1
|
Suh D, Arattu Thodika AR, Kim S, Nam K, Im W. CHARMM-GUI QM/MM Interfacer for a Quantum Mechanical and Molecular Mechanical (QM/MM) Simulation Setup: 1. Semiempirical Methods. J Chem Theory Comput 2024; 20:5337-5351. [PMID: 38856971 PMCID: PMC11209942 DOI: 10.1021/acs.jctc.4c00439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/17/2024] [Accepted: 05/24/2024] [Indexed: 06/11/2024]
Abstract
Quantum mechanical (QM) treatments, when combined with molecular mechanical (MM) force fields, can effectively handle enzyme-catalyzed reactions without significantly increasing the computational cost. In this context, we present CHARMM-GUI QM/MM Interfacer, a web-based cyberinfrastructure designed to streamline the preparation of various QM/MM simulation inputs with ligand modification. The development of QM/MM Interfacer has been achieved through integration with existing CHARMM-GUI modules, such as PDB Reader and Manipulator, Solution Builder, and Membrane Builder. In addition, new functionalities have been developed to facilitate the one-stop preparation of QM/MM systems and enable interactive and intuitive ligand modifications and QM atom selections. QM/MM Interfacer offers support for a range of semiempirical QM methods, including AM1(+/d), PM3(+/PDDG), MNDO(+/d, +/PDDG), PM6, RM1, and SCC-DFTB, tailored for both AMBER and CHARMM. A nontrivial setup related to ligand modification, link-atom insertion, and charge distribution is automatized through intuitive user interfaces. To illustrate the robustness of QM/MM Interfacer, we conducted QM/MM simulations of three enzyme-substrate systems: dihydrofolate reductase, insulin receptor kinase, and oligosaccharyltransferase. In addition, we have created three tutorial videos about building these systems, which can be found at https://www.charmm-gui.org/demo/qmi. QM/MM Interfacer is expected to be a valuable and accessible web-based tool that simplifies and accelerates the setup process for hybrid QM/MM simulations.
Collapse
Affiliation(s)
- Donghyuk Suh
- Department
of Biological Sciences, Chemistry, Bioengineering, and Computer Science
and Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Abdul Raafik Arattu Thodika
- Department
of Chemistry and Biochemistry, The University
of Texas at Arlington, Arlington, Texas 76019-9800, United States
| | - Seonghoon Kim
- Department
of Biological Sciences, Chemistry, Bioengineering, and Computer Science
and Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Kwangho Nam
- Department
of Chemistry and Biochemistry, The University
of Texas at Arlington, Arlington, Texas 76019-9800, United States
| | - Wonpil Im
- Department
of Biological Sciences, Chemistry, Bioengineering, and Computer Science
and Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| |
Collapse
|
2
|
Persichetti JR, Jiang Y, Hudson PS, O'Brien EP. Modeling Ensembles of Enzyme Reaction Pathways with Hi-MSM Reveals the Importance of Accounting for Pathway Diversity. J Phys Chem B 2022; 126:9748-9758. [PMID: 36383711 DOI: 10.1021/acs.jpcb.2c04496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Conventional quantum mechanical-molecular mechanics (QM/MM) simulation approaches for modeling enzyme reactions often assume that there is one dominant reaction pathway and that this pathway can be sampled starting from an X-ray structure of the enzyme. These assumptions reduce computational cost; however, their validity has not been extensively tested. This is due in part to the lack of a rigorous formalism for integrating disparate pathway information from dynamical QM/MM calculations. Here, we present a way to model ensembles of reaction pathways efficiently using a divide-and-conquer strategy through Hierarchical Markov State Modeling (Hi-MSM). This approach allows information on multiple, distinct pathways to be incorporated into a chemical kinetic model, and it allows us to test these two assumptions. Applying Hi-MSM to the reaction carried out by dihydrofolate reductase (DHFR) we find (i) there are multiple, distinct pathways significantly contributing to the overall flux of the reaction that the conventional approach does not identify and (ii) that the conventional approach does not identify the dominant reaction pathway. Thus, both assumptions underpinning the conventional approach are violated. Since DHFR is a relatively small enzyme, and configuration space scales exponentially with protein size, accounting for multiple reaction pathways is likely to be necessary for most enzymes.
Collapse
|
3
|
Nath SS. Evaluation of thermodynamic consistency of kinetic parameters in cyclic enzyme-catalyzed reaction networks. Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2022.139890] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
4
|
Zhou S, Wang Y, Gao J. Solvation Induction of Free Energy Barriers of Decarboxylation Reactions in Aqueous Solution from Dual-Level QM/MM Simulations. JACS AU 2021; 1:233-244. [PMID: 34467287 PMCID: PMC8395672 DOI: 10.1021/jacsau.0c00110] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Indexed: 06/13/2023]
Abstract
Carbon dioxide capture, corresponding to the recombination process of decarboxylation reactions of organic acids, is typically barrierless in the gas phase and has a relatively low barrier in aprotic solvents. However, these processes often encounter significant solvent-reorganization-induced barriers in aqueous solution if the decarboxylation product is not immediately protonated. Both the intrinsic stereoelectronic effects and solute-solvent interactions play critical roles in determining the overall decarboxylation equilibrium and free energy barrier. An understanding of the interplay of these factors is important for designing novel materials applied to greenhouse gas capture and storage as well as for unraveling the catalytic mechanisms of a range of carboxy lyases in biological CO2 production. A range of decarboxylation reactions of organic acids with rates spanning nearly 30 orders of magnitude have been examined through dual-level combined quantum mechanical and molecular mechanical simulations to help elucidate the origin of solvation-induced free energy barriers for decarboxylation and the reverse carboxylation reactions in water.
Collapse
Affiliation(s)
- Shaoyuan Zhou
- Institute
of Theoretical Chemistry, Jilin University, Changchun 130023, China
- Institute
of Systems and Physical Biology, Shenzhen
Bay Laboratory, Shenzhen 518055, China
| | - Yingjie Wang
- Institute
of Systems and Physical Biology, Shenzhen
Bay Laboratory, Shenzhen 518055, China
| | - Jiali Gao
- Institute
of Systems and Physical Biology, Shenzhen
Bay Laboratory, Shenzhen 518055, China
- Beijing
University Shenzhen Graduate School, Shenzhen 518055, China
- Department
of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
| |
Collapse
|
5
|
Mhashal AR, Major DT. Temperature-Dependent Kinetic Isotope Effects in R67 Dihydrofolate Reductase from Path-Integral Simulations. J Phys Chem B 2021; 125:1369-1377. [PMID: 33522797 PMCID: PMC7883348 DOI: 10.1021/acs.jpcb.0c10318] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/05/2021] [Indexed: 11/28/2022]
Abstract
Calculation of temperature-dependent kinetic isotope effects (KIE) in enzymes presents a significant theoretical challenge. Additionally, it is not trivial to identify enzymes with available experimental accurate intrinsic KIEs in a range of temperatures. In the current work, we present a theoretical study of KIEs in the primitive R67 dihydrofolate reductase (DHFR) enzyme and compare with experimental work. The advantage of R67 DHFR is its significantly lower kinetic complexity compared to more evolved DHFR isoforms. We employ mass-perturbation-based path-integral simulations in conjunction with umbrella sampling and a hybrid quantum mechanics-molecular mechanics Hamiltonian. We obtain temperature-dependent KIEs in good agreement with experiments and ascribe the temperature-dependent KIEs primarily to zero-point energy effects. The active site in the primitive enzyme is found to be poorly preorganized, which allows excessive water access to the active site and results in loosely bound reacting ligands.
Collapse
Affiliation(s)
- Anil R. Mhashal
- Department of Chemistry and Institute
for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Dan Thomas Major
- Department of Chemistry and Institute
for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
| |
Collapse
|
6
|
Perkal O, Qasem Z, Turgeman M, Schwartz R, Gevorkyan-Airapetov L, Pavlin M, Magistrato A, Major DT, Ruthstein S. Cu(I) Controls Conformational States in Human Atox1 Metallochaperone: An EPR and Multiscale Simulation Study. J Phys Chem B 2020; 124:4399-4411. [PMID: 32396355 PMCID: PMC7294806 DOI: 10.1021/acs.jpcb.0c01744] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
![]()
Atox1 is a human
copper metallochaperone that is responsible for
transferring copper ions from the main human copper transporter, hCtr1,
to ATP7A/B in the Golgi apparatus. Atox1 interacts with the Ctr1 C-terminal
domain as a dimer, although it transfers the copper ions to ATP7A/B
in a monomeric form. The copper binding site in the Atox1 dimer involves
Cys12 and Cys15, while Lys60 was also suggested to play a role in
the copper binding. We recently showed that Atox1 can adopt various
conformational states, depending on the interacting protein. In the
current study, we apply EPR experiments together with hybrid quantum
mechanics–molecular mechanics molecular dynamics simulations
using a recently developed semiempirical density functional theory
approach, to better understand the effect of Atox1’s conformational
states on copper coordination. We propose that the flexibility of
Atox1 occurs owing to protonation of one or more of the cysteine residues,
and that Cys15 is an important residue for Atox1 dimerization, while
Cys12 is a critical residue for Cu(I) binding. We also show that Lys60
electrostatically stabilizes the Cu(I)–Atox1 dimer.
Collapse
Affiliation(s)
- Ortal Perkal
- Department of Chemistry and Institute for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Zena Qasem
- Department of Chemistry, Faculty of Exact Sciences, Bar Ilan University, Ramat-Gan 5290002, Israel
| | - Meital Turgeman
- Department of Chemistry, Faculty of Exact Sciences, Bar Ilan University, Ramat-Gan 5290002, Israel
| | - Renana Schwartz
- Department of Chemistry and Institute for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Lada Gevorkyan-Airapetov
- Department of Chemistry, Faculty of Exact Sciences, Bar Ilan University, Ramat-Gan 5290002, Israel
| | - Matic Pavlin
- CNR-IOM at SISSA, via Bonomea 265, 34135, Trieste, Italy
| | | | - Dan Thomas Major
- Department of Chemistry and Institute for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Sharon Ruthstein
- Department of Chemistry, Faculty of Exact Sciences, Bar Ilan University, Ramat-Gan 5290002, Israel
| |
Collapse
|
7
|
Kannath S, Adamczyk P, Ferro-Costas D, Fernández-Ramos A, Major DT, Dybala-Defratyka A. Role of Microsolvation and Quantum Effects in the Accurate Prediction of Kinetic Isotope Effects: The Case of Hydrogen Atom Abstraction in Ethanol by Atomic Hydrogen in Aqueous Solution. J Chem Theory Comput 2020; 16:847-859. [PMID: 31904954 PMCID: PMC7588029 DOI: 10.1021/acs.jctc.9b00774] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Hydrogen abstraction from ethanol
by atomic hydrogen in aqueous
solution is studied using two theoretical approaches: the multipath
variational transition state theory (MP-VTST) and a path-integral
formalism in combination with free-energy perturbation and umbrella
sampling (PI-FEP/UM). The performance of the models is compared to
experimental values of H kinetic isotope effects (KIE). Solvation
models used in this study ranged from purely implicit, via mixed–microsolvation
treated quantum mechanically via the density functional theory (DFT)
to fully explicit representation of the solvent, which was incorporated
using a combined quantum mechanical-molecular mechanical (QM/MM) potential.
The effects of the transition state conformation and the position
of microsolvating water molecules interacting with the solute on the
KIE are discussed. The KIEs are in good agreement with experiment
when MP-VTST is used together with a model that includes microsolvation
of the polar part of ethanol by five or six water molecules, emphasizing
the importance of explicit solvation in KIE calculations. Both, MP-VTST
and PI-FEP/UM enable detailed characterization of nuclear quantum
effects accompanying the hydrogen atom transfer reaction in aqueous
solution.
Collapse
Affiliation(s)
- Suraj Kannath
- Institute of Applied Radiation Chemistry, Faculty of Chemistry , Lodz University of Technology , Zeromskiego 116 , 90-924 Lodz , Poland
| | - Paweł Adamczyk
- Institute of Applied Radiation Chemistry, Faculty of Chemistry , Lodz University of Technology , Zeromskiego 116 , 90-924 Lodz , Poland
| | - David Ferro-Costas
- LAQV@REQUIMTE, Department of Chemistry & Biochemistry, Faculty of Sciences , University of Porto , Rua do Campo Alegre , 4169-007 Porto , Portugal.,Center for Research in Biological Chemistry and Molecular Materials (CIQUS) , Universidade de Santiago de Compostela , 15782 Santiago de Compostela , Spain
| | - Antonio Fernández-Ramos
- Center for Research in Biological Chemistry and Molecular Materials (CIQUS) , Universidade de Santiago de Compostela , 15782 Santiago de Compostela , Spain
| | - Dan Thomas Major
- Department of Chemistry and Institute for Nanotechnology & Advanced Materials , Bar-Ilan University , Ramat-Gan 52900 , Israel
| | - Agnieszka Dybala-Defratyka
- Institute of Applied Radiation Chemistry, Faculty of Chemistry , Lodz University of Technology , Zeromskiego 116 , 90-924 Lodz , Poland
| |
Collapse
|
8
|
Examination of the performance of semiempirical methods in QM/MM studies of the SN2-like reaction of an adenylyl group transfer catalysed by ANT4′. Theor Chem Acc 2019. [DOI: 10.1007/s00214-019-2507-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
9
|
Ruiz-Pernía JJ, Tuñón I, Moliner V, Allemann RK. Why are some Enzymes Dimers? Flexibility and Catalysis in Thermotoga Maritima Dihydrofolate Reductase. ACS Catal 2019; 9:5902-5911. [PMID: 31289693 PMCID: PMC6614790 DOI: 10.1021/acscatal.9b01250] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Dihydrofolate
reductase from Thermotoga maritima (TmDFHFR) is a
dimeric thermophilic enzyme that catalyzes the hydride
transfer from the cofactor NADPH to dihydrofolate less efficiently
than other DHFR enzymes, such as the mesophilic analogue Escherichia
coli DHFR (EcDHFR). Using QM/MM potentials, we show that
the reduced catalytic efficiency of TmDHFR is most likely due to differences
in the amino acid sequence that stabilize the M20 loop in an open
conformation, which prevents the formation of some interactions in
the transition state and increases the number of water molecules in
the active site. However, dimerization provides two advantages to
the thermophilic enzyme: it protects its structure against denaturation
by reducing thermal fluctuations and it provides a less negative activation
entropy, toning down the increase of the activation free energy with
temperature. Our molecular picture is confirmed by the analysis of
the temperature dependence of enzyme kinetic isotope effects in different
DHFR enzymes.
Collapse
Affiliation(s)
- J. Javier Ruiz-Pernía
- Departamento de Química Física, Universitat de Valencia, 46100 Burjassot, Valencia, Spain
| | - Iñaki Tuñón
- Departamento de Química Física, Universitat de Valencia, 46100 Burjassot, Valencia, Spain
| | - Vicent Moliner
- Departamento de Química Física y Analítica, Universitat Jaume I, 12071 Castellón, Spain
| | - Rudolf K. Allemann
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
| |
Collapse
|
10
|
Delgado M, Görlich S, Longbotham JE, Scrutton NS, Hay S, Moliner V, Tuñón I. Convergence of theory and experiment on the role of preorganization, quantum tunneling and enzyme motions into flavoenzyme-catalyzed hydride transfer. ACS Catal 2019; 7:3190-3198. [PMID: 31157122 DOI: 10.1021/acscatal.7b00201] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Hydride transfer is one of the most common reactions catalyzed by enzymatic systems and it has become an object of study due to possible significant quantum tunneling effects. In the present work, we provide a combination of theoretical QM/MM simulations and experimental measurements of the rate constants and kinetic isotopic effects (KIEs) for the hydride transfer reaction catalyzed by morphinone reductase, MR. Quantum mechanical tunneling coefficients, computed in the framework of variational transition-state theory, play a significant role in this reaction, reaching values of 23.8 ± 5.5 for the lightest isotopologue; one of the largest values reported for enzymatic systems. This prediction is supported by the agreement between the theoretically predicted rate constants and the corresponding experimental values. Simulations indicate that the role of protein motions can be satisfactorily described as equilibrium fluctuations along the reaction coordinate, in line with a high degree of preorganization displayed by this enzyme.
Collapse
Affiliation(s)
- Manuel Delgado
- Department
of Physical and Analytical Chemistry, University Jaume I, 12071 Castelló de la Plana, Spain
| | - Stefan Görlich
- Manchester
Institute of Biotechnology and School of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - James E. Longbotham
- Manchester
Institute of Biotechnology and School of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Nigel S. Scrutton
- Manchester
Institute of Biotechnology and School of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Sam Hay
- Manchester
Institute of Biotechnology and School of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Vicent Moliner
- Department
of Physical and Analytical Chemistry, University Jaume I, 12071 Castelló de la Plana, Spain
- Department
of Chemistry, University of Bath, Bath BA2 7AY, United Kingdom
| | - Iñaki Tuñón
- Department
of Physical Chemistry, University of València, 46100 Burjassot, Spain
| |
Collapse
|
11
|
Mhashal AR, Pshetitsky Y, Cheatum CM, Kohen A, Major DT. Evolutionary Effects on Bound Substrate pKa in Dihydrofolate Reductase. J Am Chem Soc 2018; 140:16650-16660. [DOI: 10.1021/jacs.8b09089] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Anil R. Mhashal
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Yaron Pshetitsky
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | | | - Amnon Kohen
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - Dan Thomas Major
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 5290002, Israel
| |
Collapse
|
12
|
Li P, Jia X, Pan X, Shao Y, Mei Y. Accelerated Computation of Free Energy Profile at ab Initio Quantum Mechanical/Molecular Mechanics Accuracy via a Semi-Empirical Reference Potential. I. Weighted Thermodynamics Perturbation. J Chem Theory Comput 2018; 14:5583-5596. [DOI: 10.1021/acs.jctc.8b00571] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Pengfei Li
- State Key Laboratory of Precision Spectroscopy, School of Physics and Materials Science, East China Normal University, Shanghai 200062, China
| | - Xiangyu Jia
- State Key Laboratory of Precision Spectroscopy, School of Physics and Materials Science, East China Normal University, Shanghai 200062, China
| | - Xiaoliang Pan
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Yihan Shao
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Ye Mei
- State Key Laboratory of Precision Spectroscopy, School of Physics and Materials Science, East China Normal University, Shanghai 200062, China
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| |
Collapse
|
13
|
Husch T, Reiher M. Comprehensive Analysis of the Neglect of Diatomic Differential Overlap Approximation. J Chem Theory Comput 2018; 14:5169-5179. [DOI: 10.1021/acs.jctc.8b00601] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Tamara Husch
- Laboratorium für Physikalische Chemie, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Markus Reiher
- Laboratorium für Physikalische Chemie, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| |
Collapse
|
14
|
Mhashal AR, Pshetitsky Y, Eitan R, Cheatum CM, Kohen A, Major DT. Effect of Asp122 Mutation on the Hydride Transfer in E. coli DHFR Demonstrates the Goldilocks of Enzyme Flexibility. J Phys Chem B 2018; 122:8006-8017. [PMID: 30040418 DOI: 10.1021/acs.jpcb.8b05556] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Dihydrofolate reductase (DHFR) catalyzes the reduction of dihydrofolate (DHF) to tetrahydrofolate (THF) in the presence of NADPH. The key hydride transfer step in the reaction is facilitated by a combination of enzyme active site preorganization and correlated protein motions in the Michaelis-Menten (E:NADPH:DHF) complex. The present theoretical study employs mutagenesis to examine the relation between structural and functional properties of the enzyme. We mutate Asp122 in Escherichia coli DHFR, which is a conserved amino acid in the DHFR family. The consequent effect of the mutation on enzyme catalysis is examined from an energetic, structural and short-time dynamic perspective. Our investigations suggest that the structural and short-time dynamic perturbations caused by Asp122X mutations (X = Asn, Ser, Ala) are along the reaction coordinate and lower the rate of hydride transfer. Importantly, analysis of the correlated and principle component motions in the enzyme suggest that the mutation alters the coupled motions that are present in the wild-type enzyme. In the case of D122N and D122S, the mutations inhibit coupled motion, whereas in the case of D122A, the mutation enhances coupled motion, although all mutations result in similar rate reduction. These results emphasize a Goldilocks principle of enzyme flexibility, that is, enzymes should neither be too rigid nor too flexible.
Collapse
Affiliation(s)
- Anil R Mhashal
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry , Bar-Ilan University , Ramat-Gan 52900 , Israel
| | - 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
| | - Christopher M Cheatum
- Department of Chemistry , University of Iowa , Iowa City , Iowa 52242 , United States
| | - 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
|
15
|
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
|
16
|
Zinovjev K, Tuñón I. Quantifying the limits of transition state theory in enzymatic catalysis. Proc Natl Acad Sci U S A 2017; 114:12390-12395. [PMID: 29101125 PMCID: PMC5703300 DOI: 10.1073/pnas.1710820114] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
While being one of the most popular reaction rate theories, the applicability of transition state theory to the study of enzymatic reactions has been often challenged. The complex dynamic nature of the protein environment raised the question about the validity of the nonrecrossing hypothesis, a cornerstone in this theory. We present a computational strategy to quantify the error associated to transition state theory from the number of recrossings observed at the equicommittor, which is the best possible dividing surface. Application of a direct multidimensional transition state optimization to the hydride transfer step in human dihydrofolate reductase shows that both the participation of the protein degrees of freedom in the reaction coordinate and the error associated to the nonrecrossing hypothesis are small. Thus, the use of transition state theory, even with simplified reaction coordinates, provides a good theoretical framework for the study of enzymatic catalysis.
Collapse
Affiliation(s)
- Kirill Zinovjev
- Departament de Química Física, Universitat de València, 46100 Burjassot, Spain
| | - Iñaki Tuñón
- Departament de Química Física, Universitat de València, 46100 Burjassot, Spain
| |
Collapse
|
17
|
Okumura H, Higashi M, Yoshida Y, Sato H, Akiyama R. Theoretical approaches for dynamical ordering of biomolecular systems. Biochim Biophys Acta Gen Subj 2017; 1862:212-228. [PMID: 28988931 DOI: 10.1016/j.bbagen.2017.10.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 09/30/2017] [Accepted: 10/04/2017] [Indexed: 01/21/2023]
Abstract
BACKGROUND Living systems are characterized by the dynamic assembly and disassembly of biomolecules. The dynamical ordering mechanism of these biomolecules has been investigated both experimentally and theoretically. The main theoretical approaches include quantum mechanical (QM) calculation, all-atom (AA) modeling, and coarse-grained (CG) modeling. The selected approach depends on the size of the target system (which differs among electrons, atoms, molecules, and molecular assemblies). These hierarchal approaches can be combined with molecular dynamics (MD) simulation and/or integral equation theories for liquids, which cover all size hierarchies. SCOPE OF REVIEW We review the framework of quantum mechanical/molecular mechanical (QM/MM) calculations, AA MD simulations, CG modeling, and integral equation theories. Applications of these methods to the dynamical ordering of biomolecular systems are also exemplified. MAJOR CONCLUSIONS The QM/MM calculation enables the study of chemical reactions. The AA MD simulation, which omits the QM calculation, can follow longer time-scale phenomena. By reducing the number of degrees of freedom and the computational cost, CG modeling can follow much longer time-scale phenomena than AA modeling. Integral equation theories for liquids elucidate the liquid structure, for example, whether the liquid follows a radial distribution function. GENERAL SIGNIFICANCE These theoretical approaches can analyze the dynamic behaviors of biomolecular systems. They also provide useful tools for exploring the dynamic ordering systems of biomolecules, such as self-assembly. This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato.
Collapse
Affiliation(s)
- Hisashi Okumura
- Research Center for Computational Science, Institute for Molecular Science, Okazaki, Aichi 444-8585, Japan; Department of Structural Molecular Science, The Graduate University for Advanced Studies, Okazaki, Aichi 444-8585, Japan.
| | - Masahiro Higashi
- Department of Chemistry, Biology and Marine Science, University of the Ryukyus, Nishihara, Okinawa 903-0213, Japan
| | - Yuichiro Yoshida
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Hirofumi Sato
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan; Elements Strategy Initiative for Catalysts and Batteries, Kyoto University, Japan
| | - Ryo Akiyama
- Department of Chemistry, Kyushu University, Fukuoka 819-0395, Japan
| |
Collapse
|
18
|
Mhashal AR, Vardi-Kilshtain A, Kohen A, Major DT. The role of the Met 20 loop in the hydride transfer in Escherichia coli dihydrofolate reductase. J Biol Chem 2017; 292:14229-14239. [PMID: 28620051 DOI: 10.1074/jbc.m117.777136] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 05/24/2017] [Indexed: 11/06/2022] Open
Abstract
A key question concerning the catalytic cycle of Escherichia coli dihydrofolate reductase (ecDHFR) is whether the Met20 loop is dynamically coupled to the chemical step during catalysis. A more basic, yet unanswered question is whether the Met20 loop adopts a closed conformation during the chemical hydride transfer step. To examine the most likely conformation of the Met20 loop during the chemical step, we studied the hydride transfer in wild type (WT) ecDHFR using hybrid quantum mechanics-molecular mechanics free energy simulations with the Met20 loop in a closed and disordered conformation. Additionally, we investigated three mutant forms (I14X; X = Val, Ala, Gly) of the enzyme that have increased active site flexibility and donor-acceptor distance dynamics in closed and disordered Met20 loop states. We found that the conformation of the Met20 loop has a dramatic effect on the ordering of active site hydration, although the Met20 loop conformation only has a moderate effect on the hydride transfer rate and donor-acceptor distance dynamics. Finally, we evaluated the pKa of the substrate N5 position in closed and disordered Met20 loop states and found a strong correlation between N5 basicity and the conformation of the Met20 loop.
Collapse
Affiliation(s)
- Anil R Mhashal
- From the Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Alexandra Vardi-Kilshtain
- From the Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Amnon Kohen
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242
| | - Dan Thomas Major
- From the Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry, Bar-Ilan University, Ramat-Gan 5290002, Israel.
| |
Collapse
|
19
|
Świderek K, Arafet K, Kohen A, Moliner V. Benchmarking Quantum Mechanics/Molecular Mechanics (QM/MM) Methods on the Thymidylate Synthase-Catalyzed Hydride Transfer. J Chem Theory Comput 2017; 13:1375-1388. [PMID: 28192669 PMCID: PMC5371049 DOI: 10.1021/acs.jctc.6b01032] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Given the ubiquity of hydride-transfer reactions in enzyme-catalyzed processes, identifying the appropriate computational method for evaluating such biological reactions is crucial to perform theoretical studies of these processes. In this paper, the hydride-transfer step catalyzed by thymidylate synthase (TSase) is studied by examining hybrid quantum mechanics/molecular mechanics (QM/MM) potentials via multiple semiempirical methods and the M06-2X hybrid density functional. Calculations of protium and tritium transfer in these reactions across a range of temperatures allowed calculation of the temperature dependence of kinetic isotope effects (KIE). Dynamics and quantum-tunneling effects are revealed to have little effect on the reaction rate, but are significant in determining the KIEs and their temperature dependence. A good agreement with experiments is found, especially when computed for RM1/MM simulations. The small temperature dependence of quantum tunneling corrections and the quasiclassical contribution term cancel each other, while the recrossing transmission coefficient seems to be temperature-independent over the interval of 5-40 °C.
Collapse
Affiliation(s)
- Katarzyna Świderek
- Departament de Química Física i Analítica, Universitat Jaume I , 12071 Castelló, Spain
- Institute of Applied Radiation Chemistry, Lodz University of Technology , 90-924 Lodz, Poland
| | - Kemel Arafet
- Departament de Química Física i Analítica, Universitat Jaume I , 12071 Castelló, Spain
| | - Amnon Kohen
- Department of Chemistry, University of Iowa , Iowa City, Iowa 52242, United States
| | - Vicent Moliner
- Departament de Química Física i Analítica, Universitat Jaume I , 12071 Castelló, Spain
| |
Collapse
|
20
|
Roston D, Cui Q. Substrate and Transition State Binding in Alkaline Phosphatase Analyzed by Computation of Oxygen Isotope Effects. J Am Chem Soc 2016; 138:11946-57. [PMID: 27541005 PMCID: PMC5705178 DOI: 10.1021/jacs.6b07347] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Enzymes are powerful catalysts, and a thorough understanding of the sources of their catalytic power will facilitate many medical and industrial applications. Here we have studied the catalytic mechanism of alkaline phosphatase (AP), which is one of the most catalytically proficient enzymes known. We have used quantum mechanics calculations and hybrid quantum mechanics/molecular mechanics (QM/MM) simulations to model a variety of isotope effects relevant to the reaction of AP. We have calculated equilibrium isotope effects (EIEs), binding isotope effects (BIEs), and kinetic isotope effects (KIEs) for a range of phosphate mono- and diester substrates. The results agree well with experimental values, but the model for the reaction's transition state (TS) differs from the original interpretation of those experiments. Our model indicates that isotope effects on binding make important contributions to measured KIEs on V/K, which complicated interpretation of the measured values. Our results provide a detailed interpretation of the measured isotope effects and make predictions that can test the proposed model. The model indicates that the substrate is deformed in the ground state (GS) of the reaction and partially resembles the TS. The highly preorganized active site preferentially binds conformations that resemble the TS and not the GS, which induces the substrate to adapt to the enzyme, rather than the other way around-as with classic "induced fit" models. The preferential stabilization of the TS over the GS is what lowers the barrier to the chemical step.
Collapse
Affiliation(s)
- Daniel Roston
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin , Madison, Wisconsin 53706, United States
| | - Qiang Cui
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin , Madison, Wisconsin 53706, United States
| |
Collapse
|
21
|
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
|
22
|
Roston D, Cui Q. QM/MM Analysis of Transition States and Transition State Analogues in Metalloenzymes. Methods Enzymol 2016; 577:213-50. [PMID: 27498640 DOI: 10.1016/bs.mie.2016.05.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Enzymology is approaching an era where many problems can benefit from computational studies. While ample challenges remain in quantitatively predicting behavior for many enzyme systems, the insights that often come from computations are an important asset for the enzymology community. Here we provide a primer for enzymologists on the types of calculations that are most useful for mechanistic problems in enzymology. In particular, we emphasize the integration of models that range from small active-site motifs to fully solvated enzyme systems for cross-validation and dissection of specific contributions from the enzyme environment. We then use a case study of the enzyme alkaline phosphatase to illustrate specific application of the methods. The case study involves examination of the binding modes of putative transition state analogues (tungstate and vanadate) to the enzyme. The computations predict covalent binding of these ions to the enzymatic nucleophile and that they adopt the trigonal bipyramidal geometry of the expected transition state. By comparing these structures with transition states found through free energy simulations, we assess the degree to which the transition state analogues mimic the true transition states. Technical issues worth treating with care as well as several remaining challenges to quantitative analysis of metalloenzymes are also highlighted during the discussion.
Collapse
Affiliation(s)
- D Roston
- Theoretical Chemistry Institute, University of Wisconsin-Madison, Madison, WI, United States.
| | - Q Cui
- Theoretical Chemistry Institute, University of Wisconsin-Madison, Madison, WI, United States.
| |
Collapse
|
23
|
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]
|
24
|
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]
|
25
|
Chung LW, Sameera WMC, Ramozzi R, Page AJ, Hatanaka M, Petrova GP, Harris TV, Li X, Ke Z, Liu F, Li HB, Ding L, Morokuma K. The ONIOM Method and Its Applications. Chem Rev 2015; 115:5678-796. [PMID: 25853797 DOI: 10.1021/cr5004419] [Citation(s) in RCA: 738] [Impact Index Per Article: 82.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Lung Wa Chung
- †Department of Chemistry, South University of Science and Technology of China, Shenzhen 518055, China
| | - W M C Sameera
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Romain Ramozzi
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Alister J Page
- §Newcastle Institute for Energy and Resources, The University of Newcastle, Callaghan 2308, Australia
| | - Miho Hatanaka
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Galina P Petrova
- ∥Faculty of Chemistry and Pharmacy, University of Sofia, Bulgaria Boulevard James Bourchier 1, 1164 Sofia, Bulgaria
| | - Travis V Harris
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan.,⊥Department of Chemistry, State University of New York at Oswego, Oswego, New York 13126, United States
| | - Xin Li
- #State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Zhuofeng Ke
- ∇School of Chemistry and Chemical Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Fengyi Liu
- ○Key Laboratory of Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, Shaanxi 710119, China
| | - Hai-Bei Li
- ■School of Ocean, Shandong University, Weihai 264209, China
| | - Lina Ding
- ▲School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Keiji Morokuma
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| |
Collapse
|
26
|
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]
|
27
|
Doron D, Stojković V, Gakhar L, Vardi-Kilshtain A, Kohen A, Major DT. Free energy simulations of active-site mutants of dihydrofolate reductase. J Phys Chem B 2014; 119:906-16. [PMID: 25382260 DOI: 10.1021/jp5059963] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
This study employs hybrid quantum mechanics-molecular mechanics (QM/MM) simulations to investigate the effect of mutations of the active-site residue I14 of E. coli dihydrofolate reductase (DHFR) on the hydride transfer. Recent kinetic measurements of the I14X mutants (X = V, A, and G) indicated slower hydride transfer rates and increasingly temperature-dependent kinetic isotope effects (KIEs) with systematic reduction of the I14 side chain. The QM/MM simulations show that when the original isoleucine residue is substituted in silico by valine, alanine, or glycine (I14V, I14A, and I14G DHFR, respectively), the free energy barrier height of the hydride transfer reaction increases relative to the wild-type enzyme. These trends are in line with the single-turnover rate measurements reported for these systems. In addition, extended dynamics simulations of the reactive Michaelis complex reveal enhanced flexibility in the mutants, and in particular for the I14G mutant, including considerable fluctuations of the donor-acceptor distance (DAD) and the active-site hydrogen bonding network compared with those detected in the native enzyme. These observations suggest that the perturbations induced by the mutations partly impair the active-site environment in the reactant state. On the other hand, the average DADs at the transition state of all DHFR variants are similar. Crystal structures of I14 mutants (V, A, and G) confirmed the trend of increased flexibility of the M20 and other loops.
Collapse
Affiliation(s)
- Dvir Doron
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry, Bar-Ilan University , Ramat-Gan 5290002, Israel
| | | | | | | | | | | |
Collapse
|
28
|
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: 43] [Impact Index Per Article: 4.3] [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
|
29
|
Zhou Y, Pu J. Reaction Path Force Matching: A New Strategy of Fitting Specific Reaction Parameters for Semiempirical Methods in Combined QM/MM Simulations. J Chem Theory Comput 2014; 10:3038-54. [PMID: 26588275 DOI: 10.1021/ct4009624] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present a general strategy of reparametrizing semiempirical (SE) methods against ab initio (AI) methods for combined quantum mechanical and molecular mechanical (QM/MM) simulations of specific chemical reactions in condensed phases. The resulting approach, designated Reaction Path Force Matching (RP-FM), features cycles of sampling configurations along a reaction path on an efficient SE/MM potential energy surface (PES) and adjusting specific reaction parameters (SRPs) in the SE method such that the atomic forces computed at the target AI/MM level are reproduced. Iterative applications of the RP-FM cycle make possible achieving the accuracy of AI/MM simulations without explicitly sampling the computationally expensive AI/MM PES. The bypassed sampling, nevertheless, is implicitly accomplished through the aid of the efficient SE-SRP/MM PES, on which the target-level reaction path is expected to be obtained upon convergence. We demonstrate the effectiveness of the RP-FM procedure for a symmetric proton transfer reaction in the gas phase and in solution. The remarkable agreements between the RP-FM optimized SE-SRP methods and the target AI method on various properties, including energy profiles, potential of mean force free energy profiles, atomic forces, charge populations, and solvation effects, suggest that RP-FM can be used as an efficient and reliable strategy for simulating condensed-phase chemical reactions.
Collapse
Affiliation(s)
- Yan Zhou
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis , 402 N. Blackford St., LD326, Indianapolis, Indiana 46202, United States
| | - Jingzhi Pu
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis , 402 N. Blackford St., LD326, Indianapolis, Indiana 46202, United States
| |
Collapse
|
30
|
Doron D, Kohen A, Nam K, Major DT. How Accurate Are Transition States from Simulations of Enzymatic Reactions? J Chem Theory Comput 2014; 10:1863-1871. [PMID: 24860275 PMCID: PMC4025581 DOI: 10.1021/ct5000742] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Indexed: 11/30/2022]
Abstract
The rate expression of traditional transition state theory (TST) assumes no recrossing of the transition state (TS) and thermal quasi-equilibrium between the ground state and the TS. Currently, it is not well understood to what extent these assumptions influence the nature of the activated complex obtained in traditional TST-based simulations of processes in the condensed phase in general and in enzymes in particular. Here we scrutinize these assumptions by characterizing the TSs for hydride transfer catalyzed by the enzyme Escherichia coli dihydrofolate reductase obtained using various simulation approaches. Specifically, we compare the TSs obtained with common TST-based methods and a dynamics-based method. Using a recently developed accurate hybrid quantum mechanics/molecular mechanics potential, we find that the TST-based and dynamics-based methods give considerably different TS ensembles. This discrepancy, which could be due equilibrium solvation effects and the nature of the reaction coordinate employed and its motion, raises major questions about how to interpret the TSs determined by common simulation methods. We conclude that further investigation is needed to characterize the impact of various TST assumptions on the TS phase-space ensemble and on the reaction kinetics.
Collapse
Affiliation(s)
- Dvir Doron
- Department
of Chemistry and the Lise Meitner-Minerva Center of Computational
Quantum Chemistry, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Amnon Kohen
- Department
of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - Kwangho Nam
- Department
of Chemistry and Computational Life Science Cluster (CLiC), Umeå University, 901 87 Umeå, Sweden
| | - Dan Thomas Major
- Department
of Chemistry and the Lise Meitner-Minerva Center of Computational
Quantum Chemistry, Bar-Ilan University, Ramat-Gan 5290002, Israel
| |
Collapse
|
31
|
Roston D, Kohen A, Doron D, Major DT. Simulations of remote mutants of dihydrofolate reductase reveal the nature of a network of residues coupled to hydride transfer. J Comput Chem 2014; 35:1411-7. [PMID: 24798860 DOI: 10.1002/jcc.23629] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 03/11/2014] [Accepted: 04/06/2014] [Indexed: 11/07/2022]
Abstract
Recent experimental and theoretical studies have proposed that enzymes involve networks of coupled residues throughout the protein that participate in motions accompanying chemical barrier crossing. Here, we have examined portions of a proposed network in dihydrofolate reductase (DHFR) using quantum mechanics/molecular mechanics simulations. The simulations use a hybrid quantum mechanics-molecular mechanics approach with a recently developed semiempirical AM1-SRP Hamiltonian that provides accurate results for this reaction. The simulations reproduce experimentally determined catalytic rates for the wild type and distant mutants of E. coli DHFR, underscoring the accuracy of the simulation protocol. Additionally, the simulations provide detailed insight into how residues remote from the active site affect the catalyzed chemistry, through changes in the thermally averaged properties along the reaction coordinate. The mutations do not greatly affect the structure of the transition state near the bond activation, but we observe differences somewhat removed from the point of C-H cleavage that affect the rate. The mutations have global effects on the thermally averaged structure that propagate throughout the enzyme and the current simulations highlight several interactions that appear to be particularly important.
Collapse
Affiliation(s)
- Daniel Roston
- Department of Chemistry, University of Iowa, Iowa City, Iowa, 52242
| | | | | | | |
Collapse
|
32
|
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]
|
33
|
Gerber RB, Shemesh D, Varner ME, Kalinowski J, Hirshberg B. Ab initio and semi-empirical Molecular Dynamics simulations of chemical reactions in isolated molecules and in clusters. Phys Chem Chem Phys 2014; 16:9760-75. [DOI: 10.1039/c3cp55239j] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Recent progress in “on-the-fly” trajectory simulations of molecular reactions, using different electronic structure methods is discussed, with analysis of the insights that such calculations can provide and of the strengths and limitations of the algorithms available.
Collapse
Affiliation(s)
- R. B. Gerber
- Institute of Chemistry and The Fritz Haber Research Center
- The Hebrew University of Jerusalem
- Jerusalem 91904, Israel
- Department of Chemistry
- University of California
| | - D. Shemesh
- Institute of Chemistry and The Fritz Haber Research Center
- The Hebrew University of Jerusalem
- Jerusalem 91904, Israel
| | - M. E. Varner
- Department of Chemistry
- University of California
- Irvine 92697, USA
| | - J. Kalinowski
- Department of Chemistry
- University of Helsinki
- , Finland
| | - B. Hirshberg
- Institute of Chemistry and The Fritz Haber Research Center
- The Hebrew University of Jerusalem
- Jerusalem 91904, Israel
| |
Collapse
|
34
|
Liang S, Roitberg AE. AM1 Specific Reaction Parameters for Reactions of Hydroxide Ion with Halomethanes in Complex Environments: Development and Testing. J Chem Theory Comput 2013; 9:4470-80. [DOI: 10.1021/ct400471m] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Shuai Liang
- Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, Florida 32611, United States
| | - Adrian E. Roitberg
- Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, Florida 32611, United States
| |
Collapse
|
35
|
Thiel W. Semiempirical quantum–chemical methods. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2013. [DOI: 10.1002/wcms.1161] [Citation(s) in RCA: 171] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Walter Thiel
- Max‐Planck‐Institut für KohlenforschungMülheimGermany
| |
Collapse
|
36
|
Wu X, Thiel W, Pezeshki S, Lin H. Specific Reaction Path Hamiltonian for Proton Transfer in Water: Reparameterized Semiempirical Models. J Chem Theory Comput 2013; 9:2672-86. [PMID: 26583861 DOI: 10.1021/ct400224n] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The semiempirical MNDO-based AM1 and PM3 methods and the orthogonalization-corrected OM1, OM2, and OM3 models were reparameterized to improve their description of bulk water and of proton transfer in water. Reference data included the gas-phase geometries and energies of the water molecule, small water clusters, the hydronium ion, and small hydronium ion-water clusters, as well as the gas-phase potential energy surface for proton transfer between the two water molecules in a Zundel ion, all calculated at the MP2/aug-cc-pVTZ level of theory. Combined QM/MM molecular dynamics simulations were carried out for bulk water and for a proton solvated in water using large cluster models. Both the authentic and reparameterized semiempirical models were employed in the simulations. The reparameterization led to significantly better results in all cases. The new set of OM3 parameters gave the best overall results for the structural and dynamic properties of water and the hydrated proton, with a small but finite barrier of 0.1-0.2 kcal/mol in the potential of mean force for proton transfer, in agreement with ab initio path-integral molecular dynamics simulations. The reparameterized OM3 model is expected to be useful for efficient modeling of proton transfer in aqueous solution.
Collapse
Affiliation(s)
- Xin Wu
- Max-Planck-Institut für Kohlenforschung , 45470 Mülheim an der Ruhr, Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung , 45470 Mülheim an der Ruhr, Germany
| | - Soroosh Pezeshki
- Chemistry Department, University of Colorado, Denver , Denver, Colorado 80217, United States
| | - Hai Lin
- Chemistry Department, University of Colorado, Denver , Denver, Colorado 80217, United States
| |
Collapse
|
37
|
Fan Y, Cembran A, Ma S, Gao J. Connecting protein conformational dynamics with catalytic function as illustrated in dihydrofolate reductase. Biochemistry 2013; 52:2036-49. [PMID: 23297871 DOI: 10.1021/bi301559q] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Combined quantum mechanics/molecular mechanics molecular dynamics simulations reveal that the M20 loop conformational dynamics of dihydrofolate reductase (DHFR) is severely restricted at the transition state of the hydride transfer as a result of the M42W/G121V double mutation. Consequently, the double-mutant enzyme has a reduced entropy of activation, i.e., increased entropic barrier, and altered temperature dependence of kinetic isotope effects in comparison with those of wild-type DHFR. Interestingly, in both wild-type DHFR and the double mutant, the average donor-acceptor distances are essentially the same in the Michaelis complex state (~3.5 Å) and the transition state (2.7 Å). It was found that an additional hydrogen bond is formed to stabilize the M20 loop in the closed conformation in the M42W/G121V double mutant. The computational results reflect a similar aim designed to knock out precisely the dynamic flexibility of the M20 loop in a different double mutant, N23PP/S148A.
Collapse
Affiliation(s)
- Yao Fan
- Department of Chemistry, Digital Technology Center, and Supercomputing Institute, University of Minnesota , 207 Pleasant Street Southeast, Minneapolis, Minnesota 55455, United States
| | | | | | | |
Collapse
|
38
|
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
|
39
|
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
|
40
|
Engel H, Doron D, Kohen A, Major DT. Momentum Distribution as a Fingerprint of Quantum Delocalization in Enzymatic Reactions: Open-Chain Path-Integral Simulations of Model Systems and the Hydride Transfer in Dihydrofolate Reductase. J Chem Theory Comput 2012; 8:1223-34. [DOI: 10.1021/ct200874q] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- 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
| | - 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
|
41
|
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]
|