1
|
Major DT, Gupta PK, Gao J. Origin of Catalysis by Nitroalkane Oxidase. J Phys Chem B 2023; 127:151-162. [PMID: 36580021 DOI: 10.1021/acs.jpcb.2c07357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The rate of proton abstraction of the carbon acid nitroethane by Asp402 is accelerated by a factor of 108 in the enzyme nitroalkane oxidase (NAO) relative to that by the organic base acetate ion in water. The Cα proton of nitroalkanes is known to exhibit an abnormal correlation between its acidity strength and the rate of deprotonation, with an unusually slow rate of deprotonation in water. This work examines the origin of NAO catalysis, revealing that the rate enhancement by the enzyme is due to transition-state stabilization, restoring the normal behavior of the linear free energy relationship of Bronsted acids. Interestingly, NAO employs the ubiquitous cofactor flavin adenosine diphosphate (FAD) to perform the subsequent oxidation. Does the FAD cofactor also affect the catalytic rate of the initial proton transfer process of the overall nitroalkane oxidation? Classical molecular dynamics and path-integral simulations using a reaction-specific combined quantum mechanics/molecular mechanics (QM/MM) approach were carried out to obtain the free energy reaction profiles, or the potentials of mean force, for the enzymatic reaction and for a model reaction in aqueous solution, as well as for the 2'-deoxy-FAD co-factor-modified NAO. Free energy perturbation calculations suggest that transition-state stabilization of the reactive fragment is the primary cause of the catalytic effect. It is found that the FAD cofactor plays a crucial role in increasing the Cα proton acidity, via specific hydrogen bonding and π-stacking interactions, although these factors have a smaller effect on the enhancement of the rate of deprotonation. Model QM calculations of the π-stacking complexes between the FAD isoalloxazine ring and the neutral and anionic nitroethane, respectively, reveal that the anionic π-stacking complex is more stable than the neutral one by 15.7 kcal/mol, and a net π-stacking energy of 17.3 kcal/mol is obtained. Hence, the isoalloxazine ring, in addition to serving as a very potent oxidizing agent via the formation of covalent intermediate structures, is able to exert a considerable amount of catalytic effect through noncovalent π-stacking interactions.
Collapse
Affiliation(s)
- Dan Thomas Major
- Department of Chemistry and Institute for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan52900, Israel
| | - Prashant Kumar Gupta
- Department of Chemistry and Institute for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan52900, Israel
| | - Jiali Gao
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota55455, United States.,Shenzhen Bay Laboratory, Institute of Systems and Physical Biology, Shenzhen, Guangdong581055, China
| |
Collapse
|
2
|
Shimo S, Ushimaru R, Engelbrecht A, Harada M, Miyamoto K, Kulik A, Uchiyama M, Kaysser L, Abe I. Stereodivergent Nitrocyclopropane Formation during Biosynthesis of Belactosins and Hormaomycins. J Am Chem Soc 2021; 143:18413-18418. [PMID: 34710328 DOI: 10.1021/jacs.1c10201] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Belactosins and hormaomycins are peptide natural products containing 3-(2-aminocyclopropyl)alanine and 3-(2-nitrocyclopropyl)alanine residues, respectively, with opposite stereoconfigurations of the cyclopropane ring. Herein we demonstrate that the heme oxygenase-like enzymes BelK and HrmI catalyze the N-oxygenation of l-lysine to generate 6-nitronorleucine. The nonheme iron enzymes BelL and HrmJ then cyclize the nitroalkane moiety to the nitrocyclopropane ring with the desired stereochemistry found in the corresponding natural products. We also show that both cyclopropanases remove the 4-proS-H of 6-nitronorleucine during the cyclization, establishing the inversion and retention of the configuration at C4 during the BelL and HrmJ reactions, respectively. This study reveals the unique strategy for stereocontrolled cyclopropane synthesis in nature.
Collapse
Affiliation(s)
- Shotaro Shimo
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Richiro Ushimaru
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan.,ACT-X, Japan Science and Technology Agency (JST), Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Alicia Engelbrecht
- Pharmaceutical Institute, Department of Pharmaceutical Biology, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Mei Harada
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kazunori Miyamoto
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Andreas Kulik
- Interfaculty Institute of Microbiology and Infection Medicine (IMIT), University of Tübingen, 72076 Tübingen, Germany
| | - Masanobu Uchiyama
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan.,Research Initiative for Supra-Materials (RISM), Shinshu University, Ueda, 386-8567, Japan
| | - Leonard Kaysser
- Institute for Drug Discovery, Department of Pharmaceutical Biology, University of Leipzig, Eilenburger Str. 14, 04317 Leipzig, Germany
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| |
Collapse
|
3
|
Zhou S, Nguyen BT, Richard JP, Kluger R, Gao J. Origin of Free Energy Barriers of Decarboxylation and the Reverse Process of CO 2 Capture in Dimethylformamide and in Water. J Am Chem Soc 2021; 143:137-141. [PMID: 33375792 DOI: 10.1021/jacs.0c12414] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In aqueous solution, biological decarboxylation reactions proceed irreversibly to completion, whereas the reverse carboxylation processes are typically powered by the hydrolysis of ATP. The exchange of the carboxylate of ring-substituted arylacetates with isotope-labeled CO2 in polar aprotic solvents reported recently suggests a dramatic change in the partition of reaction pathways. Yet, there is little experimental data pertinent to the kinetic barriers for protonation and thermodynamic data on CO2 capture by the carbanions of decarboxylation reactions. Employing a combined quantum mechanical and molecular mechanical simulation approach, we investigated the decarboxylation reactions of a series of organic carboxylate compounds in aqueous and in dimethylformamide solutions, revealing that the reverse carboxylation barriers in solution are fully induced by solvent effects. A linear Bell-Evans-Polanyi relationship was found between the rates of decarboxylation and the Gibbs energies of reaction, indicating diminishing recombination barriers in DMF. In contrast, protonation of the carbanions by the DMF solvent has large free energy barriers, rendering the competing exchange of isotope-labeled CO2 reversible in DMF. The finding of an intricate interplay of carbanion stability and solute-solvent interaction in decarboxylation and carboxylation could be useful to designing novel materials for CO2 capture.
Collapse
Affiliation(s)
- Shaoyuan Zhou
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 581055, China.,Institute of Theoretical Chemistry, Jilin University, Changchun 100231, China
| | - Bach T Nguyen
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - John P Richard
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 47907, United States
| | - Ronald Kluger
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Jiali Gao
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 581055, China.,Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
| |
Collapse
|
4
|
Liu M, Youmans KN, Gao J. Dual QM and MM Approach for Computing Equilibrium Isotope Fractionation Factor of Organic Species in Solution. Molecules 2018; 23:E2644. [PMID: 30326599 PMCID: PMC6222756 DOI: 10.3390/molecules23102644] [Citation(s) in RCA: 2] [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: 09/17/2018] [Revised: 10/10/2018] [Accepted: 10/11/2018] [Indexed: 11/17/2022] Open
Abstract
A dual QM and MM approach for computing equilibrium isotope effects has been described. In the first partition, the potential energy surface is represented by a combined quantum mechanical and molecular mechanical (QM/MM) method, in which a solute molecule is treated quantum mechanically, and the remaining solvent molecules are approximated classically by molecular mechanics. In the second QM/MM partition, differential nuclear quantum effects responsible for the isotope effect are determined by a statistical mechanical double-averaging formalism, in which the nuclear centroid distribution is sampled classically by Newtonian molecular dynamics and the quantum mechanical spread of quantized particles about the centroid positions is treated using the path integral (PI) method. These partitions allow the potential energy surface to be properly represented such that the solute part is free of nuclear quantum effects for nuclear quantum mechanical simulations, and the double-averaging approach has the advantage of sampling efficiency for solvent configuration and for path integral convergence. Importantly, computational precision is achieved through free energy perturbation (FEP) theory to alchemically mutate one isotope into another. The PI-FEP approach is applied to model systems for the 18O enrichment found in cellulose of trees to determine the isotope enrichment factor of carbonyl compounds in water. The present method may be useful as a general tool for studying isotope fractionation in biological and geochemical systems.
Collapse
Affiliation(s)
- Meiyi Liu
- Laboratory of Theoretical and Computational Chemistry, Theoretical Chemistry Institute, Jilin University, Changchun 130023, China.
| | - Katelyn N Youmans
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Jiali Gao
- Laboratory of Theoretical and Computational Chemistry, Theoretical Chemistry Institute, Jilin University, Changchun 130023, China.
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA.
| |
Collapse
|
5
|
Das S, Nam K, Major DT. Rapid Convergence of Energy and Free Energy Profiles with Quantum Mechanical Size in Quantum Mechanical–Molecular Mechanical Simulations of Proton Transfer in DNA. J Chem Theory Comput 2018; 14:1695-1705. [DOI: 10.1021/acs.jctc.7b00964] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Susanta Das
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Kwangho Nam
- Department of Chemistry, Umeå University, 901 87 Umeå, Sweden
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas 76019-0065, United States
| | - Dan Thomas Major
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 5290002, Israel
| |
Collapse
|
6
|
Pshetitsky Y, Eitan R, Verner G, Kohen A, Major DT. Improved Sugar Puckering Profiles for Nicotinamide Ribonucleoside for Hybrid QM/MM Simulations. J Chem Theory Comput 2016; 12:5179-5189. [PMID: 27490188 DOI: 10.1021/acs.jctc.6b00401] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The coenzyme nicotinamide adenine dinucleotide (NAD+) and its reduced form (NADH) play ubiquitous roles as oxidizing and reducing agents in nature. The binding, and possibly the chemical redox step, of NAD+/NADH may be influenced by the cofactor conformational distribution and, in particular, by the ribose puckering of its nicotinamide-ribonucleoside (NR) moiety. In many hybrid quantum mechanics-molecular mechanics (QM/MM) studies of NAD+/NADH dependent enzymes, the QM region is treated by semiempirical (SE) methods. Recent work suggests that SE methods do not adequately describe the ring puckering in sugar molecules. In the present work we adopt an efficient and practical strategy to correct for this deficiency for NAD+/NADH. We have implemented a cost-effective correction to a SE Hamiltonian by adding a correction potential, which is defined as the difference between an accurate benchmark density functional theory (DFT) potential energy surface (PES) and the SE PES. In practice, this is implemented via a B-spline interpolation scheme for the grid-based potential energy difference surface. We find that the puckering population distributions obtained from free energy QM(SE)/MM simulations are in good agreement with DFT and in fair accord with experimental results. The corrected PES should facilitate a more accurate description of the ribose puckering in the NAD+/NADH cofactor in simulations of biological systems.
Collapse
Affiliation(s)
- Yaron Pshetitsky
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry, Bar-Ilan University , Ramat-Gan 52900, Israel
| | - Reuven Eitan
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry, Bar-Ilan University , Ramat-Gan 52900, Israel
| | - Gilit Verner
- Department of Chemistry and 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
| | - Dan Thomas Major
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry, Bar-Ilan University , Ramat-Gan 52900, Israel
| |
Collapse
|
7
|
Abstract
Path-integral free energy perturbation (PI-FEP) theory is presented to directly determine the ratio of quantum mechanical partition functions of different isotopologs in a single simulation. Furthermore, a double averaging strategy is used to carry out the practical simulation, separating the quantum mechanical path integral exactly into two separate calculations, one corresponding to a classical molecular dynamics simulation of the centroid coordinates, and another involving free-particle path-integral sampling over the classical, centroid positions. An integrated centroid path-integral free energy perturbation and umbrella sampling (PI-FEP/UM, or simply, PI-FEP) method along with bisection sampling was summarized, which provides an accurate and fast convergent method for computing kinetic isotope effects for chemical reactions in solution and in enzymes. The PI-FEP method is illustrated by a number of applications, to highlight the computational precision and accuracy, the rule of geometrical mean in kinetic isotope effects, enhanced nuclear quantum effects in enzyme catalysis, and protein dynamics on temperature dependence of kinetic isotope effects.
Collapse
Affiliation(s)
- J Gao
- Theoretical Chemistry Institute, Jilin University, Changchun, Jilin Province, PR China; University of Minnesota, Minneapolis, MN, United States.
| |
Collapse
|
8
|
Dixit M, Das S, Mhashal A, Eitan R, Major D. Practical Aspects of Multiscale Classical and Quantum Simulations of Enzyme Reactions. Methods Enzymol 2016; 577:251-86. [DOI: 10.1016/bs.mie.2016.05.046] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
|
9
|
Vardi-Kilshtain A, Nitoker N, Major DT. Nuclear quantum effects and kinetic isotope effects in enzyme reactions. Arch Biochem Biophys 2015; 582:18-27. [DOI: 10.1016/j.abb.2015.03.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 03/02/2015] [Accepted: 03/03/2015] [Indexed: 11/28/2022]
|
10
|
Engel H, Eitan R, Azuri A, Major DT. Nuclear quantum effects in chemical reactions via higher-order path-integral calculations. Chem Phys 2015. [DOI: 10.1016/j.chemphys.2015.01.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
11
|
Alabugin IV, Bresch S, dos Passos Gomes G. Orbital hybridization: a key electronic factor in control of structure and reactivity. J PHYS ORG CHEM 2014. [DOI: 10.1002/poc.3382] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Igor V. Alabugin
- Department of Chemistry and Biochemistry; Florida State University; Tallahassee FL 32306-4390 USA
| | - Stefan Bresch
- Department of Chemistry and Biochemistry; Florida State University; Tallahassee FL 32306-4390 USA
| | - Gabriel dos Passos Gomes
- Department of Chemistry and Biochemistry; Florida State University; Tallahassee FL 32306-4390 USA
| |
Collapse
|
12
|
Carvalho ATP, Barrozo A, Doron D, Kilshtain AV, Major DT, Kamerlin SCL. Challenges in computational studies of enzyme structure, function and dynamics. J Mol Graph Model 2014; 54:62-79. [PMID: 25306098 DOI: 10.1016/j.jmgm.2014.09.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 09/13/2014] [Accepted: 09/16/2014] [Indexed: 01/23/2023]
Abstract
In this review we give an overview of the field of Computational enzymology. We start by describing the birth of the field, with emphasis on the work of the 2013 chemistry Nobel Laureates. We then present key features of the state-of-the-art in the field, showing what theory, accompanied by experiments, has taught us so far about enzymes. We also briefly describe computational methods, such as quantum mechanics-molecular mechanics approaches, reaction coordinate treatment, and free energy simulation approaches. We finalize by discussing open questions and challenges.
Collapse
Affiliation(s)
- Alexandra T P Carvalho
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden
| | - Alexandre Barrozo
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden
| | - Dvir Doron
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Alexandra Vardi Kilshtain
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Dan Thomas Major
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry Bar-Ilan University, Ramat-Gan 52900, Israel.
| | - Shina Caroline Lynn Kamerlin
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden.
| |
Collapse
|
13
|
Alabugin IV, Bresch S, Manoharan M. Hybridization trends for main group elements and expanding the Bent's rule beyond carbon: more than electronegativity. J Phys Chem A 2014; 118:3663-77. [PMID: 24773162 DOI: 10.1021/jp502472u] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Trends in hybridization were systematically analyzed through the combination of DFT calculations with NBO analysis for the five elements X (X = B, C, N, O, and F) in 75 HnX-YHm compounds, where Y spans the groups 13-17 of the periods 2-4. This set of substrates probes the flexibility of the hybridization at five atoms X through variations in electronegativity, polarizability, and orbital size of Y. The results illustrate the scope and limitations of the Bent's rule, the classic correlation between electronegativity and hybridization, commonly used in analyzing structural effects in carbon compounds. The rehybridization effects are larger for fluorine- and oxygen-bonds than they are in the similar bonds to carbon. For bonds with the larger elements Y of the lower periods, trends in orbital hybridization depend strongly on both electronegativity and orbital size. For charged species, the effects of substituent orbital size in the more polarizable bonds to heavier elements show a particularly strong response to the charge introduction at the central atom. In the final section, we provide an example of the interplay between hybridization effects with molecular structure and reactivity. In particular, the ability to change hybridization without changes in polarization provides an alternative way to control structure and reactivity, as illustrated by the strong correlation of strain in monosubstituted cyclopropanes with hybridization in the bond to the substituent.
Collapse
Affiliation(s)
- Igor V Alabugin
- Department of Chemistry and Biochemistry, Florida State University , Tallahassee, Florida 32306-4390, United States
| | | | | |
Collapse
|
14
|
Doron D, Weitman M, Vardi-Kilshtain A, Azuri A, Engel H, Major DT. Multiscale Quantum-Classical Simulations of Enzymes. Isr J Chem 2014. [DOI: 10.1002/ijch.201400026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
15
|
Vardi-Kilshtain A, Doron D, Major DT. Quantum and classical simulations of orotidine monophosphate decarboxylase: support for a direct decarboxylation mechanism. Biochemistry 2013; 52:4382-90. [PMID: 23692207 DOI: 10.1021/bi400190v] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Orotidine 5'-monophosphate (OMP) decarboxylase (ODCase) catalyzes the decarboxylation of OMP to uridine 5'-monophosphate (UMP). Numerous studies of this reaction have suggested a plethora of mechanisms including covalent addition, ylide or carbene formation, and concerted or stepwise protonation. Recent experiments and simulations present strong evidence for a direct decarboxylation mechanism, although direct comparison between experiment and theory is still lacking. In the current work we present hybrid quantum mechanics-molecular mechanics simulations that address the detailed decarboxylation mechanisms for OMP and 5-fluoro-OMP by ODCase. Multidimensional potentials of mean force are computed as functions of structural progress coordinates for the Methanobacterium thermoautotrophicum ODCase reaction: the decarboxylation reaction coordinate, an orbital rehybridization coordinate, and the proton transfer coordinate between Lys72 and the substrate. The computed free energy profiles are in accord with the available experimental data. To facilitate further direct comparison with experiment, we compute the kinetic isotope effects (KIEs) for the enzyme-catalyzed reactions using a mass-perturbation-based path-integral method. The computed KIE provide further support for a direct decarboxylation mechanism. In agreement with experiment, the data suggest a role for Lys72 in stabilizing the transition state in the catalysis of OMP and, to a somewhat lesser extent, in 5-fluoro-OMP.
Collapse
Affiliation(s)
- Alexandra Vardi-Kilshtain
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
| | | | | |
Collapse
|
16
|
Gadda G, Fitzpatrick PF. Solvent isotope and viscosity effects on the steady-state kinetics of the flavoprotein nitroalkane oxidase. FEBS Lett 2013; 587:2785-9. [PMID: 23660407 DOI: 10.1016/j.febslet.2013.04.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Revised: 04/22/2013] [Accepted: 04/23/2013] [Indexed: 01/13/2023]
Abstract
The flavoprotein nitroalkane oxidase catalyzes the oxidative denitrification of a broad range of primary and secondary nitroalkanes to yield the respective aldehydes or ketones, hydrogen peroxide and nitrite. With nitroethane as substrate the D2O(k(cat)/K(M)) value is 0.6 and the D2Ok(cat) value is 2.4. The k(cat) proton inventory is consistent with a single exchangeable proton in flight, while the k(cat)/K(M) is consistent with either a single proton in flight in the transition state or a medium effect. Increasing the solvent viscosity did not affect the k(cat) or k(cat)/K(M) value significantly, establishing that nitroethane binding is at equilibrium and that product release does not limit k(cat).
Collapse
Affiliation(s)
- Giovanni Gadda
- Department of Chemistry and the Center for Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30303, USA
| | | |
Collapse
|
17
|
Vardi-Kilshtain A, Major DT, Kohen A, Engel H, Doron D. Hybrid Quantum and Classical Simulations of the Formate Dehydrogenase Catalyzed Hydride Transfer Reaction on an Accurate Semiempirical Potential Energy Surface. J Chem Theory Comput 2012; 8:4786-96. [DOI: 10.1021/ct300628e] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alexandra Vardi-Kilshtain
- Department
of Chemistry and the Lise Meitner-Minerva Center of Computational
Quantum Chemistry, Bar-Ilan University,
Ramat-Gan 52900, Israel
| | - Dan Thomas Major
- Department
of Chemistry and 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
| | - Hamutal Engel
- Department
of Chemistry and the Lise Meitner-Minerva Center of Computational
Quantum Chemistry, Bar-Ilan University,
Ramat-Gan 52900, Israel
| | - Dvir Doron
- Department
of Chemistry and the Lise Meitner-Minerva Center of Computational
Quantum Chemistry, Bar-Ilan University,
Ramat-Gan 52900, Israel
| |
Collapse
|
18
|
Doron D, Kohen A, Major DT. Collective Reaction Coordinate for Hybrid Quantum and Molecular Mechanics Simulations: A Case Study of the Hydride Transfer in Dihydrofolate Reductase. J Chem Theory Comput 2012; 8:2484-96. [PMID: 26588977 DOI: 10.1021/ct300235k] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The optimal description of the reaction coordinate in chemical systems is of great importance in simulating condensed phase reactions. In the current work, we present a collective reaction coordinate which is composed of several geometric coordinates which represent structural progress during the course of a hydride transfer reaction: the antisymmetric reactive stretch coordinate, the donor-acceptor distance (DAD) coordinate, and an orbital rehybridization coordinate. In this approach, the former coordinate serves as a distinguished reaction coordinate, while the latter two serve as environmental, Marcus-type inner-sphere reorganization coordinates. The classical free energy surface is obtained from multidimensional quantum mechanics-molecular mechanics (QM/MM) potential of mean force (PMF) simulations in conjunction with a general and efficient multidimensional weighted histogram method implementation. The minimum free energy path, or the collective reaction coordinate, connecting the dividing hypersurface to reactants and products, is obtained using an iterative scheme. In this approach, the string method is used to find the minimum free energy path. This path guides the multidimensional sampling, while the path is adaptively refined until convergence is achieved. As a model system, we choose the hydride transfer reaction in Escherichia coli dihydrofolate reductase (ecDHFR) using a recently developed accurate semiempirical potential energy surface. To estimate the advantages of the collective reaction coordinate, we perform activated dynamics simulations to obtain the reaction transmission coefficient. The results show that the combination of a distinguished reaction coordinate and an inner-sphere reorganization coordinate considerably reduces the dividing surface recrossing.
Collapse
Affiliation(s)
- Dvir Doron
- Department of Chemistry and 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
| | - Dan Thomas Major
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
| |
Collapse
|
19
|
Kostal J, Voutchkova AM, Jorgensen WL. Investigation of solvent effects on the rate and stereoselectivity of the Henry reaction. Org Lett 2011; 14:260-3. [PMID: 22168236 DOI: 10.1021/ol2030394] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A combined computational and experimental kinetic study on the Henry reaction is reported. The effects of solvation on the transition structures and the rates of reaction between nitromethane and formaldehyde, and between nitropropane and benzaldehyde are elucidated with QM/MM calculations.
Collapse
Affiliation(s)
- Jakub Kostal
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520-8107, USA
| | | | | |
Collapse
|
20
|
Vardi-Kilshtain A, Azuri A, Major DT. Path-integral calculations of heavy atom kinetic isotope effects in condensed phase reactions using higher-order trotter factorizations. J Comput Chem 2011; 33:435-41. [DOI: 10.1002/jcc.21986] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Revised: 10/14/2011] [Accepted: 10/14/2011] [Indexed: 01/07/2023]
|
21
|
Abstract
We describe a computational approach, incorporating quantum mechanics into enzyme kinetics modeling with a special emphasis on computation of kinetic isotope effects. Two aspects are highlighted: (1) the potential energy surface is represented by a combined quantum mechanical and molecular mechanical (QM/MM) potential in which the bond forming and breaking processes are modeled by electronic structure theory, and (2) a free energy perturbation method in path integral simulation is used to determine both kinetic isotope effects (KIEs). In this approach, which is called the PI-FEP/UM method, a light (heavy) isotope is mutated into a heavy (light) counterpart in centroid path integral simulations. The method is illustrated in the study of primary and secondary KIEs in two enzyme systems. In the case of nitroalkane oxidase, the enzymatic reaction exhibits enhanced quantum tunneling over that of the uncatalyzed process in water. In the dopa delarboxylase reaction, there appears to be distinguishable primary carbon-13 and secondary deuterium KIEs when the internal proton tautomerism is in the N-protonated or in the O-protonated positions. These examples show that the incorporation of quantum mechanical effects in enzyme kinetics modeling offers an opportunity to accurately and reliably model the mechanisms and free energies of enzymatic reactions.
Collapse
|
22
|
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.
Collapse
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
| |
Collapse
|
23
|
Azuri A, Engel H, Doron D, Major DT. Path-Integral Calculations of Nuclear Quantum Effects in Model Systems, Small Molecules, and Enzymes via Gradient-Based Forward Corrector Algorithms. J Chem Theory Comput 2011; 7:1273-86. [DOI: 10.1021/ct100716c] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Asaf Azuri
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Hamutal Engel
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Dvir Doron
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Dan Thomas Major
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
| |
Collapse
|
24
|
Abstract
A mixed centroid path integral and free energy perturbation method (PI-FEP/UM) has been used to investigate the primary carbon and secondary hydrogen kinetic isotope effects (KIEs) in the amino acid decarboxylation of L-Dopa catalyzed by the enzyme L-Dopa decarboxylase (DDC) along with the corresponding uncatalyzed reaction in water. DDC is a pyridoxal 5'-phosphate (PLP) dependent enzyme. The cofactor undergoes an internal proton transfer between the zwitterionic protonated Schiff base configuration and the neutral hydroxyimine tautomer. It was found that the cofactor PLP makes significant contributions to lowering the decarboxylation barrier, while the enzyme active site provides further stabilization of the transition state. Interestingly, the O-protonated configuration is preferred both in the Michaelis complex and at the decarboxylation transition state. The computed kinetic isotope effects (KIE) on the carboxylate C-13 are consistent with that observed on decarboxylation reactions of other PLP-dependent enzymes, whereas the KIEs on the α carbon and secondary proton, which can easily be validated experimentally, may be used as a possible identification for the active form of the PLP tautomer in the active site of DDC.
Collapse
Affiliation(s)
- Yen-lin Lin
- Department of Chemistry, Digital Technology Center and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | | |
Collapse
|
25
|
Weitman M, Major DT. Challenges posed to bornyl diphosphate synthase: diverging reaction mechanisms in monoterpenes. J Am Chem Soc 2010; 132:6349-60. [PMID: 20394387 DOI: 10.1021/ja910134x] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The simplest form of terpenoid chemistry is found for the monoterpenes, which give plants fragrance, flavor, and medicinal properties. Monoterpene synthases employ geranyl diphosphate as a substrate to generate an assortment of cyclic products. In the current study we present a detailed analysis of the multiple gas-phase reaction pathways in the synthesis of bornyl cation from geranyl diphosphate. Additionally, the fate of the proposed bornyl cation intermediate in the bornyl diphosphate synthase reaction is investigated by molecular dynamics simulations. We employ accurate density functional theory (DFT) methods after careful validation against high-level ab initio data for a set of model carbocations. The gas-phase results for the monoterpene reactions indicate a diverging reaction mechanism with multiple products in the absence of enzymatic control. This complex potential energy surface includes several possible bifurcation points due to the presence of secondary cations. Additionally, the suggested bornyl cation intermediate in the bornyl diphosphate synthase reaction is studied by molecular dynamics simulations employing a hybrid quantum mechanics (DFT)-molecular mechanics potential energy function. The simulations suggest that the bornyl cation is a transient species as in the gas phase and that electrostatic steering directs the formation of the final product, bornyl diphosphate.
Collapse
Affiliation(s)
- Michal Weitman
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
| | | |
Collapse
|
26
|
Tormos JR, Taylor AB, Daubner SC, Hart PJ, Fitzpatrick PF. Identification of a hypothetical protein from Podospora anserina as a nitroalkane oxidase. Biochemistry 2010; 49:5035-41. [PMID: 20481475 PMCID: PMC2889615 DOI: 10.1021/bi100610e] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The flavoprotein nitroalkane oxidase (NAO) from Fusarium oxysporum catalyzes the oxidation of primary and secondary nitroalkanes to their respective aldehydes and ketones. Structurally, the enzyme is a member of the acyl-CoA dehydrogenase superfamily. To date no enzymes other than that from F. oxysporum have been annotated as NAOs. To identify additional potential NAOs, the available database was searched for enzymes in which the active site residues Asp402, Arg409, and Ser276 were conserved. Of the several fungal enzymes identified in this fashion, PODANSg2158 from Podospora anserina was selected for expression and characterization. The recombinant enzyme is a flavoprotein with activity on nitroalkanes comparable to the F. oxysporum NAO, although the substrate specificity is somewhat different. Asp399, Arg406, and Ser273 in PODANSg2158 correspond to the active site triad in F. oxysporum NAO. The k(cat)/K(M)-pH profile with nitroethane shows a pK(a) of 5.9 that is assigned to Asp399 as the active site base. Mutation of Asp399 to asparagine decreases the k(cat)/K(M) value for nitroethane over 2 orders of magnitude. The R406K and S373A mutations decrease this kinetic parameter by 64- and 3-fold, respectively. The structure of PODANSg2158 has been determined at a resolution of 2.0 A, confirming its identification as an NAO.
Collapse
Affiliation(s)
- José R Tormos
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, Texas 78229, USA
| | | | | | | | | |
Collapse
|
27
|
Valley MP, Fenny NS, Ali SR, Fitzpatrick PF. Characterization of active site residues of nitroalkane oxidase. Bioorg Chem 2010; 38:115-9. [PMID: 20056514 PMCID: PMC2847678 DOI: 10.1016/j.bioorg.2009.12.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2009] [Revised: 12/03/2009] [Accepted: 12/04/2009] [Indexed: 11/30/2022]
Abstract
The flavoenzyme nitroalkane oxidase catalyzes the oxidation of primary and secondary nitroalkanes to the corresponding aldehydes and ketones plus nitrite. The structure of the enzyme shows that Ser171 forms a hydrogen bond to the flavin N5, suggesting that it plays a role in catalysis. Cys397 and Tyr398 were previously identified by chemical modification as potential active site residues. To more directly probe the roles of these residues, the S171A, S171V, S171T, C397S, and Y398F enzymes have been characterized with nitroethane as substrate. The C397S and Y398 enzymes were less stable than the wild-type enzyme, and the C397S enzyme routinely contained a substoichiometric amount of FAD. Analysis of the steady-state kinetic parameters for the mutant enzymes, including deuterium isotope effects, establishes that all of the mutations result in decreases in the rate constants for removal of the substrate proton by approximately 5-fold and decreases in the rate constant for product release of approximately 2-fold. Only the S171V and S171T mutations alter the rate constant for flavin oxidation. These results establish that these residues are not involved in catalysis, but rather are required for maintaining the protein structure.
Collapse
Affiliation(s)
- Michael P. Valley
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843
| | - Nana S. Fenny
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843
| | - Shah R. Ali
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843
| | - Paul F. Fitzpatrick
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229
| |
Collapse
|
28
|
Kamerlin SCL, Warshel A. An Analysis of All the Relevant Facts and Arguments Indicates that Enzyme Catalysis Does Not Involve Large Contributions from Nuclear Tunneling. J PHYS ORG CHEM 2010; 23:677-684. [PMID: 21494414 DOI: 10.1002/poc.1620] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Shina C L Kamerlin
- Department of Chemistry, University of Southern California, 3620 McClintock Ave., Los Angeles CA-90089, USA
| | | |
Collapse
|
29
|
Molecular dynamics simulations and mechanism of organic reactions: non-TST behaviors. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2010. [DOI: 10.1016/s0065-3160(08)44004-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
|
30
|
Differential quantum tunneling contributions in nitroalkane oxidase catalyzed and the uncatalyzed proton transfer reaction. Proc Natl Acad Sci U S A 2009; 106:20734-9. [PMID: 19926855 DOI: 10.1073/pnas.0911416106] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The proton transfer reaction between the substrate nitroethane and Asp-402 catalyzed by nitroalkane oxidase and the uncatalyzed process in water have been investigated using a path-integral free-energy perturbation method. Although the dominating effect in rate acceleration by the enzyme is the lowering of the quasiclassical free energy barrier, nuclear quantum effects also contribute to catalysis in nitroalkane oxidase. In particular, the overall nuclear quantum effects have greater contributions to lowering the classical barrier in the enzyme, and there is a larger difference in quantum effects between proton and deuteron transfer for the enzymatic reaction than that in water. Both experiment and computation show that primary KIEs are enhanced in the enzyme, and the computed Swain-Schaad exponent for the enzymatic reaction is exacerbated relative to that in the absence of the enzyme. In addition, the computed tunneling transmission coefficient is approximately three times greater for the enzyme reaction than the uncatalyzed reaction, and the origin of the difference may be attributed to a narrowing effect in the effective potentials for tunneling in the enzyme than that in aqueous solution.
Collapse
|
31
|
Backstrom N, Burton NA, Watt CIF. Primary kinetic hydrogen isotope effects in deprotonations of a nitroalkane by intramolecular phenolate groups. J PHYS ORG CHEM 2009. [DOI: 10.1002/poc.1631] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
|
32
|
Gao J, Wong KY, Major DT, Cembran A, Song L, Lin YL, Fan Y, Ma S. Kinetic Isotope Effects from Hybrid Classical and Quantum Path Integral Computations. QUANTUM TUNNELLING IN ENZYME-CATALYSED REACTIONS 2009. [DOI: 10.1039/9781847559975-00105] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Jiali Gao
- Department of Chemistry, Digital Technology Center and Supercomputer Institute, University of Minnesota 207 Pleasant Street S.E. Minneapolis MN 55455-0431 USA
| | - Kin-Yiu Wong
- Department of Chemistry, Digital Technology Center and Supercomputer Institute, University of Minnesota 207 Pleasant Street S.E. Minneapolis MN 55455-0431 USA
| | - Dan T. Major
- Department of Chemistry, Digital Technology Center and Supercomputer Institute, University of Minnesota 207 Pleasant Street S.E. Minneapolis MN 55455-0431 USA
| | - Alessandro Cembran
- Department of Chemistry, Digital Technology Center and Supercomputer Institute, University of Minnesota 207 Pleasant Street S.E. Minneapolis MN 55455-0431 USA
| | - Lingchun Song
- Department of Chemistry, Digital Technology Center and Supercomputer Institute, University of Minnesota 207 Pleasant Street S.E. Minneapolis MN 55455-0431 USA
| | - Yen-lin Lin
- Department of Chemistry, Digital Technology Center and Supercomputer Institute, University of Minnesota 207 Pleasant Street S.E. Minneapolis MN 55455-0431 USA
| | - Yao Fan
- Department of Chemistry, Digital Technology Center and Supercomputer Institute, University of Minnesota 207 Pleasant Street S.E. Minneapolis MN 55455-0431 USA
| | - Shuhua Ma
- Department of Chemistry, Digital Technology Center and Supercomputer Institute, University of Minnesota 207 Pleasant Street S.E. Minneapolis MN 55455-0431 USA
| |
Collapse
|
33
|
Hybrid quantum and classical methods for computing kinetic isotope effects of chemical reactions in solutions and in enzymes. Methods Mol Biol 2008; 443:37-62. [PMID: 18446281 DOI: 10.1007/978-1-59745-177-2_3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2023]
Abstract
A method for incorporating quantum mechanics into enzyme kinetics modeling is presented. Three aspects are emphasized: 1) combined quantum mechanical and molecular mechanical methods are used to represent the potential energy surface for modeling bond forming and breaking processes, 2) instantaneous normal mode analyses are used to incorporate quantum vibrational free energies to the classical potential of mean force, and 3) multidimensional tunneling methods are used to estimate quantum effects on the reaction coordinate motion. Centroid path integral simulations are described to make quantum corrections to the classical potential of mean force. In this method, the nuclear quantum vibrational and tunneling contributions are not separable. An integrated centroid path integral-free energy perturbation and umbrella sampling (PI-FEP/UM) method along with a bisection sampling procedure was summarized, which provides an accurate, easily convergent method for computing kinetic isotope effects for chemical reactions in solution and in enzymes. In the ensemble-averaged variational transition state theory with multidimensional tunneling (EA-VTST/MT), these three aspects of quantum mechanical effects can be individually treated, providing useful insights into the mechanism of enzymatic reactions. These methods are illustrated by applications to a model process in the gas phase, the decarboxylation reaction of N-methyl picolinate in water, and the proton abstraction and reprotonation process catalyzed by alanine racemase. These examples show that the incorporation of quantum mechanical effects is essential for enzyme kinetics simulations.
Collapse
|
34
|
Backstrom N, Burton NA, Turega S, Watt CIF. The primary kinetic hydrogen isotope effect in the deprotonation of a nitroalkane by an intramolecular carboxylate group. J PHYS ORG CHEM 2008. [DOI: 10.1002/poc.1330] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
35
|
Gao J, Wong KY, Major DT. Combined QM/MM and path integral simulations of kinetic isotope effects in the proton transfer reaction between nitroethane and acetate ion in water. J Comput Chem 2008; 29:514-22. [PMID: 17722009 PMCID: PMC2827405 DOI: 10.1002/jcc.20810] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
An integrated Feynman path integral-free energy perturbation and umbrella sampling (PI-FEP/UM) method has been used to investigate the kinetic isotope effects (KIEs) in the proton transfer reaction between nitroethane and acetate ion in water. In the present study, both nuclear and electronic quantum effects are explicitly treated for the reacting system. The nuclear quantum effects are represented by bisection sampling centroid path integral simulations, while the potential energy surface is described by a combined quantum mechanical and molecular mechanical (QM/MM) potential. The accuracy essential for computing KIEs is achieved by a FEP technique that transforms the mass of a light isotope into a heavy one, which is equivalent to the perturbation of the coordinates for the path integral quasiparticle in the bisection sampling scheme. The PI-FEP/UM method is applied to the proton abstraction of nitroethane by acetate ion in water through molecular dynamics simulations. The rule of the geometric mean and the Swain-Schaad exponents for various isotopic substitutions at the primary and secondary sites have been examined. The computed total deuterium KIEs are in accord with experiments. It is found that the mixed isotopic Swain-Schaad exponents are very close to the semiclassical limits, suggesting that tunneling effects do not significantly affect this property for the reaction between nitroethane and acetate ion in aqueous solution.
Collapse
Affiliation(s)
- Jiali Gao
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, Minnesota 55455-0431, USA.
| | | | | |
Collapse
|
36
|
Giese TJ, York DM. Charge-dependent model for many-body polarization, exchange, and dispersion interactions in hybrid quantum mechanical/molecular mechanical calculations. J Chem Phys 2008; 127:194101. [PMID: 18035873 DOI: 10.1063/1.2778428] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
This work explores a new charge-dependent energy model consisting of van der Waals and polarization interactions between the quantum mechanical (QM) and molecular mechanical (MM) regions in a combined QMMM calculation. van der Waals interactions are commonly treated using empirical Lennard-Jones potentials, whose parameters are often chosen based on the QM atom type (e.g., based on hybridization or specific covalent bonding environment). This strategy for determination of QMMM nonbonding interactions becomes tedious to parametrize and lacks robust transferability. Problems occur in the study of chemical reactions where the "atom type" is a complex function of the reaction coordinate. This is particularly problematic for reactions, where atoms or localized functional groups undergo changes in charge state and hybridization. In the present work we propose a new model for nonelectrostatic nonbonded interactions in QMMM calculations that overcomes many of these problems. The model is based on a scaled overlap model for repulsive exchange and attractive dispersion interactions that is a function of atomic charge. The model is chemically significant since it properly correlates atomic size, softness, polarizability, and dispersion terms with minimal one-body parameters that are functions of the atomic charge. Tests of the model are examined for rare-gas interactions with neutral and charged atoms in order to demonstrate improved transferability. The present work provides a new framework for modeling QMMM interactions with improved accuracy and transferability.
Collapse
Affiliation(s)
- Timothy J Giese
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | | |
Collapse
|
37
|
Sato M, Yamataka H, Komeiji Y, Mochizuki Y, Ishikawa T, Nakano T. How Does an SN2 Reaction Take Place in Solution? Full Ab Initio MD Simulations for the Hydrolysis of the Methyl Diazonium Ion. J Am Chem Soc 2008; 130:2396-7. [DOI: 10.1021/ja710038c] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Makoto Sato
- Department of Chemistry, Rikkyo University, Toshima-ku, Tokyo 171-8501, Japan, National Institute of Advanced Industrial Science and Technology, AIST Central 2, Tsukuba 305-8568, Japan, and Division of Medicinal Safety Science, National Institute of Health Sciences, Setagaya-ku, Tokyo 158-8501, Japan
| | - Hiroshi Yamataka
- Department of Chemistry, Rikkyo University, Toshima-ku, Tokyo 171-8501, Japan, National Institute of Advanced Industrial Science and Technology, AIST Central 2, Tsukuba 305-8568, Japan, and Division of Medicinal Safety Science, National Institute of Health Sciences, Setagaya-ku, Tokyo 158-8501, Japan
| | - Yuto Komeiji
- Department of Chemistry, Rikkyo University, Toshima-ku, Tokyo 171-8501, Japan, National Institute of Advanced Industrial Science and Technology, AIST Central 2, Tsukuba 305-8568, Japan, and Division of Medicinal Safety Science, National Institute of Health Sciences, Setagaya-ku, Tokyo 158-8501, Japan
| | - Yuji Mochizuki
- Department of Chemistry, Rikkyo University, Toshima-ku, Tokyo 171-8501, Japan, National Institute of Advanced Industrial Science and Technology, AIST Central 2, Tsukuba 305-8568, Japan, and Division of Medicinal Safety Science, National Institute of Health Sciences, Setagaya-ku, Tokyo 158-8501, Japan
| | - Takeshi Ishikawa
- Department of Chemistry, Rikkyo University, Toshima-ku, Tokyo 171-8501, Japan, National Institute of Advanced Industrial Science and Technology, AIST Central 2, Tsukuba 305-8568, Japan, and Division of Medicinal Safety Science, National Institute of Health Sciences, Setagaya-ku, Tokyo 158-8501, Japan
| | - Tatsuya Nakano
- Department of Chemistry, Rikkyo University, Toshima-ku, Tokyo 171-8501, Japan, National Institute of Advanced Industrial Science and Technology, AIST Central 2, Tsukuba 305-8568, Japan, and Division of Medicinal Safety Science, National Institute of Health Sciences, Setagaya-ku, Tokyo 158-8501, Japan
| |
Collapse
|
38
|
Sharma R, Thorley M, McNamara JP, Watt CIF, Burton NA. A computational study of the intramolecular deprotonation of a carbon acid in aqueous solution. Phys Chem Chem Phys 2008; 10:2475-87. [DOI: 10.1039/b717524h] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
39
|
Fitzpatrick PF, Bozinovski DM, Héroux A, Shaw PG, Valley MP, Orville AM. Mechanistic and structural analyses of the roles of Arg409 and Asp402 in the reaction of the flavoprotein nitroalkane oxidase. Biochemistry 2007; 46:13800-8. [PMID: 17994768 DOI: 10.1021/bi701557k] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The flavoprotein nitroalkane oxidase (NAO) catalyzes the oxidation of primary and secondary nitroalkanes to the corresponding aldehydes and ketones. The enzyme is a homologue of acyl-CoA dehydrogenase. Asp402 in NAO has been proposed to be the active site base responsible for removing the substrate proton in the first catalytic step; structurally it corresponds to the glutamate which acts as the base in medium chain acyl-CoA dehydrogenase. In the active site of NAO, the carboxylate of Asp402 forms an ionic interaction with the side chain of Arg409. The R409K enzyme has now been characterized kinetically and structurally. The mutation results in a decrease in the rate constant for proton abstraction of 100-fold. Analysis of the three-dimensional structure of the R409K enzyme, determined by X-ray crystallography to a resolution of 2.65 A, shows that the critical structural change is an increase in the distance between the carboxylate of Asp402 and the positively charged nitrogen in the side chain of the residue at position 409. The D402E mutation results in a smaller decrease in the rate constant for proton abstraction of 18-fold. The structure of the D402E enzyme, determined at 2.4 A resolution, shows that there is a smaller increase in the distance between Arg409 and the carboxylate at position 402, and the interaction of this residue with Ser276 is perturbed. These results establish the critical importance of the interaction between Asp402 and Arg409 for proton abstraction by nitroalkane oxidase.
Collapse
Affiliation(s)
- Paul F Fitzpatrick
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128, USA
| | | | | | | | | | | |
Collapse
|
40
|
Yang H, Yi T, Zhou Z, Zhou Y, Wu J, Xu M, Li F, Huang C. Switchable fluorescent organogels and mesomorphic superstructure based on naphthalene derivatives. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2007; 23:8224-30. [PMID: 17580919 DOI: 10.1021/la7005919] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Bisurea-functionalized naphthalene organogelators via cooperative hydrogen bonding and pi-pi stacking interaction were designed and synthesized. The gelators showed excellent gelling capability in various solvents and performed switchable fluorescence in the gel state. The fluorescent emission of these compounds strongly depends on the aggregation of the fluorophore and is very sensitive to the temperature and chemical stimuli. A stronger and red-shifted emission was found in the gel state compared with the original solution. The gel-sol transition of the systems, as well as the fluorescent emission, is reversibly controlled by a change of the temperature or upon alternative addition of fluoride anions and protons. The influence of fluoride anions on the fluorescence and gel-sol processes is a result of the dissociation of intermolecular hydrogen bonds by bonding of fluoride anions with urea groups of the gelator. The obtained sol is turned to the gel state again upon addition of trifluoroacetic acid. Furthermore, polarizing optical microscopy and small-angle X-ray scattering indicated that the gelator exhibited the liquid crystalline property and displayed the column phase.
Collapse
Affiliation(s)
- Hong Yang
- Department of Chemistry & Laboratory of Advanced Materials, Fudan University, Shanghai 200433, People's Republic of China
| | | | | | | | | | | | | | | |
Collapse
|
41
|
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
| |
Collapse
|
42
|
Li Y, Liu K, Liu J, Peng J, Feng X, Fang Y. Amino acid derivatives of cholesterol as "latent" organogelators with hydrogen chloride as a protonation reagent. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2006; 22:7016-20. [PMID: 16863254 DOI: 10.1021/la060394t] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
A series of low molecular weight organic gelator (LMOG) gel systems sensitive to alkaline/acidic stimuli was established by employing amino acid derivatives of cholesterol as "latent" gelators, which are cholesteryl glycinate (1), cholesteryl L-alaninate, cholesteryl D-alaninate, cholesteryl L-phenyl alaninate, and cholesteryl D-phenyl alaninate. The hydrochloric salts are denoted as 2, 3, 4, 5, and 6, respectively. For the 18 solvents tested, one proved to be a weak gelator and gels only two of the solvents. Its gelation ability, however, was greatly improved by bubbling HCl gas, which was produced by reaction of concentrated sulfuric acid with NaCl, through its solution owing to protonation of its amino group. It was demonstrated that the protonated form of it gelled 14 of the solvents tested. Further investigation revealed that the gels changed into solution with addition of any of the amines, including triethylamine (TEA), diethylamine, ethylenediamine, and NH3. The phase transition could be reversed by further introduction of the acidic gas. SEM measurements showed that 1 self-assembled into different supramolecular structures in different gels. Salt effect studies proved that electrostatic interaction is one of the driving forces for formation of the gels.
Collapse
Affiliation(s)
- Yuangang Li
- Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry and Materials Science, Shaanxi Normal University, Xi'an 710062, P. R. China
| | | | | | | | | | | |
Collapse
|