Alessandro Sergi
- Department of Chemistry, 104 Chemistry Building, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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Hammes-Schiffer S. Quantum-classical simulation methods for hydrogen transfer in enzymes: a case study of dihydrofolate reductase. Curr Opin Struct Biol 2005; 14:192-201. [PMID: 15093834 DOI: 10.1016/j.sbi.2004.03.008] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A variety of theoretical approaches have been used to investigate hydrogen transfer in enzymatic reactions. The free energy barriers for hydrogen transfer in enzymes have been calculated using classical molecular dynamics simulations in conjunction with quantum mechanical/molecular mechanical and empirical valence bond potentials. Nuclear quantum effects have been included with several different approaches. Applications of these approaches to hydride transfer in dihydrofolate reductase are consistent with experimental measurements and provide significant insight into the protein conformational changes that facilitate the hydride transfer reaction.
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Affiliation(s)
- Sharon Hammes-Schiffer
- Department of Chemistry, 152 Davey Laboratory, Pennsylvania State University, University Park, Pennsylvania 16802, USA.
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6
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Wong KF, Watney JB, Hammes-Schiffer S. Analysis of Electrostatics and Correlated Motions for Hydride Transfer in Dihydrofolate Reductase. J Phys Chem B 2004. [DOI: 10.1021/jp048565v] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kim F. Wong
- Department of Chemistry, 152 Davey Laboratory, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - James B. Watney
- Department of Chemistry, 152 Davey Laboratory, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Sharon Hammes-Schiffer
- Department of Chemistry, 152 Davey Laboratory, The Pennsylvania State University, University Park, Pennsylvania 16802
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7
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Cummins PL, Greatbanks SP, Rendell AP, Gready JE. Computational Methods for the Study of Enzymic Reaction Mechanisms. 1. Application to the Hydride Transfer Step in the Catalysis of Dihydrofolate Reductase. J Phys Chem B 2002. [DOI: 10.1021/jp021070q] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Peter L. Cummins
- Computational Proteomics and Therapy Design Group, John Curtin School of Medical Research, Australian National University, P.O. Box 334, Canberra ACT 2601, Australia, and Department of Computer Science, Faculty of Engineering and Information Technology, Australian National University, P.O. Box 334, Canberra ACT 2601, Australia
| | - Stephen P. Greatbanks
- Computational Proteomics and Therapy Design Group, John Curtin School of Medical Research, Australian National University, P.O. Box 334, Canberra ACT 2601, Australia, and Department of Computer Science, Faculty of Engineering and Information Technology, Australian National University, P.O. Box 334, Canberra ACT 2601, Australia
| | - Alistair P. Rendell
- Computational Proteomics and Therapy Design Group, John Curtin School of Medical Research, Australian National University, P.O. Box 334, Canberra ACT 2601, Australia, and Department of Computer Science, Faculty of Engineering and Information Technology, Australian National University, P.O. Box 334, Canberra ACT 2601, Australia
| | - Jill E. Gready
- Computational Proteomics and Therapy Design Group, John Curtin School of Medical Research, Australian National University, P.O. Box 334, Canberra ACT 2601, Australia, and Department of Computer Science, Faculty of Engineering and Information Technology, Australian National University, P.O. Box 334, Canberra ACT 2601, Australia
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8
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Dybala-Defratyka A, Paneth P. Theoretical evaluation of the hydrogen kinetic isotope effect on the first step of the methylmalonyl-CoA mutase reaction. J Inorg Biochem 2001; 86:681-9. [PMID: 11583786 DOI: 10.1016/s0162-0134(01)00230-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
We have calculated hydrogen kinetic isotope effects (KIEs) for the first step of the methylmalonyl-CoA mutase reaction, including multidimensional tunneling correction at the zero curvature (ZCT) level, and compared them with the experimental values. Both alternative mechanisms of this step, concerted and stepwise, can be accommodated. It turned out to be essential to include Arg207 hydrogen-bonded to the reactant in the mechanism predicting simultaneous breaking of the Co-C bond of AdoCbl and hydrogen atom transfer. The consequence of the stepwise mechanism is a much larger facilitation of the homolytic dissociation of the carbon-cobalt bond by the enzyme than currently appreciated; our results suggest lowering of the activation energy by about 23 kcal mol(-1). We have also shown that large hydrogen KIEs of tunneling origin do not necessarily break the Swain-Schaad equation. Furthermore, when this equation does not hold, the exponent may be smaller in the presence of tunneling than it is at the semi-classical limit, indicating that nonclassical behavior may be a more common phenomenon than expected.
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Affiliation(s)
- A Dybala-Defratyka
- Institute of Applied Radiation Chemistry, Department of Chemistry, Technical University of Lodz, Zeromskiego 116, 90-924, Lodz, Poland
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9
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Lewandowicz A, Rudziński J, Tronstad L, Widersten M, Ryberg P, Matsson O, Paneth P. Chlorine kinetic isotope effects on the haloalkane dehalogenase reaction. J Am Chem Soc 2001; 123:4550-5. [PMID: 11457241 DOI: 10.1021/ja003503d] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have found chlorine kinetic isotope effects on the dehalogenation catalyzed by haloalkane dehalogenase from Xanthobacter autotrophicus GJ10 to be 1.0045 +/- 0.0004 for 1,2-dichloroethane and 1.0066 +/- 0.0004 for 1-chlorobutane. The latter isotope effect approaches the intrinsic chlorine kinetic isotope effect for the dehalogenation step. The intrinsic isotope effect has been modeled using semiempirical and DFT theory levels using the ONIOM QM/QM scheme. Our results indicate that the dehalogenation step is reversible; the overall irreversibility of the enzyme-catalyzed reaction is brought about by a step following the dehalogenation.
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Affiliation(s)
- A Lewandowicz
- Department of Chemistry, Technical University of Lodz, Zeromskiego 116, 90-924 Lodz, Poland
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10
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Castillo R, Andrés J, Moliner V. Catalytic Mechanism of Dihydrofolate Reductase Enzyme. A Combined Quantum-Mechanical/Molecular-Mechanical Characterization of Transition State Structure for the Hydride Transfer Step. J Am Chem Soc 1999. [DOI: 10.1021/ja9843019] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- R. Castillo
- Contribution from the Departament de Ciències Experimentals, Universitat Jaume I, Castelló, Spain
| | - J. Andrés
- Contribution from the Departament de Ciències Experimentals, Universitat Jaume I, Castelló, Spain
| | - V. Moliner
- Contribution from the Departament de Ciències Experimentals, Universitat Jaume I, Castelló, Spain
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11
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Greatbanks SP, Gready JE, Limaye AC, Rendell AP. Enzyme polarization of substrates of dihydrofolate reductase by different theoretical methods. Proteins 1999. [DOI: 10.1002/(sici)1097-0134(19991101)37:2<157::aid-prot2>3.0.co;2-j] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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12
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Torres RA, Schiøtt B, Bruice TC. Molecular Dynamics Simulations of Ground and Transition States for the Hydride Transfer from Formate to NAD+ in the Active Site of Formate Dehydrogenase. J Am Chem Soc 1999. [DOI: 10.1021/ja9912731] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rhonda A. Torres
- Contribution from the Department of Chemistry, University of California, Santa Barbara, California 93106
| | - Birgit Schiøtt
- Contribution from the Department of Chemistry, University of California, Santa Barbara, California 93106
| | - Thomas C. Bruice
- Contribution from the Department of Chemistry, University of California, Santa Barbara, California 93106
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13
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Rucker J, Klinman JP. Computational Study of Tunneling and Coupled Motion in Alcohol Dehydrogenase-Catalyzed Reactions: Implication for Measured Hydrogen and Carbon Isotope Effects. J Am Chem Soc 1999. [DOI: 10.1021/ja9824425] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Joseph Rucker
- Contribution from the Department of Chemistry, University of California, Berkeley, California 94720
| | - Judith P. Klinman
- Contribution from the Department of Chemistry, University of California, Berkeley, California 94720
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14
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Schiøtt B, Zheng YJ, Bruice TC. Theoretical Investigation of the Hydride Transfer from Formate to NAD+ and the Implications for the Catalytic Mechanism of Formate Dehydrogenase. J Am Chem Soc 1998. [DOI: 10.1021/ja9807338] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Birgit Schiøtt
- Contribution from the Department of Chemistry, University of California at Santa Barbara, Santa Barbara, California 93106
| | - Ya-Jun Zheng
- Contribution from the Department of Chemistry, University of California at Santa Barbara, Santa Barbara, California 93106
| | - Thomas C. Bruice
- Contribution from the Department of Chemistry, University of California at Santa Barbara, Santa Barbara, California 93106
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15
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Mesecar AD, Stoddard BL, Koshland DE. Orbital steering in the catalytic power of enzymes: small structural changes with large catalytic consequences. Science 1997; 277:202-6. [PMID: 9211842 DOI: 10.1126/science.277.5323.202] [Citation(s) in RCA: 178] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Small structural perturbations in the enzyme isocitrate dehydrogenase (IDH) were made in order to evaluate the contribution of precise substrate alignment to the catalytic power of an enzyme. The reaction trajectory of IDH was modified (i) after the adenine moiety of nicotinamide adenine dinucleotide phosphate was changed to hypoxanthine (the 6-amino was changed to 6-hydroxyl), and (ii) by replacing Mg2+, which has six coordinating ligands, with Ca2+, which has eight coordinating ligands. Both changes make large (10(-3) to 10(-5)) changes in the reaction velocity but only small changes in the orientation of the substrates (both distance and angle) as revealed by cryocrystallographic trapping of active IDH complexes. The results provide evidence that orbital overlap produced by optimal orientation of reacting orbitals plays a major quantitative role in the catalytic power of enzymes.
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Affiliation(s)
- A D Mesecar
- Department of Molecular and Cell Biology, Stanley Hall, University of California, Berkeley, CA 94720, USA
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16
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Hurley MM, Hammes-Schiffer S. Development of a Potential Surface for Simulation of Proton and Hydride Transfer Reactions in Solution: Application to NADH Hydride Transfer. J Phys Chem A 1997. [DOI: 10.1021/jp970269d] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- M. M. Hurley
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
| | - Sharon Hammes-Schiffer
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
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17
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Transition structures for hydride transfer reactions in vacuo and their role in enzyme catalysis. ACTA ACUST UNITED AC 1996. [DOI: 10.1016/s0166-1280(96)04670-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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18
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Olson LP, Luo J, Almarsson O, Bruice TC. Mechanism of aldehyde oxidation catalyzed by horse liver alcohol dehydrogenase. Biochemistry 1996; 35:9782-91. [PMID: 8703951 DOI: 10.1021/bi952020x] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The mechanism of oxidation of benzaldehyde to benzoic acid catalyzed by horse liver alcohol dehydrogenase (HLADH) has been investigated using the HLADH structure at 2.1 A resolution with NAD+ and pentafluorobenzyl alcohol in the active site [Ramaswamy et al. (1994) Biochemistry 33,5230-5237]. Constructs for molecular dynamics (MD) investigations with HLADH were obtained by a best-fit superimposition of benzaldehyde or its hydrate on the pentafluorobenzyl alcohol bound to the active site Zn(II)ion. Equilibrium bond lengths, angles, and dihedral parameters for Zn(II) bonding residues His67, Cys46, and Cys174 were obtained from small-molecule X-ray crystal structures and an ab initio-derived parameterization of zinc in HLADH [Ryde, U. (1995) Proteins: Struct., Funct., Genet. 21,40-56]. Dynamic simulations in CHARMM were carried out on the following three constructs to 100 ps: (MD1) enzyme with NAD+, benzaldehyde, and zinc-ligated HO-in the active site; (MD2) enzyme with NAD+ and hydrated benzaldehyde monoanion bound to zinc via the pro-R oxygen, with a proton residing on the pro-S oxygen; and (MD3) enzyme with NAD+ and hydrated benzaldehyde monoanion bound to zinc via the pro-S oxygen, with a proton residing on the pro-R oxygen. Analyses were done of 800 sample conformations taken in the last 40 ps of dynamics. Structures from MD1 and MD3 were used to define the initial spatial arrangements of reactive functionalities for semiempirical PM3 calculations. Using PM3, model systems were calculated of ground states and some transition states for aldehyde hydration, hydride transfer, and subsequent proton shuttling. With benzaldehyde and zinc-bound hydroxide ion in the active site, the oxygen of Zn(II)-OH resided at a distance of 2.8-5.5 A from the aldehyde carbonyl carbon during the dynamics simulation. This may be compared to the PM3 transition state for attack of the Zn(II)-OH oxygen on the benzaldehyde carbonyl carbon, which has an O...C distance of 1.877 A. HLADH catalysis of the aldehyde hydration would require very little motion aside from that in the ground state. Two simulations of benzaldehyde hydrate ligated to zinc (MD2 and MD3) both showed close approach of the aldehyde hydrate hydrogen to NAD+C4, varying from 2.3 to 3.3 A, seemingly favorable for the hydride transfer reaction. The MD2 configuration does not allow proton shuttling. On the other hand, when the pro-S oxygen is ligated to zinc (MD3), the proton on the pro-R oxygen averages 2.09 A from the hydroxyl oxygen of Ser48 such that initiation of shuttling of protons via Ser48 to the ribose 2'-hydroxyl oxygen to the 3'-hydroxyl oxygen to His51 nitrogen is sterically favorable. PM3 calculations suggest that this proton shuttle represents a stepwise reaction which occurs subsequent to hydride transfer. The PM3 transition state for hydride transfer based on the MD3 configuration has the transferring hydride 1.476 A from C4 of NAD+ and 1.433 A from the aldehyde alpha-carbon.
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Affiliation(s)
- L P Olson
- Department of Chemistry, University of California at Santa Barbara, Santa Barbara, California 93106, USA
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19
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Andrés J, Moliner V, Krechl J, Silla E. Transition state structures for the molecular mechanism of lactate dehydrogenase enzyme. ACTA ACUST UNITED AC 1995. [DOI: 10.1039/p29950001551] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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20
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Ranganathan S, Gready JE. Mechanistic aspects of biological redox reactions involving NADH. Part 5.—AM1 transition-state studies for the pyruvate–L-lactate interconversion inL-lactate dehydrogenase. ACTA ACUST UNITED AC 1994. [DOI: 10.1039/ft9949002047] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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21
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von Onciul AR, Clark T. Molecular orbital studies of enzyme mechanisms. II. Catalytic oxidation of alcohols by liver alcohol dehydrogenase. J Comput Chem 1993. [DOI: 10.1002/jcc.540140403] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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22
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Jurema MW, Shields GC. Ability of the PM3 quantum-mechanical method to modelintermolecular hydrogen bonding between neutral molecules. J Comput Chem 1993. [DOI: 10.1002/jcc.540140113] [Citation(s) in RCA: 139] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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23
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24
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Mestres J, Lledós A, Duran M, Bertrán J. Analysis of the hydride transfer in the [CH3-H-CH3]+ system in terms of valence bond structures. ACTA ACUST UNITED AC 1992. [DOI: 10.1016/0166-1280(92)87048-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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25
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Gerres T, Heesing A. Wasserstoffübertragungen, 20[1a] Konkurrierende pericyclische Reaktionen von Dihydroarenen mit gespannten Cycloalkenen und -alkinen. ACTA ACUST UNITED AC 1992. [DOI: 10.1002/cber.19921250621] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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26
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