1
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Hudspeth J, Rogge K, Dörner S, Müll M, Hoffmeister D, Rupp B, Werten S. Methyl transfer in psilocybin biosynthesis. Nat Commun 2024; 15:2709. [PMID: 38548735 PMCID: PMC10978996 DOI: 10.1038/s41467-024-46997-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 03/17/2024] [Indexed: 04/01/2024] Open
Abstract
Psilocybin, the natural hallucinogen produced by Psilocybe ("magic") mushrooms, holds great promise for the treatment of depression and several other mental health conditions. The final step in the psilocybin biosynthetic pathway, dimethylation of the tryptophan-derived intermediate norbaeocystin, is catalysed by PsiM. Here we present atomic resolution (0.9 Å) crystal structures of PsiM trapped at various stages of its reaction cycle, providing detailed insight into the SAM-dependent methylation mechanism. Structural and phylogenetic analyses suggest that PsiM derives from epitranscriptomic N6-methyladenosine writers of the METTL16 family, which is further supported by the observation that bound substrates physicochemically mimic RNA. Inherent limitations of the ancestral monomethyltransferase scaffold hamper the efficiency of psilocybin assembly and leave PsiM incapable of catalysing trimethylation to aeruginascin. The results of our study will support bioengineering efforts aiming to create novel variants of psilocybin with improved therapeutic properties.
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Affiliation(s)
- Jesse Hudspeth
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
- Department of Chemistry, Colorado School of Mines, Golden, CO, USA
| | - Kai Rogge
- Institute of Pharmacy, Friedrich Schiller University, Jena, Germany
- Research Group Pharmaceutical Microbiology, Leibniz Institute of Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
| | - Sebastian Dörner
- Institute of Pharmacy, Friedrich Schiller University, Jena, Germany
- Research Group Pharmaceutical Microbiology, Leibniz Institute of Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
| | - Maximilian Müll
- Research Group Biosynthetic Design of Natural Products, Leibniz Institute of Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
| | - Dirk Hoffmeister
- Institute of Pharmacy, Friedrich Schiller University, Jena, Germany
- Research Group Pharmaceutical Microbiology, Leibniz Institute of Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
| | - Bernhard Rupp
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
- k.-k. Hofkristallamt, San Diego, California, USA
| | - Sebastiaan Werten
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria.
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2
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Zhao F, Moriwaki Y, Noguchi T, Shimizu K, Kuzuyama T, Terada T. QM/MM Study of the Catalytic Mechanism and Substrate Specificity of the Aromatic Substrate C-Methyltransferase Fur6. Biochemistry 2024; 63:806-814. [PMID: 38422553 DOI: 10.1021/acs.biochem.3c00556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
In the field of medical chemistry and other organic chemistry, introducing a methyl group into a designed position has been difficult to achieve. However, owing to the vigorous developments in the field of enzymology, methyltransferases are considered potential tools for addressing this problem. Within the methyltransferase family, Fur6 catalyzes the methylation of C3 of 1,2,4,5,7-pentahydroxynaphthalene (PHN) using S-adenosyl-l-methionine (SAM) as the methyl donor. Here, we report the catalytic mechanism and substrate specificity of Fur6 based on computational studies. Our molecular dynamics (MD) simulation studies reveal the reactive form of PHN and its interactions with the enzyme. Our hybrid quantum mechanics/molecular mechanics (QM/MM) calculations suggest the reaction pathway of the methyl transfer step in which the energy barrier is 8.6 kcal mol-1. Our free-energy calculations with a polarizable continuum model (PCM) indicate that the final deprotonation step of the methylated intermediate occurs after it is ejected into the water solvent from the active center pocket of Fur6. Additionally, our studies on the protonation states, the highest occupied molecular orbital (HOMOs), and the energy barriers of the methylation reaction for the analogs of PHN demonstrate the mechanism of the specificity to PHN. Our study provides valuable insights into Fur6 chemistry, contributing to a deeper understanding of molecular mechanisms and offering an opportunity to engineer the enzyme to achieve high yields of the desired product(s).
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Affiliation(s)
- Fan Zhao
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yoshitaka Moriwaki
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
- Graduate School of Agricultural and Life Sciences and Collaborative Research Institute for Innovative Microbiology (CRIIM), The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Tomohiro Noguchi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Kentaro Shimizu
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Tomohisa Kuzuyama
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
- Graduate School of Agricultural and Life Sciences and Collaborative Research Institute for Innovative Microbiology (CRIIM), The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Tohru Terada
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
- Graduate School of Agricultural and Life Sciences and Collaborative Research Institute for Innovative Microbiology (CRIIM), The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
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3
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Jiang Y, Ding N, Shao Q, Stull SL, Cheng Z, Yang ZJ. Substrate Positioning Dynamics Involves a Non-Electrostatic Component to Mediate Catalysis. J Phys Chem Lett 2023; 14:11480-11489. [PMID: 38085952 PMCID: PMC11211065 DOI: 10.1021/acs.jpclett.3c02444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
Substrate positioning dynamics (SPD) orients the substrate in the active site, thereby influencing catalytic efficiency. However, it remains unknown whether SPD effects originate primarily from electrostatic perturbation inside the enzyme or can independently mediate catalysis with a significant non-electrostatic component. In this work, we investigated how the non-electrostatic component of SPD affects transition state (TS) stabilization. Using high-throughput enzyme modeling, we selected Kemp eliminase variants with similar electrostatics inside the enzyme but significantly different SPD. The kinetic parameters of these mutants were experimentally characterized. We observed a valley-shaped, two-segment linear correlation between the TS stabilization free energy (converted from kinetic parameters) and substrate positioning index (a metric to quantify SPD). The energy varies by approximately 2 kcal/mol. Favorable SPD was observed for the distal mutant R154W, increasing the proportion of reactive conformations and leading to the lowest activation free energy. These results indicate the substantial contribution of the non-electrostatic component of SPD to enzyme catalytic efficiency.
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Affiliation(s)
- Yaoyukun Jiang
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Ning Ding
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Qianzhen Shao
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Sebastian L. Stull
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Zihao Cheng
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Zhongyue J. Yang
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
- Data Science Institute, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
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4
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Cheng Q, DeYonker NJ. The Glycine N-Methyltransferase Case Study: Another Challenge for QM-Cluster Models? J Phys Chem B 2023; 127:9282-9294. [PMID: 37870315 PMCID: PMC11018112 DOI: 10.1021/acs.jpcb.3c04138] [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] [Indexed: 10/24/2023]
Abstract
The methyl transfer reaction between SAM and glycine catalyzed by glycine N-methyltransferase (GNMT) was examined using QM-cluster models generated by Residue Interaction Network ResidUe Selector (RINRUS). RINRUS is a Python-based tool that can build QM-cluster models with rules-based processing of the active site residue interaction network. This way of enzyme model-building allows quantitative analysis of residue and fragment contributions to kinetic and thermodynamic properties of the enzyme. Many residue fragments are important for the GNMT catalytic reaction, such as Gly137, Asn138, and Arg175, which interact with the glycine substrate, and Trp30, Asp85, and Tyr242, which interact with the SAM cofactor. Our study shows that active site fragments that interact with the glycine substrate and the SAM cofactor must both be included in the QM-cluster models. Even though the proposed mechanism is a simple one-step reaction, GNMT may be a rather challenging case study for QM-cluster models because convergence in energetics requires models with >350 atoms. "Maximal" QM-cluster models built with either qualitative contact count ranking or quantitative interaction energies from functional group symmetry adapted perturbation theory provide acceptable results. Hence, important residue fragments that contribute to the energetics of the methyl-transfer reaction in GNMT are correctly identified in the RIN. Observations from this work suggest new directions to better establish an effective approach for constructing atomic-level enzyme models.
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Affiliation(s)
- Qianyi Cheng
- Department of Chemistry, University of Memphis, Memphis, TN 38152, U.S.A
| | - Nathan J. DeYonker
- Department of Chemistry, University of Memphis, Memphis, TN 38152, U.S.A
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5
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Jurich C, Yang ZJ. High-throughput computational investigation of protein electrostatics and cavity for SAM-dependent methyltransferases. Protein Sci 2023; 32:e4690. [PMID: 37278582 PMCID: PMC10273352 DOI: 10.1002/pro.4690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/25/2023] [Accepted: 05/29/2023] [Indexed: 06/07/2023]
Abstract
S-adenosyl methionine (SAM)-dependent methyl transferases (MTases) are a ubiquitous class of enzymes catalyzing dozens of essential life processes. Despite targeting a large space of substrates with diverse intrinsic reactivity, SAM MTases have similar catalytic efficiency. While understanding of MTase mechanism has grown tremendously through the integration of structural characterization, kinetic assays, and multiscale simulations, it remains elusive how these enzymes have evolved to fit the diverse chemical needs of their respective substrates. In this work, we performed a high-throughput molecular modeling analysis of 91 SAM MTases to better understand how their properties (i.e., electric field [EF] strength and active site volumes) help achieve similar catalytic efficiency toward substrates of different reactivity. We found that EF strengths have largely adjusted to make the target atom a better methyl acceptor. For MTases that target RNA/DNA and histone proteins, our results suggest that EF strength accommodates formal hybridization state and variation in cavity volume trends with diversity of substrate classes. Metal ions in SAM MTases contribute negatively to EF strength for methyl donation and enzyme scaffolds tend to offset these contributions.
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Affiliation(s)
| | - Zhongyue J. Yang
- Department of ChemistryVanderbilt UniversityNashvilleTennesseeUSA
- Center for Structural BiologyVanderbilt UniversityNashvilleTennesseeUSA
- Vanderbilt Institute of Chemical Biology, Vanderbilt UniversityNashvilleTennesseeUSA
- Data Science InstituteVanderbilt UniversityNashvilleTennesseeUSA
- Department of Chemical and Biomolecular EngineeringVanderbilt UniversityNashvilleTennesseeUSA
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6
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Yan S, Ji X, Peng W, Wang B. Evaluating the Transition State Stabilization/Destabilization Effects of the Electric Fields from Scaffold Residues by a QM/MM Approach. J Phys Chem B 2023; 127:4245-4253. [PMID: 37155960 DOI: 10.1021/acs.jpcb.3c01054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The protein scaffolds of enzymes not only provide structural support for the catalytic center but also exert preorganized electric fields for electrostatic catalysis. In recent years, uniform oriented external electric fields (OEEFs) have been widely applied to enzymatic reactions to mimic the electrostatic effects of the environment. However, the electric fields exerted by individual residues in proteins may be quite heterogeneous across the active site, with varying directions and strengths at different positions of the active site. Here, we propose a QM/MM-based approach to evaluate the effects of the electric fields exerted by individual residues in the protein scaffold. In particular, the heterogeneity of the residue electric fields and the effect of the native protein environment can be properly accounted for by this QM/MM approach. A case study of the O-O heterolysis reaction in the catalytic cycle of TyrH shows that (1) for scaffold residues that are relatively far from the active site, the heterogeneity of the residue electric field in the active site is not very significant and the electrostatic stabilization/destabilization due to each residue can be well approximated with the interaction energy between a uniform electric field and the QM region dipole; (2) for scaffold residues near the active site, the residue electric fields can be highly heterogeneous along the breaking O-O bond. In such a case, approximating the residue electric fields as uniform fields may misrepresent the overall electrostatic effect of the residue. The present QM/MM approach can be applied to evaluate the residues' electrostatic impact on enzymatic reactions, which also can be useful in computational optimization of electric fields to boost the enzyme catalysis.
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Affiliation(s)
- Shengheng Yan
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering and Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, P. R. China
| | - Xinwei Ji
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering and Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, P. R. China
| | - Wei Peng
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering and Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, P. R. China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering and Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, P. R. China
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7
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Abstract
This Perspective presents a review of our work and that of others in the highly controversial topic of the coupling of protein dynamics to reaction in enzymes. We have been involved in studying this topic for many years. Thus, this perspective will naturally present our own views, but it also is designed to present an overview of the variety of viewpoints of this topic, both experimental and theoretical. This is obviously a large and contentious topic.
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Affiliation(s)
- Steven D Schwartz
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
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8
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Balieiro AM, Anunciação ELS, Costa CHS, Qayed WS, Silva JRA. Computational Analysis of SAM Analogs as Methyltransferase Inhibitors of nsp16/nsp10 Complex from SARS-CoV-2. Int J Mol Sci 2022; 23:ijms232213972. [PMID: 36430451 PMCID: PMC9697258 DOI: 10.3390/ijms232213972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 11/03/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022] Open
Abstract
Methyltransferases (MTases) enzymes, responsible for RNA capping into severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), are emerging important targets for the design of new anti-SARS-CoV-2 agents. Here, analogs of S-adenosylmethionine (SAM), obtained from the bioisosteric substitution of the sulfonium and amino acid groups, were evaluated by rigorous computational modeling techniques such as molecular dynamics (MD) simulations followed by relative binding free analysis against nsp16/nsp10 complex from SARS-CoV-2. The most potent inhibitor (2a) shows the lowest binding free energy (-58.75 Kcal/mol) and more potency than Sinefungin (SFG) (-39.8 Kcal/mol), a pan-MTase inhibitor, which agrees with experimental observations. Besides, our results suggest that the total binding free energy of each evaluated SAM analog is driven by van der Waals interactions which can explain their poor cell permeability, as observed in experimental essays. Overall, we provide a structural and energetic analysis for the inhibition of the nsp16/nsp10 complex involving the evaluated SAM analogs as potential inhibitors.
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Affiliation(s)
- Alessandra M. Balieiro
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém 66075-110, Brazil
| | - Eduarda L. S. Anunciação
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém 66075-110, Brazil
| | - Clauber H. S. Costa
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém 66075-110, Brazil
- Institute of Chemistry and Center for Computing in Engineering & Sciences, University of Campinas, Campinas, São Paulo 13084-862, Brazil
| | - Wesam S. Qayed
- Medicinal Chemistry Department, Faculty of Pharmacy, Assiut University, Assiut 71526, Egypt
| | - José Rogério A. Silva
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém 66075-110, Brazil
- Correspondence:
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9
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Abstract
This Perspective reviews the use of Transition Path Sampling methods to study enzymatically catalyzed chemical reactions. First applied by our group to an enzymatic reaction over 15 years ago, the method has uncovered basic principles in enzymatic catalysis such as the protein promoting vibration, and it has also helped harmonize such ideas as electrostatic preorganization with dynamic views of enzyme function. It is now being used to help uncover principles of protein design necessary to artificial enzyme creation.
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Affiliation(s)
- Steven D Schwartz
- Department of Chemistry and Biochemistry University of Arizona Tucson, Arizona 85721, United States
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10
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Lawal MM, Vaissier Welborn V. Structural dynamics support electrostatic interactions in the active site of Adenylate Kinase. Chembiochem 2022; 23:e202200097. [PMID: 35303385 DOI: 10.1002/cbic.202200097] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/17/2022] [Indexed: 11/12/2022]
Abstract
Electrostatic preorganization as well as structural and dynamic heterogeneity are often used to rationalize the remarkable catalytic efficiency of enzymes. However, they are often presented as incompatible because the generation of permanent electrostatic effects implies that the protein structure remains rigid. Here, we use a metric, electric fields, that can treat electrostatic contributions and dynamics effects on equal footing, for a unique perspective on enzymatic catalysis. We find that the residues that contribute the most to electrostatic interactions with the substrate in the active site of Adenylate Kinase (our working example) are also the most flexible residues. Further, entropy-tuning mutations raise flexibility at the picosecond timescale where more conformations can be visited on short time periods, thereby softening the sharp heterogeneity normally visible at the microsecond timescale.
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Affiliation(s)
| | - Valerie Vaissier Welborn
- Virginia Polytechnic Institute and State University, Chemistry, Davidson 421A, 1040 Drillfield Drive, 24073, Blacksburg, UNITED STATES
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11
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Exploring the Catalytic Mechanism of the RNA Cap Modification by nsp16-nsp10 Complex of SARS-CoV-2 through a QM/MM Approach. Int J Mol Sci 2021; 23:ijms23010300. [PMID: 35008724 PMCID: PMC8745711 DOI: 10.3390/ijms23010300] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 12/10/2021] [Accepted: 12/23/2021] [Indexed: 11/23/2022] Open
Abstract
The inhibition of key enzymes that may contain the viral replication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have assumed central importance in drug discovery projects. Nonstructural proteins (nsps) are essential for RNA capping and coronavirus replication since it protects the virus from host innate immune restriction. In particular, nonstructural protein 16 (nsp16) in complex with nsp10 is a Cap-0 binding enzyme. The heterodimer formed by nsp16-nsp10 methylates the 5′-end of virally encoded mRNAs to mimic cellular mRNAs and thus it is one of the enzymes that is a potential target for antiviral therapy. In this study, we have evaluated the mechanism of the 2′-O methylation of the viral mRNA cap using hybrid quantum mechanics/molecular mechanics (QM/MM) approach. It was found that the calculated free energy barriers obtained at M062X/6-31+G(d,p) is in agreement with experimental observations. Overall, we provide a detailed molecular analysis of the catalytic mechanism involving the 2′-O methylation of the viral mRNA cap and, as expected, the results demonstrate that the TS stabilization is critical for the catalysis.
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12
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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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13
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Lima AH, Silva JR, Alves C, Lameira J. QM/MM Study of the Fosfomycin Resistance Mechanism Involving FosB Enzyme. ACS OMEGA 2021; 6:12507-12512. [PMID: 34056400 PMCID: PMC8154160 DOI: 10.1021/acsomega.1c00096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 03/12/2021] [Indexed: 06/01/2023]
Abstract
Multidrug-resistant organisms contain antibiotic-modifying enzymes that facilitate resistance to a variety of antimicrobial compounds. Particularly, the fosfomycin (FOF) drug can be structurally modified by several FOF-modifying enzymes before it reaches the biological target. Among them, FosB is an enzyme that utilizes l-cysteine or bacillithiol in the presence of a divalent metal to open the epoxide ring of FOF and, consequently, inactivate the drug. Here, we have used hybrid quantum mechanics/molecular mechanics (QM/MM) and molecular dynamics (MD) simulations to explore the mechanism of the reaction involving FosB and FOF. The calculated free-energy profiles show that the cost to open the epoxide ring of FOF at the C2 atom is ∼3.0 kcal/mol higher than that at the C1 atom. Besides, our QM/MM MD results revealed the critical role of conformation change of Cys9 and Asn50 to release the drug from the active site. Overall, the present study provides insights into the mechanism of FOF-resistant proteins.
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Affiliation(s)
- Anderson H. Lima
- Laboratório de Planejamento
e Desenvolvimento de Fármacos, Instituto de Ciências
Exatas e Naturais, Universidade Federal
do Pará, Rua Augusto Corrêa, 01, 66075-110, Belém, Pará, Brasil
| | - José Rogério
A. Silva
- Laboratório de Planejamento
e Desenvolvimento de Fármacos, Instituto de Ciências
Exatas e Naturais, Universidade Federal
do Pará, Rua Augusto Corrêa, 01, 66075-110, Belém, Pará, Brasil
| | - Cláudio
Nahum Alves
- Laboratório de Planejamento
e Desenvolvimento de Fármacos, Instituto de Ciências
Exatas e Naturais, Universidade Federal
do Pará, Rua Augusto Corrêa, 01, 66075-110, Belém, Pará, Brasil
| | - Jerônimo Lameira
- Laboratório de Planejamento
e Desenvolvimento de Fármacos, Instituto de Ciências
Exatas e Naturais, Universidade Federal
do Pará, Rua Augusto Corrêa, 01, 66075-110, Belém, Pará, Brasil
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14
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Cramer J, Jiang X, Schönemann W, Silbermann M, Zihlmann P, Siegrist S, Fiege B, Jakob RP, Rabbani S, Maier T, Ernst B. Enhancing the enthalpic contribution of hydrogen bonds by solvent shielding. RSC Chem Biol 2020; 1:281-287. [PMID: 34458766 PMCID: PMC8341794 DOI: 10.1039/d0cb00108b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 08/19/2020] [Indexed: 11/21/2022] Open
Abstract
In biological systems, polar interactions are heavily burdened by high desolvation penalties resulting from strong solute-solvent interactions. As a consequence thereof, enthalpic contributions of hydrogen bonds to the free energy of binding are severely diminished. However, this effect is strongly attenuated for interactions within solvent-shielded areas of proteins. In microcalorimetric experiments, we show that the bacterial lectin FimH utilizes conformational adaptions to effectively shield its binding site from solvent. The transition into a lower dielectric environment results in an enthalpic benefit of approximately -13 kJ mol-1 for mannoside binding. However, this effect can be abrogated, if the hydrogen bond network within the binding site is disturbed by deoxygenation of the ligand. Conformational adaption leading to reduced local dielectric constants could represent a general mechanism for proteins to enable enthalpy-driven recognition of polar ligands.
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Affiliation(s)
- Jonathan Cramer
- Institute of Molecular Pharmacy, University of Basel Klingelbergstrasse 50 4056 Basel Switzerland
| | - Xiaohua Jiang
- Institute of Molecular Pharmacy, University of Basel Klingelbergstrasse 50 4056 Basel Switzerland
| | - Wojciech Schönemann
- Institute of Molecular Pharmacy, University of Basel Klingelbergstrasse 50 4056 Basel Switzerland
| | - Marleen Silbermann
- Institute of Molecular Pharmacy, University of Basel Klingelbergstrasse 50 4056 Basel Switzerland
| | - Pascal Zihlmann
- Institute of Molecular Pharmacy, University of Basel Klingelbergstrasse 50 4056 Basel Switzerland
| | - Stefan Siegrist
- Institute of Molecular Pharmacy, University of Basel Klingelbergstrasse 50 4056 Basel Switzerland
| | - Brigitte Fiege
- Institute of Molecular Pharmacy, University of Basel Klingelbergstrasse 50 4056 Basel Switzerland
| | - Roman Peter Jakob
- Institute of Structural Biology, University of Basel Klingelbergstrasse 70 4056 Basel Switzerland
| | - Said Rabbani
- Institute of Molecular Pharmacy, University of Basel Klingelbergstrasse 50 4056 Basel Switzerland
| | - Timm Maier
- Institute of Structural Biology, University of Basel Klingelbergstrasse 70 4056 Basel Switzerland
| | - Beat Ernst
- Institute of Molecular Pharmacy, University of Basel Klingelbergstrasse 50 4056 Basel Switzerland
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15
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Liu F, Zhang J. Nano-second protein dynamics of key residue at Position 38 in catechol-O-methyltransferase system: a time-resolved fluorescence study. J Biochem 2020; 168:417-425. [DOI: 10.1093/jb/mvaa063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 05/17/2020] [Indexed: 02/02/2023] Open
Abstract
AbstractHuman catechol-O-methyltransferase, a key enzyme related to neurotransmitter metabolism, catalyses a methyl transfer from S-adenosylmethionine to catechol. Although extensive studies aim to understand the enzyme mechanisms, the connection of protein dynamics and enzyme catalysis is still not clear. Here, W38in (Trp143Phe) and W38in/Y68A (Trp143Phe with Tyr68Ala) mutants were carried out to study the relationship of dynamics and catalysis in nano-second timescale using time-resolved fluorescence lifetimes and Stokes shifts in various solvents. The comprehensive data implied the mutant W38in/Y68A with lower activity is more rigid than the ‘WT’−W38in, suggesting the importance of flexibility at residue 38 to maintain the optimal catalysis.
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Affiliation(s)
- Fan Liu
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, China
| | - Jianyu Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, China
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16
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Lim D, Wen X, Seebeck FP. Selenoimidazolium Salts as Supramolecular Reagents for Protein Alkylation. Chembiochem 2020; 21:3515-3520. [DOI: 10.1002/cbic.202000557] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Indexed: 12/15/2022]
Affiliation(s)
- David Lim
- Department of Chemistry University of Basel Mattenstrasse 24a Basel 4002 Switzerland
| | - Xiaojin Wen
- Department of Chemistry University of Basel Mattenstrasse 24a Basel 4002 Switzerland
| | - Florian P. Seebeck
- Department of Chemistry University of Basel Mattenstrasse 24a Basel 4002 Switzerland
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17
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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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18
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Hennefarth MR, Alexandrova AN. Direct Look at the Electric Field in Ketosteroid Isomerase and Its Variants. ACS Catal 2020. [DOI: 10.1021/acscatal.0c02795] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Matthew R. Hennefarth
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095-1569, United States
| | - Anastassia N. Alexandrova
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095-1569, United States
- California NanoSystems Institute, University of California, Los Angeles, 570 Westwood Plaza, Los Angeles, California 90095-1569, United Sates
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19
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Mehmood R, Kulik HJ. Both Configuration and QM Region Size Matter: Zinc Stability in QM/MM Models of DNA Methyltransferase. J Chem Theory Comput 2020; 16:3121-3134. [PMID: 32243149 DOI: 10.1021/acs.jctc.0c00153] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Quantum-mechanical/molecular-mechanical (QM/MM) methods are essential to the study of metalloproteins, but the relative importance of sampling and degree of QM treatment in achieving quantitative predictions is poorly understood. We study the relative magnitude of configurational and QM-region sensitivity of energetic and electronic properties in a representative Zn2+ metal binding site of a DNA methyltransferase. To quantify property variations, we analyze snapshots extracted from 250 ns of molecular dynamics simulation. To understand the degree of QM-region sensitivity, we perform analysis using QM regions ranging from a minimal 49-atom region consisting only of the Zn2+ metal and its four coordinating Cys residues up to a 628-atom QM region that includes residues within 12 Å of the metal center. Over the configurations sampled, we observe that illustrative properties (e.g., rigid Zn2+ removal energy) exhibit large fluctuations that are well captured with even minimal QM regions. Nevertheless, for both energetic and electronic properties, we observe a slow approach to asymptotic limits with similarly large changes in absolute values that converge only with larger (ca. 300-atom) QM region sizes. For the smaller QM regions, the electronic description of Zn2+ binding is incomplete: the metal binds too tightly and is too stabilized by the strong electrostatic potential of MM point charges, and the Zn-S bond covalency is overestimated. Overall, this work suggests that efficient sampling with QM/MM in small QM regions is an effective method to explore the influence of enzyme structure on target properties. At the same time, accurate descriptions of electronic and energetic properties require a larger QM region than the minimal metal-coordinating residues in order to converge treatment of both metal-local bonding and the overall electrostatic environment.
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Affiliation(s)
- Rimsha Mehmood
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Heather J Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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20
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Pereira PRM, Araújo JDO, Silva JRA, Alves CN, Lameira J, Lima AH. Exploring Chloride Selectivity and Halogenase Regioselectivity of the SalL Enzyme through Quantum Mechanical/Molecular Mechanical Modeling. J Chem Inf Model 2020; 60:738-746. [DOI: 10.1021/acs.jcim.9b01079] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Paulo R. M. Pereira
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, 66075-110, Belém, PA, Brasil
| | - Jéssica de O. Araújo
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, 66075-110, Belém, PA, Brasil
| | - José Rogério A. Silva
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, 66075-110, Belém, PA, Brasil
| | - Cláudio N. Alves
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, 66075-110, Belém, PA, Brasil
| | - Jerônimo Lameira
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, 66075-110, Belém, PA, Brasil
- Instituto de Ciências Biológicas, Universidade Federal do Pará, 66075-110, Belém, PA, Brasil
| | - Anderson H. Lima
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, 66075-110, Belém, PA, Brasil
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21
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Bueren-Calabuig JA, G Bage M, Cowling VH, Pisliakov AV. Mechanism of allosteric activation of human mRNA cap methyltransferase (RNMT) by RAM: insights from accelerated molecular dynamics simulations. Nucleic Acids Res 2019; 47:8675-8692. [PMID: 31329932 PMCID: PMC7145595 DOI: 10.1093/nar/gkz613] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 07/01/2019] [Accepted: 07/08/2019] [Indexed: 02/04/2023] Open
Abstract
The RNA guanine-N7 methyltransferase (RNMT) in complex with RNMT-activating miniprotein (RAM) catalyses the formation of a N7-methylated guanosine cap structure on the 5' end of nascent RNA polymerase II transcripts. The mRNA cap protects the primary transcript from exonucleases and recruits cap-binding complexes that mediate RNA processing, export and translation. By using microsecond standard and accelerated molecular dynamics simulations, we provide for the first time a detailed molecular mechanism of allosteric regulation of RNMT by RAM. We show that RAM selects the RNMT active site conformations that are optimal for binding of substrates (AdoMet and the cap), thus enhancing their affinity. Furthermore, our results strongly suggest the likely scenario in which the cap binding promotes the subsequent AdoMet binding, consistent with the previously suggested cooperative binding model. By employing the network community analyses, we revealed the underlying long-range allosteric networks and paths that are crucial for allosteric regulation by RAM. Our findings complement and explain previous experimental data on RNMT activity. Moreover, this study provides the most complete description of the cap and AdoMet binding poses and interactions within the enzyme's active site. This information is critical for the drug discovery efforts that consider RNMT as a promising anti-cancer target.
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Affiliation(s)
- Juan A Bueren-Calabuig
- Computational Biology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Marcus G Bage
- Computational Biology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Victoria H Cowling
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Andrei V Pisliakov
- Computational Biology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK.,Physics, School of Science and Engineering, University of Dundee, Dundee, DD1 4HN, UK
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22
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Abstract
For decades, there has been debate regarding the origin of the catalytic power of enzymes. In this work, we use the approach of computational chemistry to study the enzyme catechol O-methyltransferase (COMT) and reveal that the two current views on the catalytic mechanism of enzymes, the rate-promoting vibrations and the electric field, may both be viewed as part of the chemical step catalyzed by COMT. However, we show that the rate-promoting vibrations cause the electrostatic effect. This work provides insight into the catalytic mechanism of COMT and resolves a longstanding controversy regarding this enzyme's mechanism.
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Affiliation(s)
- Xi Chen
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, Arizona 85721, United States
| | - Steven D. Schwartz
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, Arizona 85721, United States
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23
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Yang Z, Liu F, Steeves AH, Kulik HJ. Quantum Mechanical Description of Electrostatics Provides a Unified Picture of Catalytic Action Across Methyltransferases. J Phys Chem Lett 2019; 10:3779-3787. [PMID: 31244268 DOI: 10.1021/acs.jpclett.9b01555] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Methyl transferases (MTases) are a well-studied class of enzymes for which competing enzymatic enhancement mechanisms have been suggested, ranging from structural methyl group CH···X hydrogen bonds (HBs) to electrostatic- and charge-transfer-driven stabilization of the transition state (TS). We identified all Class I MTases for which reasonable resolution (<2.0 Å) crystal structures could be used to form catalytically competent ternary complexes for multiscale (i.e., quantum-mechanical/molecular-mechanical or QM/MM) simulation of the SN2 methyl transfer reaction coordinate. The four Class I MTases studied have both distinct functions (e.g., protein repair or biosynthesis) and substrate nucleophiles (i.e., C, N, or O). While CH···X HBs stabilize all reactant complexes, no universal TS stabilization role is found for these interactions in MTases. A consistent picture is instead obtained through analysis of charge transfer and electrostatics, wherein much of cofactor-substrate charge separation is maintained in the TS region, and electrostatic potential is correlated with substrate nucleophilicity (i.e., intrinsic reactivity).
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Affiliation(s)
- Zhongyue Yang
- Department of Chemical Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Fang Liu
- Department of Chemical Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Adam H Steeves
- Department of Chemical Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Heather J Kulik
- Department of Chemical Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
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24
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Calixto AR, Moreira C, Pabis A, Kötting C, Gerwert K, Rudack T, Kamerlin SCL. GTP Hydrolysis Without an Active Site Base: A Unifying Mechanism for Ras and Related GTPases. J Am Chem Soc 2019; 141:10684-10701. [PMID: 31199130 DOI: 10.1021/jacs.9b03193] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
GTP hydrolysis is a biologically crucial reaction, being involved in regulating almost all cellular processes. As a result, the enzymes that catalyze this reaction are among the most important drug targets. Despite their vital importance and decades of substantial research effort, the fundamental mechanism of enzyme-catalyzed GTP hydrolysis by GTPases remains highly controversial. Specifically, how do these regulatory proteins hydrolyze GTP without an obvious general base in the active site to activate the water molecule for nucleophilic attack? To answer this question, we perform empirical valence bond simulations of GTPase-catalyzed GTP hydrolysis, comparing solvent- and substrate-assisted pathways in three distinct GTPases, Ras, Rab, and the Gαi subunit of a heterotrimeric G-protein, both in the presence and in the absence of the corresponding GTPase activating proteins. Our results demonstrate that a general base is not needed in the active site, as the preferred mechanism for GTP hydrolysis is a conserved solvent-assisted pathway. This pathway involves the rate-limiting nucleophilic attack of a water molecule, leading to a short-lived intermediate that tautomerizes to form H2PO4- and GDP as the final products. Our fundamental biochemical insight into the enzymatic regulation of GTP hydrolysis not only resolves a decades-old mechanistic controversy but also has high relevance for drug discovery efforts. That is, revisiting the role of oncogenic mutants with respect to our mechanistic findings would pave the way for a new starting point to discover drugs for (so far) "undruggable" GTPases like Ras.
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Affiliation(s)
- Ana R Calixto
- Department of Chemistry-BMC , Uppsala University , Box 576, S-751 23 Uppsala , Sweden
| | - Cátia Moreira
- Department of Chemistry-BMC , Uppsala University , Box 576, S-751 23 Uppsala , Sweden
| | - Anna Pabis
- Department of Cell and Molecular Biology , Uppsala University , BMC Box 596, S-751 24 , Uppsala , Sweden
| | - Carsten Kötting
- Department of Biophysics , Ruhr University Bochum , 44801 Bochum , Germany
| | - Klaus Gerwert
- Department of Biophysics , Ruhr University Bochum , 44801 Bochum , Germany
| | - Till Rudack
- Department of Biophysics , Ruhr University Bochum , 44801 Bochum , Germany
| | - Shina C L Kamerlin
- Department of Chemistry-BMC , Uppsala University , Box 576, S-751 23 Uppsala , Sweden
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25
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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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26
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Yang Z, Mehmood R, Wang M, Qi HW, Steeves AH, Kulik HJ. Revealing quantum mechanical effects in enzyme catalysis with large-scale electronic structure simulation. REACT CHEM ENG 2019; 4:298-315. [PMID: 31572618 PMCID: PMC6768422 DOI: 10.1039/c8re00213d] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Enzymes have evolved to facilitate challenging reactions at ambient conditions with specificity seldom matched by other catalysts. Computational modeling provides valuable insight into catalytic mechanism, and the large size of enzymes mandates multi-scale, quantum mechanical-molecular mechanical (QM/MM) simulations. Although QM/MM plays an essential role in balancing simulation cost to enable sampling with full QM treatment needed to understand electronic structure in enzyme active sites, the relative importance of these two strategies for understanding enzyme mechanism is not well known. We explore challenges in QM/MM for studying the reactivity and stability of three diverse enzymes: i) Mg2+-dependent catechol O-methyltransferase (COMT), ii) radical enzyme choline trimethylamine lyase (CutC), and iii) DNA methyltransferase (DNMT1), which has structural Zn2+ binding sites. In COMT, strong non-covalent interactions lead to long range coupling of electronic structure properties across the active site, but the more isolated nature of the metallocofactor in DNMT1 leads to faster convergence of some properties. We quantify these effects in COMT by computing covariance matrices of by-residue electronic structure properties during dynamics and along the reaction coordinate. In CutC, we observe spontaneous bond cleavage following initiation events, highlighting the importance of sampling and dynamics. We use electronic structure analysis to quantify the relative importance of CHO and OHO non-covalent interactions in imparting reactivity. These three diverse cases enable us to provide some general recommendations regarding QM/MM simulation of enzymes.
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Affiliation(s)
- Zhongyue Yang
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Rimsha Mehmood
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Mengyi Wang
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Helena W. Qi
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Adam H. Steeves
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Heather J. Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
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27
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Crystallographic and Computational Characterization of Methyl Tetrel Bonding in S-Adenosylmethionine-Dependent Methyltransferases. Molecules 2018; 23:molecules23112965. [PMID: 30428636 PMCID: PMC6278250 DOI: 10.3390/molecules23112965] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 10/19/2018] [Accepted: 10/20/2018] [Indexed: 11/17/2022] Open
Abstract
Tetrel bonds represent a category of non-bonding interaction wherein an electronegative atom donates a lone pair of electrons into the sigma antibonding orbital of an atom in the carbon group of the periodic table. Prior computational studies have implicated tetrel bonding in the stabilization of a preliminary state that precedes the transition state in SN2 reactions, including methyl transfer. Notably, the angles between the tetrel bond donor and acceptor atoms coincide with the prerequisite geometry for the SN2 reaction. Prompted by these findings, we surveyed crystal structures of methyltransferases in the Protein Data Bank and discovered multiple instances of carbon tetrel bonding between the methyl group of the substrate S-adenosylmethionine (AdoMet) and electronegative atoms of small molecule inhibitors, ions, and solvent molecules. The majority of these interactions involve oxygen atoms as the Lewis base, with the exception of one structure in which a chlorine atom of an inhibitor functions as the electron donor. Quantum mechanical analyses of a representative subset of the methyltransferase structures from the survey revealed that the calculated interaction energies and spectral properties are consistent with the values for bona fide carbon tetrel bonds. The discovery of methyl tetrel bonding offers new insights into the mechanism underlying the SN2 reaction catalyzed by AdoMet-dependent methyltransferases. These findings highlight the potential of exploiting these interactions in developing new methyltransferase inhibitors.
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28
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Saez DA, Zinovjev K, Tuñón I, Vöhringer-Martinez E. Catalytic Reaction Mechanism in Native and Mutant Catechol-O-methyltransferase from the Adaptive String Method and Mean Reaction Force Analysis. J Phys Chem B 2018; 122:8861-8871. [DOI: 10.1021/acs.jpcb.8b07339] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- David Adrian Saez
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, 4070371 Concepcion, Chile
| | - Kirill Zinovjev
- Departament de Química Física, Universitat de València, 46100 Burjassot, Spain
| | - Iñaki Tuñón
- Departament de Química Física, Universitat de València, 46100 Burjassot, Spain
| | - Esteban Vöhringer-Martinez
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, 4070371 Concepcion, Chile
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29
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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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30
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Song H, van der Velden NS, Shiran SL, Bleiziffer P, Zach C, Sieber R, Imani AS, Krausbeck F, Aebi M, Freeman MF, Riniker S, Künzler M, Naismith JH. A molecular mechanism for the enzymatic methylation of nitrogen atoms within peptide bonds. SCIENCE ADVANCES 2018; 4:eaat2720. [PMID: 30151425 PMCID: PMC6108569 DOI: 10.1126/sciadv.aat2720] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 07/17/2018] [Indexed: 05/04/2023]
Abstract
The peptide bond, the defining feature of proteins, governs peptide chemistry by abolishing nucleophilicity of the nitrogen. This and the planarity of the peptide bond arise from the delocalization of the lone pair of electrons on the nitrogen atom into the adjacent carbonyl. While chemical methylation of an amide bond uses a strong base to generate the imidate, OphA, the precursor protein of the fungal peptide macrocycle omphalotin A, self-hypermethylates amides at pH 7 using S-adenosyl methionine (SAM) as cofactor. The structure of OphA reveals a complex catenane-like arrangement in which the peptide substrate is clamped with its amide nitrogen aligned for nucleophilic attack on the methyl group of SAM. Biochemical data and computational modeling suggest a base-catalyzed reaction with the protein stabilizing the reaction intermediate. Backbone N-methylation of peptides enhances their protease resistance and membrane permeability, a property that holds promise for applications to medicinal chemistry.
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Affiliation(s)
- Haigang Song
- Biomedical Sciences Research Complex, North Haugh, University of St. Andrews, Fife KY16 9ST, UK
- Division of Structural Biology, Wellcome Trust Centre of Human Genomics, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Niels S. van der Velden
- Institute of Microbiology, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Sally L. Shiran
- Biomedical Sciences Research Complex, North Haugh, University of St. Andrews, Fife KY16 9ST, UK
| | - Patrick Bleiziffer
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Christina Zach
- Institute of Microbiology, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Ramon Sieber
- Institute of Microbiology, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Aman S. Imani
- Department of Biochemistry, Molecular Biology, and Biophysics, and BioTechnology Institute, University of Minnesota–Twin Cities, St. Paul, MN 55108, USA
| | - Florian Krausbeck
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Markus Aebi
- Institute of Microbiology, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Michael F. Freeman
- Department of Biochemistry, Molecular Biology, and Biophysics, and BioTechnology Institute, University of Minnesota–Twin Cities, St. Paul, MN 55108, USA
| | - Sereina Riniker
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
- Corresponding author. (S.R.); (M.K.); (J.H.N.)
| | - Markus Künzler
- Institute of Microbiology, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
- Corresponding author. (S.R.); (M.K.); (J.H.N.)
| | - James H. Naismith
- Division of Structural Biology, Wellcome Trust Centre of Human Genomics, Roosevelt Drive, Oxford OX3 7BN, UK
- State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
- Research Complex at Harwell, Rutherford Laboratory, Didcot, Oxfordshire OX11 0FA, UK
- Corresponding author. (S.R.); (M.K.); (J.H.N.)
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31
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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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32
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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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33
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Almeida MO, Costa CHS, Gomes GC, Lameira J, Alves CN, Honorio KM. Computational analyses of interactions between ALK-5 and bioactive ligands: insights for the design of potential anticancer agents. J Biomol Struct Dyn 2017; 36:4010-4022. [PMID: 29132261 DOI: 10.1080/07391102.2017.1404938] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Activin Receptor-Like Kinase 5 (ALK-5) is related to some types of cancer, such as breast, lung, and pancreas. In this study, we have used molecular docking, molecular dynamics simulations, and free energy calculations in order to explore key interactions between ALK-5 and six bioactive ligands with different ranges of biological activity. The motivation of this work is the lack of crystal structure for inhibitor-protein complexes for this set of ligands. The understanding of the molecular structure and the protein-ligand interaction could give support for the development of new drugs against cancer. The results show that the calculated binding free energy using MM-GBSA, MM-PBSA, and SIE is correlated with experimental data with r2 = 0.88, 0.80, and 0.94, respectively, which indicates that the calculated binding free energy is in excellent agreement with experimental data. In addition, the results demonstrate that H bonds with Lys232, Glu245, Tyr249, His283, Asp351, and one structural water molecule play an important role for the inhibition of ALK-5. Overall, we discussed the main interactions between ALK-5 and six inhibitors that may be used as starting points for designing new molecules to the treatment of cancer.
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Affiliation(s)
- Michell O Almeida
- a Center of Natural Sciences and Humanities , Federal University of ABC , Santo Andre , SP , Brazil
| | - Clauber H S Costa
- b Laboratório de Planejamento e Desenvolvimento de Fármacos , Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará , CP 11101, 66075-110 , Belém , PA , Brazil
| | - Guelber C Gomes
- b Laboratório de Planejamento e Desenvolvimento de Fármacos , Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará , CP 11101, 66075-110 , Belém , PA , Brazil
| | - Jerônimo Lameira
- b Laboratório de Planejamento e Desenvolvimento de Fármacos , Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará , CP 11101, 66075-110 , Belém , PA , Brazil
| | - Claudio N Alves
- b Laboratório de Planejamento e Desenvolvimento de Fármacos , Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará , CP 11101, 66075-110 , Belém , PA , Brazil
| | - Kathia M Honorio
- a Center of Natural Sciences and Humanities , Federal University of ABC , Santo Andre , SP , Brazil.,c School of Arts, Sciences and Humanities , University of São Paulo , Sao Paulo , Brazil
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34
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Dos Santos AM, Lima AH, Alves CN, Lameira J. Unraveling the Addition-Elimination Mechanism of EPSP Synthase through Computer Modeling. J Phys Chem B 2017; 121:8626-8637. [PMID: 28829128 DOI: 10.1021/acs.jpcb.7b05063] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Enolpyruvyl transfer from phosphoenolpyruvate (PEP) to the hydroxyl group of shikimate-5-OH-3-phosphate (S3P) is catalyzed by 5-enolpyruvylshikimate 3-phosphate (EPSP) synthase in a reaction that involves breaking the C-O bond of PEP. Catalysis involves an addition-elimination mechanism with the formation of a tetrahedral intermediate (THI). Experiments have elucidated the mechanism of THI formation and breakdown. However, the catalytic action of EPSP synthase and the individual roles of catalytic residues Asp313 and Glu341 remains unclear. We have used a hybrid quantum mechanical/molecular mechanical (QM/MM) approach to explore the free energy surface in a reaction catalyzed by EPSP synthase. The Glu341 was the most favorable acid/base catalyst. Our results indicate that the protonation of PEP C3 precedes the nucleophilic attack on PEP C2 in the addition mechanism. Also, the breaking of the C-O bond of THI to form an EPSP cation intermediate must occur before proton transfer from PEP C3 to Glu341 in the elimination mechanism. Analysis of the FES supports cationic intermediate formation during the reaction catalyzed by EPSP synthase. Finally, the computational model indicates a proton transfer shift (Hammond shift) from Glu341 to C3 for an enzyme-based reaction with the shifted transition state, earlier than in the reference reaction in water.
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Affiliation(s)
- Alberto M Dos Santos
- Institute of Biological Sciences, Federal University of Pará , Belém, PA 66075-110, Brazil
| | - Anderson H Lima
- Institute of Biological Sciences, Federal University of Pará , Belém, PA 66075-110, Brazil
| | - Cláudio Nahum Alves
- Institute of Exact and Natural Sciences, Federal University of Pará , Belém, PA 66075-110, Brazil
| | - Jerônimo Lameira
- Institute of Biological Sciences, Federal University of Pará , Belém, PA 66075-110, Brazil
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35
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Roy S, Schopf P, Warshel A. Origin of the Non-Arrhenius Behavior of the Rates of Enzymatic Reactions. J Phys Chem B 2017; 121:6520-6526. [PMID: 28613876 DOI: 10.1021/acs.jpcb.7b03698] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The origin of the non-Arrhenius behavior of the rate constant for hydride transfer enzymatic reactions has been a puzzling problem since its initial observation. This effect has been used originally to support the idea that enzymes work by dynamical effects and more recently to suggest an entropy funnel model. Our analysis, however, has advanced the idea that the reason for the non-Arrhenius trend reflects the temperature dependence of the rearrangements of the protein polar groups in response to the change in the charge distribution of the reacting system during the transition from the ground state (GS) to the transition state (TS). Here we examine the validity of our early proposal by simulating the catalytic reaction of alcohol dehydrogenase (ADH) and determine the microscopic origin of the entropic and enthalpic contributions to the activation barrier. The corresponding analysis establishes the origin of the non-Arrhenius behaviors and quantifies our original suggestion that the classical effect is due to the entropic contributions of the environment. We also find that the quantum effects reflect in part the temperature dependence of the donor-acceptor distance.
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Affiliation(s)
- Subhendu Roy
- Department of Chemistry, University of Southern California , 3620 McClintock Avenue, Los Angeles, California 90089, United States
| | - Patrick Schopf
- Astex Pharmaceuticals , Cambridge CB4 0QA, United Kingdom
| | - Arieh Warshel
- Department of Chemistry, University of Southern California , 3620 McClintock Avenue, Los Angeles, California 90089, United States
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36
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Warshel A, Bora RP. Perspective: Defining and quantifying the role of dynamics in enzyme catalysis. J Chem Phys 2017; 144:180901. [PMID: 27179464 DOI: 10.1063/1.4947037] [Citation(s) in RCA: 134] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Enzymes control chemical reactions that are key to life processes, and allow them to take place on the time scale needed for synchronization between the relevant reaction cycles. In addition to general interest in their biological roles, these proteins present a fundamental scientific puzzle, since the origin of their tremendous catalytic power is still unclear. While many different hypotheses have been put forward to rationalize this, one of the proposals that has become particularly popular in recent years is the idea that dynamical effects contribute to catalysis. Here, we present a critical review of the dynamical idea, considering all reasonable definitions of what does and does not qualify as a dynamical effect. We demonstrate that no dynamical effect (according to these definitions) has ever been experimentally shown to contribute to catalysis. Furthermore, the existence of non-negligible dynamical contributions to catalysis is not supported by consistent theoretical studies. Our review is aimed, in part, at readers with a background in chemical physics and biophysics, and illustrates that despite a substantial body of experimental effort, there has not yet been any study that consistently established a connection between an enzyme's conformational dynamics and a significant increase in the catalytic contribution of the chemical step. We also make the point that the dynamical proposal is not a semantic issue but a well-defined scientific hypothesis with well-defined conclusions.
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Affiliation(s)
- Arieh Warshel
- Department of Chemistry, University of Southern California, SGM 418, 3620 McClintock Avenue, Los Angeles, California 90089, USA
| | - Ram Prasad Bora
- Department of Chemistry, University of Southern California, SGM 418, 3620 McClintock Avenue, Los Angeles, California 90089, USA
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37
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Stratton CF, Poulin MB, Du Q, Schramm VL. Kinetic Isotope Effects and Transition State Structure for Human Phenylethanolamine N-Methyltransferase. ACS Chem Biol 2017; 12:342-346. [PMID: 27997103 PMCID: PMC5553282 DOI: 10.1021/acschembio.6b00922] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Phenylethanolamine N-methyltransferase (PNMT) catalyzes the S-adenosyl-l-methionine (SAM)-dependent conversion of norepinephrine to epinephrine. Epinephrine has been associated with critical processes in humans including the control of respiration and blood pressure. Additionally, PNMT activity has been suggested to play a role in hypertension and Alzheimer's disease. In the current study, labeled SAM substrates were used to measure primary methyl-14C and 36S and secondary methyl-3H, 5'-3H, and 5'-14C intrinsic kinetic isotope effects for human PNMT. The transition state of human PNMT was modeled by matching kinetic isotope effects predicted via quantum chemical calculations to intrinsic values. The model provides information on the geometry and electrostatics of the human PNMT transition state structure and indicates that human PNMT catalyzes the formation of epinephrine through an early SN2 transition state in which methyl transfer is rate-limiting.
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Affiliation(s)
- Christopher F. Stratton
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | | | - Quan Du
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
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38
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Amrein BA, Steffen-Munsberg F, Szeler I, Purg M, Kulkarni Y, Kamerlin SCL. CADEE: Computer-Aided Directed Evolution of Enzymes. IUCRJ 2017; 4:50-64. [PMID: 28250941 PMCID: PMC5331465 DOI: 10.1107/s2052252516018017] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 11/09/2016] [Indexed: 05/10/2023]
Abstract
The tremendous interest in enzymes as biocatalysts has led to extensive work in enzyme engineering, as well as associated methodology development. Here, a new framework for computer-aided directed evolution of enzymes (CADEE) is presented which allows a drastic reduction in the time necessary to prepare and analyze in silico semi-automated directed evolution of enzymes. A pedagogical example of the application of CADEE to a real biological system is also presented in order to illustrate the CADEE workflow.
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Affiliation(s)
- Beat Anton Amrein
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden
| | - Fabian Steffen-Munsberg
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden
| | - Ireneusz Szeler
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden
| | - Miha Purg
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden
| | - Yashraj Kulkarni
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden
| | - Shina Caroline Lynn Kamerlin
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden
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39
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Araújo E, Lima AH, Lameira J. Catalysis by solvation rather than the desolvation effect: exploring the catalytic efficiency of SAM-dependent chlorinase. Phys Chem Chem Phys 2017; 19:21350-21356. [DOI: 10.1039/c7cp02811c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Chlorinase SalL active sites provide electrostatic stabilization of the transition state which is the origin of its catalytic effect.
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Affiliation(s)
- Edson Araújo
- Institute of Biological Sciences
- Federal University of Pará
- Belém
- Brazil
| | - Anderson H. Lima
- Institute of Exact and Natural Sciences
- Federal University of Pará
- Belém
- Brazil
| | - Jerônimo Lameira
- Institute of Biological Sciences
- Federal University of Pará
- Belém
- Brazil
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40
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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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41
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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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42
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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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43
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Wang X, Zhang JZH, He X. Quantum mechanical calculation of electric fields and vibrational Stark shifts at active site of human aldose reductase. J Chem Phys 2016; 143:184111. [PMID: 26567650 DOI: 10.1063/1.4935176] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Recent advance in biophysics has made it possible to directly measure site-specific electric field at internal sites of proteins using molecular probes with C = O or C≡N groups in the context of vibrational Stark effect. These measurements directly probe changes of electric field at specific protein sites due to, e.g., mutation and are very useful in protein design. Computational simulation of the Stark effect based on force fields such as AMBER and OPLS, while providing good insight, shows large errors in comparison to experimental measurement due to inherent difficulties associated with point charge based representation of force fields. In this study, quantum mechanical calculation of protein's internal electrostatic properties and vibrational Stark shifts was carried out by using electrostatically embedded generalized molecular fractionation with conjugate caps method. Quantum calculated change of mutation-induced electric field and vibrational Stark shift is reported at the internal probing site of enzyme human aldose reductase. The quantum result is in much better agreement with experimental data than those predicted by force fields, underscoring the deficiency of traditional point charge models describing intra-protein electrostatic properties.
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Affiliation(s)
- Xianwei Wang
- Center for Optics and Optoelectronics Research, College of Science, Zhejiang University of Technology, Hangzhou, Zhejiang 310023, China
| | - John Z H Zhang
- State Key Laboratory of Precision Spectroscopy, Institute of Theoretical and Computational Science, East China Normal University, Shanghai 200062, China
| | - Xiao He
- State Key Laboratory of Precision Spectroscopy, Institute of Theoretical and Computational Science, East China Normal University, Shanghai 200062, China
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Abstract
Human DNA methyltransferase 1 (DNMT1) maintains the epigenetic state of DNA by replicating CpG methylation signatures from parent to daughter strands, producing heritable methylation patterns through cell divisions. The proposed catalytic mechanism of DNMT1 involves nucleophilic attack of Cys(1226) to cytosine (Cyt) C6, methyl transfer from S-adenosyl-l-methionine (SAM) to Cyt C5, and proton abstraction from C5 to form methylated CpG in DNA. Here, we report the subangstrom geometric and electrostatic structure of the major transition state (TS) of the reaction catalyzed by human DNMT1. Experimental kinetic isotope effects were used to guide quantum mechanical calculations to solve the TS structure. Methyl transfer occurs after Cys(1226) attack to Cyt C6, and the methyl transfer step is chemically rate-limiting for DNMT1. Electrostatic potential maps were compared for the TS and ground states, providing the electronic basis for interactions between the protein and reactants at the TS. Understanding the TS of DNMT1 demonstrates the possibility of using similar analysis to gain subangstrom geometric insight into the complex reactions of epigenetic modifications.
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Affiliation(s)
- Quan Du
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Zhen Wang
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Vern L Schramm
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461
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45
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Lameira J, Kupchencko I, Warshel A. Enhancing Paradynamics for QM/MM Sampling of Enzymatic Reactions. J Phys Chem B 2016; 120:2155-64. [PMID: 26866994 PMCID: PMC5380004 DOI: 10.1021/acs.jpcb.5b11966] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Despite the enormous increase in computer power, it is still extremely challenging to obtain computationally converging sampling of ab initio QM/MM (QM(ai)/MM) free energy surfaces in condensed phases. The sampling problem can be significantly reduced by the use of the reference potential paradynamics (PD) approach, but even this approach still requires major computer time in studies of enzymatic reactions. To further reduce the sampling problem we developed here a new PD version where we use an empirical valence bond reference potential that has a minimum rather than a maximum at the transition state region of the target potential (this is accomplished conveniently by shifting the EVB of the product state). Hence, we can map the TS region in a more efficient way. Here, we introduce and validate the inverted EVB PD approach. The validation involves the study of the S(N)2 step of the reaction catalyzed by haloakene dehalogenase (DhlA) and the GTP hydrolysis in the RasGAP system. In addition, we have also studied the corresponding reaction in water for each of the systems described here and the reaction involving trimethylsulfonium and dimethylamine in solution. The results are encouraging and the new strategy appears to provide a powerful way of evaluating QM(ai)/MM activation free energies.
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Affiliation(s)
- Jerônimo Lameira
- Department of Chemistry (SGM418), University of Southern California , 3620 McClintock 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, Pará, Brazil
| | - Ilya Kupchencko
- Department of Chemistry (SGM418), University of Southern California , 3620 McClintock Avenue, Los Angeles, California 90089, United States
| | - Arieh Warshel
- Department of Chemistry (SGM418), University of Southern California , 3620 McClintock Avenue, Los Angeles, California 90089, United States
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46
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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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47
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Poulin MB, Schneck JL, Matico RE, McDevitt PJ, Huddleston MJ, Hou W, Johnson NW, Thrall SH, Meek TD, Schramm VL. Transition state for the NSD2-catalyzed methylation of histone H3 lysine 36. Proc Natl Acad Sci U S A 2016; 113:1197-201. [PMID: 26787850 PMCID: PMC4747696 DOI: 10.1073/pnas.1521036113] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Nuclear receptor SET domain containing protein 2 (NSD2) catalyzes the methylation of histone H3 lysine 36 (H3K36). It is a determinant in Wolf-Hirschhorn syndrome and is overexpressed in human multiple myeloma. Despite the relevance of NSD2 to cancer, there are no potent, selective inhibitors of this enzyme reported. Here, a combination of kinetic isotope effect measurements and quantum chemical modeling was used to provide subangstrom details of the transition state structure for NSD2 enzymatic activity. Kinetic isotope effects were measured for the methylation of isolated HeLa cell nucleosomes by NSD2. NSD2 preferentially catalyzes the dimethylation of H3K36 along with a reduced preference for H3K36 monomethylation. Primary Me-(14)C and (36)S and secondary Me-(3)H3, Me-(2)H3, 5'-(14)C, and 5'-(3)H2 kinetic isotope effects were measured for the methylation of H3K36 using specifically labeled S-adenosyl-l-methionine. The intrinsic kinetic isotope effects were used as boundary constraints for quantum mechanical calculations for the NSD2 transition state. The experimental and calculated kinetic isotope effects are consistent with an SN2 chemical mechanism with methyl transfer as the first irreversible chemical step in the reaction mechanism. The transition state is a late, asymmetric nucleophilic displacement with bond separation from the leaving group at (2.53 Å) and bond making to the attacking nucleophile (2.10 Å) advanced at the transition state. The transition state structure can be represented in a molecular electrostatic potential map to guide the design of inhibitors that mimic the transition state geometry and charge.
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Affiliation(s)
- Myles B Poulin
- Department of Biochemistry, Albert Einstein College of Medicine of Yeshiva University, Bronx, NY 10461
| | - Jessica L Schneck
- Biological Sciences, Platform Technology and Science, GlaxoSmithKline, Collegeville, PA 19426
| | - Rosalie E Matico
- Biological Sciences, Platform Technology and Science, GlaxoSmithKline, Collegeville, PA 19426
| | - Patrick J McDevitt
- Biological Sciences, Platform Technology and Science, GlaxoSmithKline, Collegeville, PA 19426
| | - Michael J Huddleston
- Biological Sciences, Platform Technology and Science, GlaxoSmithKline, Collegeville, PA 19426
| | - Wangfang Hou
- Biological Sciences, Platform Technology and Science, GlaxoSmithKline, Collegeville, PA 19426
| | - Neil W Johnson
- Cancer Epigenetics Discovery Performance Unit, GlaxoSmithKline, Collegeville, PA 19426
| | - Sara H Thrall
- Biological Sciences, Platform Technology and Science, GlaxoSmithKline, Collegeville, PA 19426
| | - Thomas D Meek
- Biological Sciences, Platform Technology and Science, GlaxoSmithKline, Collegeville, PA 19426
| | - Vern L Schramm
- Department of Biochemistry, Albert Einstein College of Medicine of Yeshiva University, Bronx, NY 10461;
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48
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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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49
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Lima AH, Alves CN, Prasad R, Lameira J. Exploring the origin of the catalytic power and product specificity of SET domain protein methyltransferase. MOLECULAR BIOSYSTEMS 2016; 12:2980-3. [DOI: 10.1039/c6mb00414h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Computer simulation reveals that the origin of SET8 catalytic power is mainly due to electrostatic preorganization.
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Affiliation(s)
- A. H. Lima
- Faculdade de Biotecnologia e Laboratório de Planejamento e Desenvolvimento de Fármacos
- Universidade Federal do Pará
- Belém
- Brazil
| | - C. N. Alves
- Faculdade de Biotecnologia e Laboratório de Planejamento e Desenvolvimento de Fármacos
- Universidade Federal do Pará
- Belém
- Brazil
| | - R. Prasad
- Southern California
- Department of Chemistry
- SGM 418
- Los Angeles
- USA
| | - J. Lameira
- Faculdade de Biotecnologia e Laboratório de Planejamento e Desenvolvimento de Fármacos
- Universidade Federal do Pará
- Belém
- Brazil
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50
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Saez DA, Vogt-Geisse S, Inostroza-Rivera R, Kubař T, Elstner M, Toro-Labbé A, Vöhringer-Martinez E. The effect of the environment on the methyl transfer reaction mechanism between trimethylsulfonium and phenolate. Phys Chem Chem Phys 2016; 18:24033-42. [DOI: 10.1039/c6cp02821g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The methyl transfer reaction mechanism in different molecular environments were studied by electronic structure methods and QM/MM molecular dynamics simulations.
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Affiliation(s)
- David Adrian Saez
- Departamento de Físico-Química
- Facultad de Ciencias Químicas
- Universidad de Concepción
- Millenium Nucleus Chemical Processes and Catalysis (CPC)
- Chile
| | - Stefan Vogt-Geisse
- Departamento de Físico-Química
- Facultad de Ciencias Químicas
- Universidad de Concepción
- Millenium Nucleus Chemical Processes and Catalysis (CPC)
- Chile
| | | | - Tomáš Kubař
- Center for Functional Nanomaterials
- Karlsruhe Institute of Technology
- Germany
- Institute for Physical Chemistry
- Karlsruhe Institute of Technology
| | - Marcus Elstner
- Institute for Physical Chemistry
- Karlsruhe Institute of Technology
- 76131 Karlsruhe
- Germany
| | - Alejandro Toro-Labbé
- QTC
- Facultad de Química
- Pontificia Universidad Católica de Chile
- Millenium Nucleus Chemical Processes and Catalysis (CPC)
- Chile
| | - Esteban Vöhringer-Martinez
- Departamento de Físico-Química
- Facultad de Ciencias Químicas
- Universidad de Concepción
- Millenium Nucleus Chemical Processes and Catalysis (CPC)
- Chile
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