1
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Demapan D, Kussmann J, Ochsenfeld C, Cui Q. Factors That Determine the Variation of Equilibrium and Kinetic Properties of QM/MM Enzyme Simulations: QM Region, Conformation, and Boundary Condition. J Chem Theory Comput 2022; 18:2530-2542. [PMID: 35226489 PMCID: PMC9652774 DOI: 10.1021/acs.jctc.1c00714] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
To analyze the impact of various technical details on the results of quantum mechanical (QM)/molecular mechanical (MM) enzyme simulations, including the QM region size, catechol-O-methyltransferase (COMT) is studied as a model system using an approximate QM/MM method (DFTB3/CHARMM). The results show that key equilibrium and kinetic properties for methyl transfer in COMT exhibit limited variations with respect to the size of the QM region, which ranges from ∼100 to ∼500 atoms in this study. With extensive sampling, local and global structural characteristics of the enzyme are largely conserved across the studied QM regions, while the nature of the transition state (e.g., secondary kinetic isotope effect) and reaction exergonicity are largely maintained. Deviations in the free energy profile with different QM region sizes are similar in magnitude to those observed with changes in other simulation protocols, such as different initial enzyme conformations and boundary conditions. Electronic structural properties, such as the covariance matrix of residual charge fluctuations, appear to exhibit rather long-range correlations, especially when the peptide backbone is included in the QM region; this observation holds when a range-separated DFT approach is used as the QM region, suggesting that delocalization error is unlikely the origin. Overall, the analyses suggest that multiple simulation details determine the results of QM/MM enzyme simulations with comparable contributions.
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Affiliation(s)
- Darren Demapan
- Department of Chemistry, University of Munich (LMU), Butenandtstr. 7 (C), D-81377 Munich, Germany.,Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Jörg Kussmann
- Department of Chemistry, University of Munich (LMU), Butenandtstr. 7 (C), D-81377 Munich, Germany
| | - Christian Ochsenfeld
- Department of Chemistry, University of Munich (LMU), Butenandtstr. 7 (C), D-81377 Munich, Germany
| | - Qiang Cui
- Departments of Chemistry, Physics and Biomedical Engineering, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
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2
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Summers TJ, Cheng Q, Palma MA, Pham DT, Kelso DK, Webster CE, DeYonker NJ. Cheminformatic quantum mechanical enzyme model design: A catechol-O-methyltransferase case study. Biophys J 2021; 120:3577-3587. [PMID: 34358526 DOI: 10.1016/j.bpj.2021.07.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/26/2021] [Accepted: 07/29/2021] [Indexed: 10/20/2022] Open
Abstract
To accurately simulate the inner workings of an enzyme active site with quantum mechanics (QM), not only must the reactive species be included in the model but also important surrounding residues, solvent, or coenzymes involved in crafting the microenvironment. Our lab has been developing the Residue Interaction Network Residue Selector (RINRUS) toolkit to utilize interatomic contact network information for automated, rational residue selection and QM-cluster model generation. Starting from an x-ray crystal structure of catechol-O-methyltransferase, RINRUS was used to construct a series of QM-cluster models. The reactant, product, and transition state of the methyl transfer reaction were computed for a total of 550 models, and the resulting free energies of activation and reaction were used to evaluate model convergence. RINRUS-designed models with only 200-300 atoms are shown to converge. RINRUS will serve as a cornerstone for improved and automated cheminformatics-based enzyme model design.
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Affiliation(s)
- Thomas J Summers
- Department of Chemistry, The University of Memphis, Memphis, Tennessee
| | - Qianyi Cheng
- Department of Chemistry, The University of Memphis, Memphis, Tennessee
| | - Manuel A Palma
- Department of Chemistry, The University of Memphis, Memphis, Tennessee
| | - Diem-Trang Pham
- Department of Chemistry, The University of Memphis, Memphis, Tennessee; Department of Computer Science, The University of Memphis, Memphis, Tennessee
| | - Dudley K Kelso
- Department of Chemistry, The University of Memphis, Memphis, Tennessee
| | - Charles Edwin Webster
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi
| | - Nathan J DeYonker
- Department of Chemistry, The University of Memphis, Memphis, Tennessee.
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3
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Chitrala KN, Nagarkatti P, Nagarkatti M. Computational analysis of deleterious single nucleotide polymorphisms in catechol O-Methyltransferase conferring risk to post-traumatic stress disorder. J Psychiatr Res 2021; 138:207-218. [PMID: 33865170 PMCID: PMC8969201 DOI: 10.1016/j.jpsychires.2021.03.048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 03/18/2021] [Accepted: 03/24/2021] [Indexed: 10/21/2022]
Abstract
Post-traumatic stress disorder (PTSD) is one of the prevalent neurological disorder which is drawing increased attention over the past few decades. Major risk factors for PTSD can be categorized into environmental and genetic factors. Among the genetic risk factors, polymorphisms in the catechol-O-methyltransferase (COMT) gene is known to be associated with the risk for PTSD. In the present study, we analysed the impact of deleterious single nucleotide polymorphisms (SNPs) in the COMT gene conferring risk to PTSD using computational based approaches followed by molecular dynamic simulations. The data on COMT gene associated with PTSD were collected from several databases including Online Mendelian Inheritance in Man (OMIM) search. Datasets related to SNP were downloaded from the dbSNP database. To study the structural and dynamic effects of COMT wild type and mutant forms, we performed molecular dynamics simulations (MD simulations) at a time scale of 300 ns. Results from screening the SNPs using the computational tools SIFT and Polyphen-2 demonstrated that the SNP rs4680 (V158M) in COMT has a deleterious effect with phenotype in PTSD. Results from the MD simulations showed that there is some major fluctuations in the structural features including root mean square deviation (RMSD), radius of gyration (Rg), root mean square fluctuation (RMSF) and secondary structural elements including α-helices, sheets and turns between wild-type (WT) and mutant forms of COMT protein. In conclusion, our study provides novel insights into the deleterious effects and impact of V158M mutation on COMT protein structure which plays a key role in PTSD.
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Affiliation(s)
- Kumaraswamy Naidu Chitrala
- Dept. of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC, 29208, USA; Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA.
| | - Prakash Nagarkatti
- Dept. of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC, 29208, USA
| | - Mitzi Nagarkatti
- Dept. of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC, 29208, USA
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4
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Roca M, Williams IH. Transition-State Vibrational Analysis and Isotope Effects for COMT-Catalyzed Methyl Transfer. J Am Chem Soc 2020; 142:15548-15559. [PMID: 32812761 PMCID: PMC7498148 DOI: 10.1021/jacs.0c07344] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Isotopic partition-function ratios (IPFRs) computed for transition structures (TSs) of the methyl-transfer reaction catalyzed by catechol O-methyltransferase and modeled by hybrid QM/MM methods are analyzed. The ability of smaller Hessians to reproduce trends in α-3H3 and 14Cα IPFRs as obtained using the much larger subset QM/MM Hessians from which they are extracted is investigated critically. A 6-atom-extracted Hessian reproduces perfectly the α-T3 IPFR values from the full-subset Hessians of all the TSs but not the α-14CIPFRs. Average AM1/OPLS-AA harmonic frequencies and mean-square amplitudes are presented for the 12 normal modes of the α-CH3 moiety within the active site of several enzymic transition structures, together with QM/MM potential energy scans along each of these modes to assess the degree of anharmonicity. A novel investigation of ponderal effects upon IPFRs suggests that the value for α-14C tends toward a limiting minimum whereas that for α-T3 tends toward a limiting maximum as the mass of the rest of the system increases. The transition vector is dominated by motions of atoms within the donor and acceptor moieties and is very well described as a simple combination of Walden-inversion "umbrella" bending and asymmetric stretching of the SCα and CαO bonds. The contribution of atoms of the protein residues Met40, Tyr68, and Asp141 to the transition vector is extremely small. Average valence force constants for the COMT TS show significant differences from early BEBOVIB estimates which were used in support of the compression hypothesis for catalysis. There is no correlation between TS IPFRs and the nonbonded distances for close contacts between the S atom of SAM and Tyr68 or between any of the H atoms of the transferring methyl group and either Met40 or Asp141.
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Affiliation(s)
- Maite Roca
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castellón, Spain
| | - Ian H Williams
- Department of Chemistry, University of Bath, Bath BA2 7AY, United Kingdom
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5
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Czarnota S, Johannissen LO, Baxter NJ, Rummel F, Wilson AL, Cliff MJ, Levy CW, Scrutton NS, Waltho JP, Hay S. Equatorial Active Site Compaction and Electrostatic Reorganization in Catechol- O-methyltransferase. ACS Catal 2019; 9:4394-4401. [PMID: 31080692 PMCID: PMC6503465 DOI: 10.1021/acscatal.9b00174] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 03/26/2019] [Indexed: 12/18/2022]
Abstract
Catechol-O-methyltransferase (COMT) is a model S-adenosyl-l-methionine (SAM) dependent methyl transferase, which catalyzes the methylation of catecholamine neurotransmitters such as dopamine in the primary pathway of neurotransmitter deactivation in animals. Despite extensive study, there is no consensus view of the physical basis of catalysis in COMT. Further progress requires experimental data that directly probes active site geometry, protein dynamics and electrostatics, ideally in a range of positions along the reaction coordinate. Here we establish that sinefungin, a fungal-derived inhibitor of SAM-dependent enzymes that possess transition state-like charge on the transferring group, can be used as a transition state analog of COMT when combined with a catechol. X-ray crystal structures and NMR backbone assignments of the ternary complexes of the soluble form of human COMT containing dinitrocatechol, Mg2+ and SAM or sinefungin were determined. Comparison and further analysis with the aid of density functional theory calculations and molecular dynamics simulations provides evidence for active site "compaction", which is driven by electrostatic stabilization between the transferring methyl group and "equatorial" active site residues that are orthogonal to the donor-acceptor (pseudo reaction) coordinate. We propose that upon catecholamine binding and subsequent proton transfer to Lys 144, the enzyme becomes geometrically preorganized, with little further movement along the donor-acceptor coordinate required for methyl transfer. Catalysis is then largely facilitated through stabilization of the developing charge on the transferring methyl group via "equatorial" H-bonding and electrostatic interactions orthogonal to the donor-acceptor coordinate.
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Affiliation(s)
- Sylwia Czarnota
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
- School
of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - Linus O. Johannissen
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Nicola J. Baxter
- Krebs
Institute for Biomolecular Research, Department of Molecular Biology
and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, United Kingdom
| | - Felix Rummel
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
- School
of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - Alex L. Wilson
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
- School
of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - Matthew J. Cliff
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Colin W. Levy
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Nigel S. Scrutton
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
- School
of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - Jonathan P. Waltho
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
- School
of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
- Krebs
Institute for Biomolecular Research, Department of Molecular Biology
and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, United Kingdom
| | - Sam Hay
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
- School
of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
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6
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Kulik HJ. Large-scale QM/MM free energy simulations of enzyme catalysis reveal the influence of charge transfer. Phys Chem Chem Phys 2018; 20:20650-20660. [PMID: 30059109 PMCID: PMC6085747 DOI: 10.1039/c8cp03871f] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Hybrid quantum mechanical-molecular mechanical (QM/MM) simulations provide key insights into enzyme structure-function relationships. Numerous studies have demonstrated that large QM regions are needed to systematically converge ground state, zero temperature properties with electrostatic embedding QM/MM. However, it is not well known if ab initio QM/MM free energy simulations have this same dependence, in part due to the hundreds of thousands of energy evaluations required for free energy estimations that in turn limit QM region size. Here, we leverage recent advances in electronic structure efficiency and accuracy to carry out range-separated hybrid density functional theory free energy simulations in a representative methyltransferase. By studying 200 ps of ab initio QM/MM dynamics for each of five QM regions from minimal (64 atoms) to one-sixth of the protein (544 atoms), we identify critical differences between large and small QM region QM/MM in charge transfer between substrates and active site residues as well as in geometric structure and dynamics that coincide with differences in predicted free energy barriers. Distinct geometric and electronic structure features in the largest QM region indicate that important aspects of enzymatic rate enhancement in methyltransferases are identified with large-scale electronic structure.
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Affiliation(s)
- Heather J Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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7
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Świderek K, Tuñón I, Williams IH, Moliner V. Insights on the Origin of Catalysis on Glycine N-Methyltransferase from Computational Modeling. J Am Chem Soc 2018; 140:4327-4334. [PMID: 29460630 PMCID: PMC6613375 DOI: 10.1021/jacs.7b13655] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The origin of enzyme catalysis remains a question of debate despite much intense study. We report a QM/MM theoretical study of the SN2 methyl transfer reaction catalyzed by a glycine N-methyltransferase (GNMT) and three mutants to test whether recent experimental observations of rate-constant reductions and variations in inverse secondary α-3H kinetic isotope effects (KIEs) should be attributed to changes in the methyl donor-acceptor distance (DAD): Is catalysis due to a compression effect? Semiempirical (AM1) and DFT (M06-2X) methods were used to describe the QM subset of atoms, while OPLS-AA and TIP3P classical force fields were used for the protein and water molecules, respectively. The computed activation free energies and KIEs are in good agreement with experimental data, but the mutations do not meaningfully affect the DAD: Compression cannot explain the experimental variations on KIEs. On the contrary, electrostatic properties in the active site correlate with the catalytic activity of wild type and mutants. The plasticity of the enzyme moderates the effects of the mutations, explaining the rather small degree of variation in KIEs and reactivities.
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Affiliation(s)
- Katarzyna Świderek
- Departament de Química Física i Analítica; Universitat Jaume I, 12071 Castellón (Spain)
- Department of Chemistry, University of Bath, Bath BA2 7AY (United Kingdom)
| | - Iñaki Tuñón
- Departament de Química Física, Universitat de València, 46100 Burjasot (Spain)
| | - Ian H. Williams
- Department of Chemistry, University of Bath, Bath BA2 7AY (United Kingdom)
| | - Vicent Moliner
- Departament de Química Física i Analítica; Universitat Jaume I, 12071 Castellón (Spain)
- Department of Chemistry, University of Bath, Bath BA2 7AY (United Kingdom)
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8
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Wilson PB, Williams IH. Computational Modeling of a Caged Methyl Cation: Structure, Energetics, and Vibrational Analysis. J Phys Chem A 2018; 122:1432-1438. [DOI: 10.1021/acs.jpca.7b11836] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Philippe B. Wilson
- Department
of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
- Leicester
School of Pharmacy, De Montfort University, The Gateway, Leicester LE1 9BH, United Kingdom
| | - Ian H. Williams
- Department
of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
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9
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Grüber R, Aranda J, Bellili A, Tuñón I, Dumont E. Free energy profiles for two ubiquitous damaging agents: methylation and hydroxylation of guanine in B-DNA. Phys Chem Chem Phys 2017; 19:14695-14701. [PMID: 28537602 DOI: 10.1039/c6cp07966k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA methylation and hydroxylation are two ubiquitous reactions in DNA damage induction, yet insights are scarce concerning the free energy of activation within B-DNA. We resort to multiscale simulations to investigate the attack of a hydroxyl radical and of the primary diazonium onto a guanine embedded in a solvated dodecamer. Reaction free energy profiles characterize two strongly exergonic processes, yet allow unprecedented quantification of the barrier towards this damage reaction, not higher than 6 kcal mol-1 and sometimes inexistent, and of the exergonicities. In the case of the [G(C8)-OH]˙ intermediate, we challenge the functional dependence of such simulations: recently-proposed functionals, such as M06-2X and LC-BLYP, agree on a ∼4 kcal mol-1 barrier, whereas the hybrid GGA B3LYP functional predicts a barrier-less pathway. In the long term, multiscale approaches can help build up a unified panorama of DNA lesion induction. These results stress the importance of DFT/MM-MD simulations involving new functionals towards the sound modelling of biomolecule damage even in the ground state.
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Affiliation(s)
- R Grüber
- Univ. Lyon, Ens de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F-69342 Lyon, France.
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10
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Uggerud E. The Factors Determining Reactivity in Nucleophilic Substitution. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2017. [DOI: 10.1016/bs.apoc.2017.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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11
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Kulik H, Zhang J, Klinman J, Martínez TJ. How Large Should the QM Region Be in QM/MM Calculations? The Case of Catechol O-Methyltransferase. J Phys Chem B 2016; 120:11381-11394. [PMID: 27704827 PMCID: PMC5108028 DOI: 10.1021/acs.jpcb.6b07814] [Citation(s) in RCA: 139] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 09/09/2016] [Indexed: 01/29/2023]
Abstract
Hybrid quantum mechanical-molecular mechanical (QM/MM) simulations are widely used in studies of enzymatic catalysis. Until recently, it has been cost prohibitive to determine the asymptotic limit of key energetic and structural properties with respect to increasingly large QM regions. Leveraging recent advances in electronic structure efficiency and accuracy, we investigate catalytic properties in catechol O-methyltransferase, a prototypical methyltransferase critical to human health. Using QM regions ranging in size from reactants-only (64 atoms) to nearly one-third of the entire protein (940 atoms), we show that properties such as the activation energy approach within chemical accuracy of the large-QM asymptotic limits rather slowly, requiring approximately 500-600 atoms if the QM residues are chosen simply by distance from the substrate. This slow approach to asymptotic limit is due to charge transfer from protein residues to the reacting substrates. Our large QM/MM calculations enable identification of charge separation for fragments in the transition state as a key component of enzymatic methyl transfer rate enhancement. We introduce charge shift analysis that reveals the minimum number of protein residues (approximately 11-16 residues or 200-300 atoms for COMT) needed for quantitative agreement with large-QM simulations. The identified residues are not those that would be typically selected using criteria such as chemical intuition or proximity. These results provide a recipe for a more careful determination of QM region sizes in future QM/MM studies of enzymes.
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Affiliation(s)
- Heather
J. Kulik
- Department
of Chemistry and PULSE Institute, Stanford
University, Stanford, California 94305, United States
- SLAC
National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Jianyu Zhang
- Departments
of Chemistry and of Molecular and Cell Biology, and California Institute
for Quantitative Biosciences, University
of California, Berkeley, California 94720, United States
| | - Judith
P. Klinman
- Departments
of Chemistry and of Molecular and Cell Biology, and California Institute
for Quantitative Biosciences, University
of California, Berkeley, California 94720, United States
| | - Todd J. Martínez
- Department
of Chemistry and PULSE Institute, Stanford
University, Stanford, California 94305, United States
- SLAC
National Accelerator Laboratory, Menlo Park, California 94025, United States
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12
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Abstract
![]()
Although QM/MM calculations
are the primary current tool for modeling enzymatic reactions, the
reliability of such calculations can be limited by the size of the
QM region. Thus, we examine in this work the dependence of QM/MM calculations
on the size of the QM region, using the reaction of catechol-O-methyl transferase (COMT) as a test case. Our study focuses
on the effect of adding residues to the QM region on the activation
free energy, obtained with extensive QM/MM sampling. It is found that
the sensitivity of the activation barrier to the size of the QM is
rather limited, while the dependence of the reaction free energy is
somewhat larger. Of course, the results depend on the inclusion of
the first solvation shell in the QM regions. For example, the inclusion
of the Mg2+ ion can change the activation barrier due to
charge transfer effects. However, such effects can easily be included
in semiempirical approaches by proper parametrization. Overall, we
establish that QM/MM calculations of activation barriers of enzymatic
reactions are not highly sensitive to the size of the QM region, beyond
the immediate region that describes the reacting atoms.
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13
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Patra N, Ioannidis EI, Kulik HJ. Computational Investigation of the Interplay of Substrate Positioning and Reactivity in Catechol O-Methyltransferase. PLoS One 2016; 11:e0161868. [PMID: 27564542 PMCID: PMC5001633 DOI: 10.1371/journal.pone.0161868] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 08/13/2016] [Indexed: 12/27/2022] Open
Abstract
Catechol O-methyltransferase (COMT) is a SAM- and Mg2+-dependent methyltransferase that regulates neurotransmitters through methylation. Simulations and experiments have identified divergent catecholamine substrate orientations in the COMT active site: molecular dynamics simulations have favored a monodentate coordination of catecholate substrates to the active site Mg2+, and crystal structures instead preserve bidentate coordination along with short (2.65 Å) methyl donor-acceptor distances. We carry out longer dynamics (up to 350 ns) to quantify interconversion between bidentate and monodentate binding poses. We provide a systematic determination of the relative free energy of the monodentate and bidentate structures in order to identify whether structural differences alter the nature of the methyl transfer mechanism and source of enzymatic rate enhancement. We demonstrate that the bidentate and monodentate binding modes are close in energy but separated by a 7 kcal/mol free energy barrier. Analysis of interactions in the two binding modes reveals that the driving force for monodentate catecholate orientations in classical molecular dynamics simulations is derived from stronger electrostatic stabilization afforded by alternate Mg2+ coordination with strongly charged active site carboxylates. Mixed semi-empirical-classical (SQM/MM) substrate C-O distances (2.7 Å) for the bidentate case are in excellent agreement with COMT X-ray crystal structures, as long as charge transfer between the substrates, Mg2+, and surrounding ligands is permitted. SQM/MM free energy barriers for methyl transfer from bidentate and monodentate catecholate configurations are comparable at around 21-22 kcal/mol, in good agreement with experiment (18-19 kcal/mol). Overall, the work suggests that both binding poses are viable for methyl transfer, and accurate descriptions of charge transfer and electrostatics are needed to provide balanced relative barriers when multiple binding poses are accessible, for example in other transferases.
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Affiliation(s)
- Niladri Patra
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, United States of America
| | - Efthymios I. Ioannidis
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, United States of America
| | - Heather J. Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, United States of America
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14
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Wilson PB, Williams IH. Influence of Equatorial CH⋅⋅⋅O Interactions on Secondary Kinetic Isotope Effects for Methyl Transfer. Angew Chem Int Ed Engl 2016; 55:3192-5. [PMID: 26823274 PMCID: PMC4770435 DOI: 10.1002/anie.201511708] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Indexed: 11/29/2022]
Abstract
DFT calculations for methyl cation complexed within a constrained cage of water molecules permit the controlled manipulation of the "axial" donor/acceptor distance and the "equatorial" distance to hydrogen-bond acceptors. The kinetic isotope effect k(CH3)/k(CT3) for methyl transfer within a cage with a short axial distance becomes less inverse for shorter equatorial C⋅⋅⋅O distances: a decrease of 0.5 Å results in a 3 % increase at 298 K. Kinetic isotope effects in AdoMet-dependent methyltransferases may be m∧odulated by CH⋅⋅⋅O hydrogen bonding, and factors other than axial compression may contribute, at least partially, to recently reported isotope-effect variations for catechol-O-methyltransferase and its mutant structures.
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Affiliation(s)
| | - Ian H Williams
- Department of Chemistry, University of Bath, Bath, BA2 7AY, UK.
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15
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Wilson PB, Williams IH. Influence of Equatorial CH⋅⋅⋅O Interactions on Secondary Kinetic Isotope Effects for Methyl Transfer. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201511708] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
| | - Ian H. Williams
- Department of Chemistry; University of Bath; Bath BA2 7AY UK
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Zhang J, Kulik HJ, Martinez TJ, Klinman JP. Mediation of donor-acceptor distance in an enzymatic methyl transfer reaction. Proc Natl Acad Sci U S A 2015; 112:7954-9. [PMID: 26080432 PMCID: PMC4491759 DOI: 10.1073/pnas.1506792112] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Enzymatic methyl transfer, catalyzed by catechol-O-methyltransferase (COMT), is investigated using binding isotope effects (BIEs), time-resolved fluorescence lifetimes, Stokes shifts, and extended graphics processing unit (GPU)-based quantum mechanics/molecular mechanics (QM/MM) approaches. The WT enzyme is compared with mutants at Tyr68, a conserved residue that is located behind the reactive sulfur of cofactor. Small (>1) BIEs are observed for an S-adenosylmethionine (AdoMet)-binary and abortive ternary complex containing 8-hydroxyquinoline, and contrast with previously reported inverse (<1) kinetic isotope effects (KIEs). Extended GPU-based computational studies of a ternary complex containing catecholate show a clear trend in ground state structures, from noncanonical bond lengths for WT toward solution values with mutants. Structural and dynamical differences that are sensitive to Tyr68 have also been detected using time-resolved Stokes shift measurements and molecular dynamics. These experimental and computational results are discussed in the context of active site compaction that requires an ionization of substrate within the enzyme ternary complex.
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Affiliation(s)
- Jianyu Zhang
- Department of Chemistry, University of California, Berkeley, CA 94720; California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720
| | - Heather J Kulik
- Department of Chemistry, University of California, Berkeley, CA 94720; Photon Ultrafast Laser Science and Engineering Institute and Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Todd J Martinez
- Photon Ultrafast Laser Science and Engineering Institute and Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Judith P Klinman
- Department of Chemistry, University of California, Berkeley, CA 94720; California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720; Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
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17
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Lameira J, Ram Prasad B, Chu ZT, Warshel A. Methyltransferases do not work by compression, cratic, or desolvation effects, but by electrostatic preorganization. Proteins 2015; 83:318-30. [PMID: 25388538 PMCID: PMC4300294 DOI: 10.1002/prot.24717] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 10/30/2014] [Accepted: 11/03/2014] [Indexed: 11/05/2022]
Abstract
The enzyme catechol O-methyltransferase (COMT) catalyzes the transfer of a methyl group from S-adenosylmethionine to dopamine and related catechols. The search for the origin of COMT catalysis has led to different proposals and hypothesis, including the entropic, the NAC, and the compression proposals as well as the more reasonable electrostatic idea. Thus, it is important to understand the catalytic power of this enzyme and to examine the validity of different proposals and in particular the repeated recent implication of the compression idea. The corresponding analysis should be done by well-defined physically-based considerations that involve computations rather than circular interpretations of experimental results. Thus, we explore here the origin of the catalytic efficiency of COMT by using the empirical valence bond and the linear response approximation approaches. The results demonstrate that the catalytic effect of COMT is mainly due to electrostatic preorganization effects. It is also shown that the compression, NAC and entropic proposals do not account for the catalytic effect.
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Affiliation(s)
- Jeronimo Lameira
- University of Southern California, Department of Chemistry, SGM 418, 3620 McClintosk Avenue, Los Angeles, California 90089, United States
- Faculdade de Biotecnologia e Laboratório de Planejamento e Desenvolvimento de Fármacos; Universidade Federal do Pará, 66075-110, Belém, PA, Brazil
| | - B Ram Prasad
- University of Southern California, Department of Chemistry, SGM 418, 3620 McClintosk Avenue, Los Angeles, California 90089, United States
| | - Zhen T. Chu
- University of Southern California, Department of Chemistry, SGM 418, 3620 McClintosk Avenue, Los Angeles, California 90089, United States
| | - Arieh Warshel
- University of Southern California, Department of Chemistry, SGM 418, 3620 McClintosk Avenue, Los Angeles, California 90089, United States
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18
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García-Meseguer R, Zinovjev K, Roca M, Ruiz-Pernía JJ, Tuñón I. Linking Electrostatic Effects and Protein Motions in Enzymatic Catalysis. A Theoretical Analysis of Catechol O-Methyltransferase. J Phys Chem B 2014; 119:873-82. [DOI: 10.1021/jp505746x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
| | - Kirill Zinovjev
- Departament de Química Física, Universitat de València, 46100 Burjassot, Spain
| | - Maite Roca
- Departament de Química Física, Universitat de València, 46100 Burjassot, Spain
| | - Javier J. Ruiz-Pernía
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castelló, Spain
| | - Iñaki Tuñón
- Departament de Química Física, Universitat de València, 46100 Burjassot, Spain
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19
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Wilson PB, Weaver PJ, Greig IR, Williams IH. Solvent effects on isotope effects: methyl cation as a model system. J Phys Chem B 2014; 119:802-9. [PMID: 25010417 DOI: 10.1021/jp505344a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The isotopic sensitivity (CH3(+) vs CD3(+)) of the equilibrium between the methyl cation in vacuum and in solution has been investigated. Two alternative options for describing the shape of the solute cavity within the widely used polarized continuum model for implicit solvation were compared; the UFF and UA0 methods give equilibrium isotope effects (EIEs) that vary as a function of the dielectric constant in opposite directions. The same isotope effect was also obtained as the average over 40 structures from a hybrid quantum mechanical/molecular mechanical molecular dynamics simulation for the methyl cation explicitly solvated by many water molecules; the inverse value of the EIE agrees with UFF but not UA0. The opposing trends may be satisfactorily explained in terms of the different degrees of exposure of the atomic charges to the dielectric continuum in cavities of different shapes.
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Affiliation(s)
- Philippe B Wilson
- Department of Chemistry, University of Bath , Bath BA2 7AY, United Kingdom
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Ruiz Pernía JJ, Williams IH. Ensemble-Averaged QM/MM Kinetic Isotope Effects for the SN2 Reaction of Cyanide Anions with Chloroethane in DMSO Solution. Chemistry 2012; 18:9405-14. [DOI: 10.1002/chem.201200443] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Indexed: 11/11/2022]
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21
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Zhang J, Klinman JP. Enzymatic methyl transfer: role of an active site residue in generating active site compaction that correlates with catalytic efficiency. J Am Chem Soc 2011; 133:17134-7. [PMID: 21958159 DOI: 10.1021/ja207467d] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Human catechol-O-methyltransferase (COMT) catalyzes a methyl transfer from S-adenosylmethionine (AdoMet) to dopamine. Site-specific mutants at three positions (Tyr68, Trp38, and Val108) have been characterized with regard to product distribution, catalytic efficiency, and secondary kinetic isotope effects. The series of mutations at Tyr68 within wild-type protein and the common polymorphic variant (Val108Met) yields a linear correlation between the catalytic efficiency and the size of the secondary kinetic isotope effect. We conclude that active site compaction in COMT is modulated by a proximal side chain residing behind the sulfur-bearing methyl group of AdoMet. These findings are discussed in the context of the active site compression that has been postulated to accompany enzyme-supported hydrogen tunneling.
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Affiliation(s)
- Jianyu Zhang
- Department of Chemistry, University of California, Berkeley, California 94720, USA
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Williams IH. Catalysis: transition-state molecular recognition? Beilstein J Org Chem 2010; 6:1026-34. [PMID: 21085499 PMCID: PMC2981812 DOI: 10.3762/bjoc.6.117] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2010] [Accepted: 10/05/2010] [Indexed: 11/23/2022] Open
Abstract
THE KEY TO UNDERSTANDING THE FUNDAMENTAL PROCESSES OF CATALYSIS IS THE TRANSITION STATE (TS): indeed, catalysis is a transition-state molecular recognition event. Practical objectives, such as the design of TS analogues as potential drugs, or the design of synthetic catalysts (including catalytic antibodies), require prior knowledge of the TS structure to be mimicked. Examples, both old and new, of computational modelling studies are discussed, which illustrate this fundamental concept. It is shown that reactant binding is intrinsically inhibitory, and that attempts to design catalysts that focus simply upon attractive interactions in a binding site may fail. Free-energy changes along the reaction coordinate for S(N)2 methyl transfer catalysed by the enzyme catechol-O-methyl transferase are described and compared with those for a model reaction in water, as computed by hybrid quantum-mechanical/molecular-mechanical molecular dynamics simulations. The case is discussed of molecular recognition in a xylanase enzyme that stabilises its sugar substrate in a (normally unfavourable) boat conformation and in which a single-atom mutation affects the free-energy of activation dramatically.
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Affiliation(s)
- Ian H Williams
- Department of Chemistry, University of Bath, Bath BA2 7AY, United Kingdom.
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