1
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Hwang W, Austin SL, Blondel A, Boittier ED, Boresch S, Buck M, Buckner J, Caflisch A, Chang HT, Cheng X, Choi YK, Chu JW, Crowley MF, Cui Q, Damjanovic A, Deng Y, Devereux M, Ding X, Feig MF, Gao J, Glowacki DR, Gonzales JE, Hamaneh MB, Harder ED, Hayes RL, Huang J, Huang Y, Hudson PS, Im W, Islam SM, Jiang W, Jones MR, Käser S, Kearns FL, Kern NR, Klauda JB, Lazaridis T, Lee J, Lemkul JA, Liu X, Luo Y, MacKerell AD, Major DT, Meuwly M, Nam K, Nilsson L, Ovchinnikov V, Paci E, Park S, Pastor RW, Pittman AR, Post CB, Prasad S, Pu J, Qi Y, Rathinavelan T, Roe DR, Roux B, Rowley CN, Shen J, Simmonett AC, Sodt AJ, Töpfer K, Upadhyay M, van der Vaart A, Vazquez-Salazar LI, Venable RM, Warrensford LC, Woodcock HL, Wu Y, Brooks CL, Brooks BR, Karplus M. CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed. J Phys Chem B 2024. [PMID: 39303207 DOI: 10.1021/acs.jpcb.4c04100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2024]
Abstract
Since its inception nearly a half century ago, CHARMM has been playing a central role in computational biochemistry and biophysics. Commensurate with the developments in experimental research and advances in computer hardware, the range of methods and applicability of CHARMM have also grown. This review summarizes major developments that occurred after 2009 when the last review of CHARMM was published. They include the following: new faster simulation engines, accessible user interfaces for convenient workflows, and a vast array of simulation and analysis methods that encompass quantum mechanical, atomistic, and coarse-grained levels, as well as extensive coverage of force fields. In addition to providing the current snapshot of the CHARMM development, this review may serve as a starting point for exploring relevant theories and computational methods for tackling contemporary and emerging problems in biomolecular systems. CHARMM is freely available for academic and nonprofit research at https://academiccharmm.org/program.
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Affiliation(s)
- Wonmuk Hwang
- Department of Biomedical Engineering, Texas A&M University, College Station, Texas 77843, United States
- Department of Materials Science and Engineering, Texas A&M University, College Station, Texas 77843, United States
- Department of Physics and Astronomy, Texas A&M University, College Station, Texas 77843, United States
- Center for AI and Natural Sciences, Korea Institute for Advanced Study, Seoul 02455, Republic of Korea
| | - Steven L Austin
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Arnaud Blondel
- Institut Pasteur, Université Paris Cité, CNRS UMR3825, Structural Bioinformatics Unit, 28 rue du Dr. Roux F-75015 Paris, France
| | - Eric D Boittier
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Stefan Boresch
- Faculty of Chemistry, Department of Computational Biological Chemistry, University of Vienna, Wahringerstrasse 17, 1090 Vienna, Austria
| | - Matthias Buck
- Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, Cleveland, Ohio 44106, United States
| | - Joshua Buckner
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zürich, CH-8057 Zürich, Switzerland
| | - Hao-Ting Chang
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan, ROC
| | - Xi Cheng
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yeol Kyo Choi
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Jhih-Wei Chu
- Institute of Bioinformatics and Systems Biology, Department of Biological Science and Technology, Institute of Molecular Medicine and Bioengineering, and Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan, ROC
| | - Michael F Crowley
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Qiang Cui
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
- Department of Physics, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, Massachusetts 02215, United States
| | - Ana Damjanovic
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Physics and Astronomy, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Yuqing Deng
- Shanghai R&D Center, DP Technology, Ltd., Shanghai 201210, China
| | - Mike Devereux
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Xinqiang Ding
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Michael F Feig
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
| | - Jiali Gao
- School of Chemical Biology & Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, Guangdong 518055, China
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, Guangdong 518055, China
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - David R Glowacki
- CiTIUS Centro Singular de Investigación en Tecnoloxías Intelixentes da USC, 15705 Santiago de Compostela, Spain
| | - James E Gonzales
- Department of Biomedical Engineering, Texas A&M University, College Station, Texas 77843, United States
- Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Mehdi Bagerhi Hamaneh
- Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, Cleveland, Ohio 44106, United States
| | | | - Ryan L Hayes
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, California 92697, United States
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, California 92697, United States
| | - Jing Huang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China
| | - Yandong Huang
- College of Computer Engineering, Jimei University, Xiamen 361021, China
| | - Phillip S Hudson
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
- Medicine Design, Pfizer Inc., Cambridge, Massachusetts 02139, United States
| | - Wonpil Im
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Shahidul M Islam
- Department of Chemistry, Delaware State University, Dover, Delaware 19901, United States
| | - Wei Jiang
- Computational Science Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Michael R Jones
- Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Silvan Käser
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Fiona L Kearns
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Nathan R Kern
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Jeffery B Klauda
- Department of Chemical and Biomolecular Engineering, Institute for Physical Science and Technology, Biophysics Program, University of Maryland, College Park, Maryland 20742, United States
| | - Themis Lazaridis
- Department of Chemistry, City College of New York, New York, New York 10031, United States
| | - Jinhyuk Lee
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
- Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34141, Republic of Korea
| | - Justin A Lemkul
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| | - Xiaorong Liu
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Yun Luo
- Department of Biotechnology and Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, Pomona, California 91766, United States
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
| | - Dan T Major
- Department of Chemistry and Institute for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Kwangho Nam
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas 76019, United States
| | - Lennart Nilsson
- Karolinska Institutet, Department of Biosciences and Nutrition, SE-14183 Huddinge, Sweden
| | - Victor Ovchinnikov
- Harvard University, Department of Chemistry and Chemical Biology, Cambridge, Massachusetts 02138, United States
| | - Emanuele Paci
- Dipartimento di Fisica e Astronomia, Universitá di Bologna, Bologna 40127, Italy
| | - Soohyung Park
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Amanda R Pittman
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Carol Beth Post
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Samarjeet Prasad
- Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Jingzhi Pu
- Department of Chemistry and Chemical Biology, Indiana University Indianapolis, Indianapolis, Indiana 46202, United States
| | - Yifei Qi
- School of Pharmacy, Fudan University, Shanghai 201203, China
| | | | - Daniel R Roe
- Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Benoit Roux
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | | | - Jana Shen
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
| | - Andrew C Simmonett
- Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Alexander J Sodt
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Kai Töpfer
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Meenu Upadhyay
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Arjan van der Vaart
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | | | - Richard M Venable
- Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Luke C Warrensford
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - H Lee Woodcock
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Yujin Wu
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Charles L Brooks
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Martin Karplus
- Harvard University, Department of Chemistry and Chemical Biology, Cambridge, Massachusetts 02138, United States
- Laboratoire de Chimie Biophysique, ISIS, Université de Strasbourg, 67000 Strasbourg, France
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2
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Deng J, Cui Q. Second-Shell Residues Contribute to Catalysis by Predominately Preorganizing the Apo State in PafA. J Am Chem Soc 2023; 145:11333-11347. [PMID: 37172218 PMCID: PMC10810092 DOI: 10.1021/jacs.3c02423] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Residues beyond the first coordination shell are often observed to make considerable cumulative contributions in enzymes. Due to typically indirect perturbations of multiple physicochemical properties of the active site, however, their individual and specific roles in enzyme catalysis and disease-causing mutations remain difficult to predict and understand at the molecular level. Here we analyze the contributions of several second-shell residues in phosphate-irrepressible alkaline phosphatase of flavobacterium (PafA), a representative system as one of the most efficient enzymes. By adopting a multifaceted approach that integrates quantum-mechanical/molecular-mechanical free energy computations, molecular-mechanical molecular dynamics simulations, and density functional theory cluster model calculations, we probe the rate-limiting phosphoryl transfer step and structural properties of all relevant enzyme states. In combination with available experimental data, our computational results show that mutations of the studied second-shell residues impact catalytic efficiency mainly by perturbation of the apo state and therefore substrate binding, while they do not affect the ground state or alter the nature of phosphoryl transfer transition state significantly. Several second-shell mutations also modulate the active site hydration level, which in turn influences the energetics of phosphoryl transfer. These mechanistic insights also help inform strategies that may improve the efficiency of enzyme design and engineering by going beyond the current focus on the first coordination shell.
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Affiliation(s)
- Jiahua Deng
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Qiang Cui
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
- Department of Physics, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, Massachusetts 02215, United States
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3
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Ahmad K, Rizzi A, Capelli R, Mandelli D, Lyu W, Carloni P. Enhanced-Sampling Simulations for the Estimation of Ligand Binding Kinetics: Current Status and Perspective. Front Mol Biosci 2022; 9:899805. [PMID: 35755817 PMCID: PMC9216551 DOI: 10.3389/fmolb.2022.899805] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 05/09/2022] [Indexed: 12/12/2022] Open
Abstract
The dissociation rate (k off) associated with ligand unbinding events from proteins is a parameter of fundamental importance in drug design. Here we review recent major advancements in molecular simulation methodologies for the prediction of k off. Next, we discuss the impact of the potential energy function models on the accuracy of calculated k off values. Finally, we provide a perspective from high-performance computing and machine learning which might help improve such predictions.
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Affiliation(s)
- Katya Ahmad
- Computational Biomedicine (IAS-5/INM-9), Forschungszentrum Jülich, Jülich, Germany
| | - Andrea Rizzi
- Computational Biomedicine (IAS-5/INM-9), Forschungszentrum Jülich, Jülich, Germany
- Atomistic Simulations, Istituto Italiano di Tecnologia, Genova, Italy
| | - Riccardo Capelli
- Department of Applied Science and Technology (DISAT), Politecnico di Torino, Torino, Italy
| | - Davide Mandelli
- Computational Biomedicine (IAS-5/INM-9), Forschungszentrum Jülich, Jülich, Germany
| | - Wenping Lyu
- Warshel Institute for Computational Biology, School of Life and Health Sciences, The Chinese University of Hong Kong (Shenzhen), Shenzhen, China
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, China
| | - Paolo Carloni
- Computational Biomedicine (IAS-5/INM-9), Forschungszentrum Jülich, Jülich, Germany
- Molecular Neuroscience and Neuroimaging (INM-11), Forschungszentrum Jülich, Jülich, Germany
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4
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Demapan D, Kussmann J, Ochsenfeld C, Cui Q. Factors That Determine the Variation of Equilibrium and Kinetic Properties of QM/MM Enzyme Simulations: QM Region, Conformation, and Boundary Condition. J Chem Theory Comput 2022; 18:2530-2542. [PMID: 35226489 PMCID: PMC9652774 DOI: 10.1021/acs.jctc.1c00714] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
To analyze the impact of various technical details on the results of quantum mechanical (QM)/molecular mechanical (MM) enzyme simulations, including the QM region size, catechol-O-methyltransferase (COMT) is studied as a model system using an approximate QM/MM method (DFTB3/CHARMM). The results show that key equilibrium and kinetic properties for methyl transfer in COMT exhibit limited variations with respect to the size of the QM region, which ranges from ∼100 to ∼500 atoms in this study. With extensive sampling, local and global structural characteristics of the enzyme are largely conserved across the studied QM regions, while the nature of the transition state (e.g., secondary kinetic isotope effect) and reaction exergonicity are largely maintained. Deviations in the free energy profile with different QM region sizes are similar in magnitude to those observed with changes in other simulation protocols, such as different initial enzyme conformations and boundary conditions. Electronic structural properties, such as the covariance matrix of residual charge fluctuations, appear to exhibit rather long-range correlations, especially when the peptide backbone is included in the QM region; this observation holds when a range-separated DFT approach is used as the QM region, suggesting that delocalization error is unlikely the origin. Overall, the analyses suggest that multiple simulation details determine the results of QM/MM enzyme simulations with comparable contributions.
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Affiliation(s)
- Darren Demapan
- Department of Chemistry, University of Munich (LMU), Butenandtstr. 7 (C), D-81377 Munich, Germany.,Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Jörg Kussmann
- Department of Chemistry, University of Munich (LMU), Butenandtstr. 7 (C), D-81377 Munich, Germany
| | - Christian Ochsenfeld
- Department of Chemistry, University of Munich (LMU), Butenandtstr. 7 (C), D-81377 Munich, Germany
| | - Qiang Cui
- Departments of Chemistry, Physics and Biomedical Engineering, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
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5
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Monitoring protein conformational changes using fluorescent nanoantennas. Nat Methods 2022; 19:71-80. [PMID: 34969985 DOI: 10.1038/s41592-021-01355-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 11/10/2021] [Indexed: 01/03/2023]
Abstract
Understanding the relationship between protein structural dynamics and function is crucial for both basic research and biotechnology. However, methods for studying the fast dynamics of structural changes are limited. Here, we introduce fluorescent nanoantennas as a spectroscopic technique to sense and report protein conformational changes through noncovalent dye-protein interactions. Using experiments and molecular simulations, we detect and characterize five distinct conformational states of intestinal alkaline phosphatase, including the transient enzyme-substrate complex. We also explored the universality of the nanoantenna strategy with another model protein, Protein G and its interaction with antibodies, and demonstrated a rapid screening strategy to identify efficient nanoantennas. These versatile nanoantennas can be used with diverse dyes to monitor small and large conformational changes, suggesting that they could be used to characterize diverse protein movements or in high-throughput screening applications.
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6
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Abstract
Machine learning (ML) techniques applied to chemical reactions have a long history. The present contribution discusses applications ranging from small molecule reaction dynamics to computational platforms for reaction planning. ML-based techniques can be particularly relevant for problems involving both computation and experiments. For one, Bayesian inference is a powerful approach to develop models consistent with knowledge from experiments. Second, ML-based methods can also be used to handle problems that are formally intractable using conventional approaches, such as exhaustive characterization of state-to-state information in reactive collisions. Finally, the explicit simulation of reactive networks as they occur in combustion has become possible using machine-learned neural network potentials. This review provides an overview of the questions that can and have been addressed using machine learning techniques, and an outlook discusses challenges in this diverse and stimulating field. It is concluded that ML applied to chemistry problems as practiced and conceived today has the potential to transform the way with which the field approaches problems involving chemical reactions, in both research and academic teaching.
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Affiliation(s)
- Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland.,Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
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7
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Structures of an engineered phospholipase D with specificity for secondary alcohol transphosphatidylation: insights into plasticity of substrate binding and activation. Biochem J 2021; 478:1749-1767. [PMID: 33843991 PMCID: PMC8133832 DOI: 10.1042/bcj20210117] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/06/2021] [Accepted: 04/09/2021] [Indexed: 11/17/2022]
Abstract
Phospholipase D (PLD) is an enzyme useful for the enzymatic modification of phospholipids. In the presence of primary alcohols, the enzyme catalyses transphosphatidylation of the head group of phospholipid substrates to synthesise a modified phospholipid product. However, the enzyme is specific for primary alcohols and thus the limitation of the molecular size of the acceptor compounds has restricted the type of phospholipid species that can be synthesised. An engineered variant of PLD from Streptomyces antibioticus termed TNYR SaPLD was developed capable of synthesising 1-phosphatidylinositol with positional specificity of up to 98%. To gain a better understanding of the substrate binding features of the TNYR SaPLD, crystal structures have been determined for the free enzyme and its complexes with phosphate, phosphatidic acid and 1-inositol phosphate. Comparisons of these structures with the wild-type SaPLD show a larger binding site able to accommodate a bulkier secondary alcohol substrate as well as changes to the position of a flexible surface loop proposed to be involved in substrate recognition. The complex of the active TNYR SaPLD with 1-inositol phosphate reveals a covalent intermediate adduct with the ligand bound to H442 rather than to H168, the proposed nucleophile in the wild-type enzyme. This structural feature suggests that the enzyme exhibits plasticity of the catalytic mechanism different from what has been reported to date for PLDs. These structural studies provide insights into the underlying mechanism that governs the recognition of myo-inositol by TNYR SaPLD, and an important foundation for further studies of the catalytic mechanism.
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8
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Recabarren R, Zinovjev K, Tuñón I, Alzate-Morales J. How a Second Mg 2+ Ion Affects the Phosphoryl-Transfer Mechanism in a Protein Kinase: A Computational Study. ACS Catal 2020. [DOI: 10.1021/acscatal.0c03304] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Rodrigo Recabarren
- Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingeniería, Universidad de Talca, 1 Poniente, 1141 Talca, Chile
| | - Kirill Zinovjev
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, U.K
| | - Iñaki Tuñón
- Departament de Química Física, Universitat de València, Valencia 46010, Spain
| | - Jans Alzate-Morales
- Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingeniería, Universidad de Talca, 1 Poniente, 1141 Talca, Chile
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9
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Borosky GL. Alkaline Phosphatases: in Silico Study on the Catalytic Effect of Conserved Active Site Residues Using Human Placental Alkaline Phosphatase (PLAP) As a Model Protein. J Chem Inf Model 2020; 60:6228-6241. [PMID: 33306371 DOI: 10.1021/acs.jcim.0c00860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The metalloenzymes from the alkaline phosphatase (AP) superfamily catalyze the hydrolysis and transphosphorylation of phosphate monoesters. The role of several amino acids highly conserved in the active site of this family of enzymes was examined, using human placental AP (PLAP) as a model protein. By employing an active-site model based on the X-ray crystal structure of PLAP, mutations of several key residues were modeled by quantum mechanical methods in order to determine their impact on the catalytic activity. Kinetic and thermodynamic estimations were achieved for each reaction step of the catalytic mechanism by characterization of the intermediates and transition states on the reaction pathway, and the effects of mutations on the activation barriers were analyzed. A good accordance was observed between the present computational results and experimental measurements reported in the literature.
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Affiliation(s)
- Gabriela L Borosky
- INFIQC, CONICET and Departamento de Química Teórica y Computacional, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, Córdoba 5000, Argentina
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10
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Lai R, Cui Q. What Does the Brønsted Slope Measure in the Phosphoryl Transfer Transition State? ACS Catal 2020; 10:13932-13945. [PMID: 34567831 DOI: 10.1021/acscatal.0c03764] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The structural and energetic features of phosphate and phosphonate hydrolysis in Protein Phosphatase-1 (PP1) and water are studied using quantum mechanical (QM) cluster models. The calculations are able to reproduce observed kinetic isotope effects and capture several key trends in the experimental Brønsted plots: the β l g values are rather different for phosphate and phosphonate ester hydrolysis in solution but are similar in PP1. Detailed analyses of structure, charge distribution and bond order of computed transition states support the general conclusion from experimental study that phosphoryl transfer transition states are different for the two classes of substrates in solution but similar in PP1. On the other hand, the microscopic models also highlight notable differences between the phosphate and phosphonate transition states, which are manifested in not only structure but also kinetic isotope effects. Overall, we find that while β l g / β E Q , l g generally correlates with the partial charge on leaving group oxygen and the fractional bond order of the breaking P- O l g bond, the precise mapping between β l g / β E Q , l g and P- O l g bond order in the transition state is difficult due largely to the cross talk between breaking and forming P-O bonds. Therefore, further supporting previous analyses of limitations of free energy relations, our results suggest that while free energy relation is a valuable tool for probing the nature of transition state, a quantitative mapping of β l g and β l g / β E Q , l g values to structure or charge in the transition state should be conducted with great care.
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Affiliation(s)
- Rui Lai
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, MA 02215
| | - Qiang Cui
- Departments of Chemistry, Physics and Biomedical Engineering, Boston University, 590 Commonwealth Avenue, Boston, MA 02215
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11
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Lai R, Cui Q. Differences in the Nature of the Phosphoryl Transfer Transition State in Protein Phosphatase 1 and Alkaline Phosphatase: Insights from QM Cluster Models. J Phys Chem B 2020; 124:9371-9384. [PMID: 33030898 PMCID: PMC7647665 DOI: 10.1021/acs.jpcb.0c07863] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Quantum mechanical (QM) cluster models are used to probe effects on the catalytic properties of protein phosphatase 1 (PP1) and alkaline phosphatase (AP) due to metal ions and active site residues. The calculations suggest that the phosphoryl transfer transition states in PP1 are synchronous in nature with a significant degree of P-Olg cleavage, while those in AP are tighter with a modest degree of P-Olg cleavage and a range of P-Onuc formation. Similar to observations made in our recent work, a significant degree of cross talk between the forming and breaking P-O bonds complicates the interpretation of the Brønsted relation, especially in regard to AP for which the computed βlg/βEQ,lg value does not correlate with the degree of P-Olg cleavage regardless of the metal ions in the active site. By comparison, the correlation between βlg/βEQ,lg and the P-Olg bond order is more applicable to PP1, which generally exhibits less variation in the transition state than AP. Results for computational models with swapped metal ions between PP1 and AP suggest that the metal ions modulate both the nature of the transition state and the degrees of sensitivity of the transition state to the leaving group. In the reactant state, the degree of the scissile bond polarization is also different in the two enzymes, although this difference appears to be largely determined by the active site residues rather than the metal ions. Therefore, both the identity of the metal ion and the positioning of polar or charged residues in the active site contribute to the distinct catalytic characteristics of these enzymes. Several discrepancies observed between the QM cluster results and the available experimental data highlight the need for further QM/MM method developments for the quantitative analysis of metalloenzymes that contain open-shell transition metal ions.
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Affiliation(s)
- Rui Lai
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Qiang Cui
- Departments of Chemistry, Physics, and Biomedical Engineering, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
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12
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Cheng R, Wu L, Lai R, Peng C, Naowarojna N, Hu W, Li X, Whelan SA, Lee N, Lopez J, Zhao C, Yong Y, Xue J, Jiang X, Grinstaff MW, Deng Z, Chen J, Cui Q, Zhou J, Liu P. Single-step Replacement of an Unreactive C-H Bond by a C-S Bond Using Polysulfide as the Direct Sulfur Source in Anaerobic Ergothioneine Biosynthesis. ACS Catal 2020; 10:8981-8994. [PMID: 34306804 DOI: 10.1021/acscatal.0c01809] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Ergothioneine, a natural longevity vitamin and antioxidant, is a thiol-histidine derivative. Recently, two types of biosynthetic pathways were reported. In the aerobic ergothioneine biosynthesis, a non-heme iron enzyme incorporates a sulfoxide to an sp2 C-H bond in trimethyl-histidine (hercynine) through oxidation reactions. In contrast, in the anaerobic ergothioneine biosynthetic pathway in a green sulfur bacterium, Chlorobium limicola, a rhodanese domain containing protein (EanB) directly replaces this unreactive hercynine C-H bond with a C-S bond. Herein, we demonstrate that polysulfide (HSSnSR) is the direct sulfur-source in EanB-catalysis. After identifying EanB's substrates, X-ray crystallography of several intermediate states along with mass spectrometry results provide additional mechanistic details for this reaction. Further, quantum mechanics/molecular mechanics (QM/MM) calculations reveal that protonation of Nπ of hercynine by Tyr353 with the assistance of Thr414 is a key activation step for the hercynine sp2 C-H bond in this trans-sulfuration reaction.
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Affiliation(s)
- Ronghai Cheng
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Lian Wu
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai 200032, China
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Shanghai 200032, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rui Lai
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Chao Peng
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Science, Shanghai 201210, China
| | - Nathchar Naowarojna
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Weiyao Hu
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xinhao Li
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Stephen A. Whelan
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Norman Lee
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Juan Lopez
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Changming Zhao
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Hubei 430072, China
| | - Youhua Yong
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Jiahui Xue
- Shanghai Key Laboratory of Green Chemistry and Chemical Process, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China
| | - Xuefeng Jiang
- Shanghai Key Laboratory of Green Chemistry and Chemical Process, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China
| | - Mark W. Grinstaff
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Zixin Deng
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Hubei 430072, China
| | - Jiesheng Chen
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qiang Cui
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Jiahai Zhou
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Pinghua Liu
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
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13
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Zhao Y, Dong H, Ren J, Song J, Yao J, Gao J, Jiang CS, Wang X. One- and Two-Proton Transfer Mechanisms Coexist in One Active Site. J Phys Chem B 2020; 124:6699-6708. [PMID: 32663399 DOI: 10.1021/acs.jpcb.0c04445] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Acibenzolar-S-methyl (ASM) is one of the most successfully commercialized plant activators of the systemic acquired resistance (SAR). However, its activation (hydrolysis) mechanism catalyzed by the salicylic acid binding protein 2 (SABP2) remains elusive. The fundamental catalytic mechanism of the SABP2-catalyzed hydrolysis of the ASM had been investigated by extensive computational and experimental studies, including QM/MM simulations, charge transfer analysis, small-molecule synthesis, and biochemical assays. Here we report that the promiscuous SABP2 shows different catalytic mechanisms toward different substrates. To catalyze the ASM hydrolysis, the SABP2 uses a two-proton transfer mechanism, and the key intermediate is stabilized by the charge transfer effect; to catalyze the ethyl 1,2,3-benzothiadiazole-7-carboxylate (BTM, an ASM analogue) hydrolysis, the SABP2 applies the one-proton transfer mechanism, and the classic tetrahedral intermediate is stabilized by the electrostatic effect. The HPLC analyses of the SABP2 esterase activities toward the ASM and the BTM show comparable results with our computaional results, suggesting that the obtained computational mechanism insights are reasonable. The obtained mechanism is not only an important supplement to the theory of enzymes' catalytic promiscuity, but it also contributes a possible strategy for the design of next generation plant SAR activators.
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Affiliation(s)
- Yueqi Zhao
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China
| | - Huaikun Dong
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China
| | - Jing Ren
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China
| | - Jiali Song
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China
| | - Jianzhuang Yao
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China
| | - Juan Gao
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China
| | - Cheng-Shi Jiang
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China
| | - Xia Wang
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China
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14
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Chen H, Snurr RQ. Insights into Catalytic Gas-Phase Hydrolysis of Organophosphate Chemical Warfare Agents by MOF-Supported Bimetallic Metal-Oxo Clusters. ACS APPLIED MATERIALS & INTERFACES 2020; 12:14631-14640. [PMID: 31909586 DOI: 10.1021/acsami.9b19484] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Zirconium-based metal-organic frameworks (Zr-MOFs) have been reported to be efficient catalysts for the hydrolysis of organophosphate chemical warfare agents (CWAs) in buffered solutions. However, for the gas-phase reaction, which is more relevant to the situation in a battlefield gas mask application, the kinetics of Zr-MOF catalysts may be severely hindered by strong product inhibition. To improve the catalytic performance, we computationally screened a series of synthetically accessible Zr-MOF-supported bimetallic metal-oxo clusters in which the metal-oxygen-metal active motif is preserved, aiming to find catalysts that have lower binding affinities to the hydrolysis product. For the promising catalyst Al2O2(OH)2@NU-1000 identified from the screening using density functional theory, we mapped out the full reaction pathway of gas-phase dimethyl p-nitrophenolphosphate (DMNP) hydrolysis and analyzed the free energy profile as well as the turnover frequency (TOF). We found that the catalytic mechanism on the new catalyst is slightly different from the one on NU-1000, which also led to a different TOF-limiting step. Additional factors that can affect the overall catalytic performance in practical application, such as the amount of ambient moisture and the existence of acid gases that may poison the catalyst, have also been evaluated.
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Affiliation(s)
- Haoyuan Chen
- Department of Chemical & Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Randall Q Snurr
- Department of Chemical & Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
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15
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Unke OT, Koner D, Patra S, Käser S, Meuwly M. High-dimensional potential energy surfaces for molecular simulations: from empiricism to machine learning. MACHINE LEARNING-SCIENCE AND TECHNOLOGY 2020. [DOI: 10.1088/2632-2153/ab5922] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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16
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Roston D, Demapan D, Cui Q. Extensive free-energy simulations identify water as the base in nucleotide addition by DNA polymerase. Proc Natl Acad Sci U S A 2019; 116:25048-25056. [PMID: 31757846 PMCID: PMC6911213 DOI: 10.1073/pnas.1914613116] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Transphosphorylation of nucleotide triphosphates is the central reaction in DNA replication by DNA polymerase as well as many other biological processes. Despite its importance, the microscopic chemical mechanism of transphosphorylation of nucleotide triphosphates is, in most cases, unknown. Here we use extensive simulations of DNA polymerase η to test mechanistic hypotheses. We systematically survey the reactive space by calculating 2D free-energy surfaces for 10 different plausible mechanisms that have been proposed. We supplement these free-energy surfaces with calculations of pKa for a number of potentially acidic protons in different states relevant to the catalytic cycle. We find that among all of the conditions that we test, the smallest activation barrier occurs for a reaction where a Mg2+-coordinated water deprotonates the nucleophilic 3'-OH, and this deprotonation is concerted with the phosphoryl transfer. The presence of a third Mg2+ in the active site lowers the activation barrier for the water-as-base mechanism, as does protonation of the pyrophosphate leaving group, which is consistent with general acid catalysis. The results demonstrate the value of simulations, when used in conjunction with experimental data, to help establish a microscopic chemical mechanism in a complex environment.
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Affiliation(s)
- Daniel Roston
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093;
| | - Darren Demapan
- Department of Chemistry, Boston University, Boston, MA 02215
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Qiang Cui
- Department of Chemistry, Boston University, Boston, MA 02215;
- Department of Physics, Boston University, Boston, MA 02215
- Department of Biomedical Engineering, Boston University, Boston, MA 02215
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17
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Recabarren R, Osorio EH, Caballero J, Tuñón I, Alzate-Morales JH. Mechanistic insights into the phosphoryl transfer reaction in cyclin-dependent kinase 2: A QM/MM study. PLoS One 2019; 14:e0215793. [PMID: 31483779 PMCID: PMC6726203 DOI: 10.1371/journal.pone.0215793] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 08/19/2019] [Indexed: 12/18/2022] Open
Abstract
Cyclin-dependent kinase 2 (CDK2) is an important member of the CDK family exerting its most important function in the regulation of the cell cycle. It catalyzes the transfer of the gamma phosphate group from an ATP (adenosine triphosphate) molecule to a Serine/Threonine residue of a peptide substrate. Due to the importance of this enzyme, and protein kinases in general, a detailed understanding of the reaction mechanism is desired. Thus, in this work the phosphoryl transfer reaction catalyzed by CDK2 was revisited and studied by means of hybrid quantum mechanics/molecular mechanics (QM/MM) calculations. Our results suggest that the base-assisted mechanism is preferred over the substrate-assisted pathway when one Mg2+ is present in the active site, in agreement with a previous theoretical study. The base-assisted mechanism resulted to be dissociative, with a potential energy barrier of 14.3 kcal/mol, very close to the experimental derived value. An interesting feature of the mechanism is the proton transfer from Lys129 to the phosphoryl group at the second transition state, event that could be helping in neutralizing the charge on the phosphoryl group upon the absence of a second Mg2+ ion. Furthermore, important insights into the mechanisms in terms of bond order and charge analysis were provided. These descriptors helped to characterize the synchronicity of bond forming and breaking events, and to characterize charge transfer effects. Local interactions at the active site are key to modulate the charge distribution on the phosphoryl group and therefore alter its reactivity.
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Affiliation(s)
- Rodrigo Recabarren
- Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingeniería, Universidad de Talca, Talca, Chile
| | - Edison H. Osorio
- Facultad de Ciencias Naturales y Matemáticas, Universidad de Ibagué, Ibagué, Colombia
| | - Julio Caballero
- Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingeniería, Universidad de Talca, Talca, Chile
| | - Iñaki Tuñón
- Departament de Química Física, Universitat de Valencia, Valencia, Spain
- * E-mail: (JAM); (IT)
| | - Jans H. Alzate-Morales
- Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingeniería, Universidad de Talca, Talca, Chile
- * E-mail: (JAM); (IT)
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18
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Chen D, Zhao M, Tan W, Li Y, Li X, Li Y, Fan X. Effects of intramolecular hydrogen bonds on lipophilicity. Eur J Pharm Sci 2019; 130:100-106. [DOI: 10.1016/j.ejps.2019.01.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 01/08/2019] [Accepted: 01/18/2019] [Indexed: 12/22/2022]
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19
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Wang X, Bakanina Kissanga GM, Li E, Li Q, Yao J. The catalytic mechanism of S-acyltransferases: acylation is triggered on by a loose transition state and deacylation is turned off by a tight transition state. Phys Chem Chem Phys 2019; 21:12163-12172. [DOI: 10.1039/c9cp02248a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The reaction of S-acyltransferase is characterized by a loose transition state.
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Affiliation(s)
- Xia Wang
- School of Biological Science and Technology
- University of Jinan
- Jinan 250022
- China
| | | | - E. Li
- School of Biological Science and Technology
- University of Jinan
- Jinan 250022
- China
| | - Qiang Li
- School of Biological Science and Technology
- University of Jinan
- Jinan 250022
- China
| | - Jianzhuang Yao
- School of Biological Science and Technology
- University of Jinan
- Jinan 250022
- China
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20
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Two symmetric arginine residues play distinct roles in Thermus thermophilus Argonaute DNA guide strand-mediated DNA target cleavage. Proc Natl Acad Sci U S A 2018; 116:845-853. [PMID: 30591565 DOI: 10.1073/pnas.1817041116] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Bacterium Thermus thermophilus Argonaute (Ago; TtAgo) is a prokaryotic Ago (pAgo) that acts as the host defense against the uptake and propagation of foreign DNA by catalyzing the DNA cleavage reaction. The TtAgo active site consists of a plugged-in glutamate finger with two arginine residues (R545 and R486) located symmetrically around it. An interesting challenge is to understand how they can collaboratively facilitate enzymatic catalysis. In Kluyveromyces polysporus Ago, a eukaryotic Ago, the evolutionarily symmetrical residues are arginine and histidine, both of which function to stabilize the plugged-in catalytic tetrad conformation. Surprisingly, our simulation results indicated that, in TtAgo, only R545 is involved in the cleavage reaction by serving as a critical structural anchor to stabilize the catalytic tetrad Asp-Glu-Asp-Asp that is completed by the insertion of the glutamate finger, whereas R486 is not involved in target cleavage. The TtAgo-mediated target DNA cleavage occurs in a substrate-assisted mechanism, in which the pro-Rp (Rp, a tetrahedral phosphorus center with "R-type" chirality) oxygen of scissile phosphate acts as a general base to activate the nucleophilic water. Our unexpected theoretical findings on distinct roles played by R545 and R486 in TtAgo catalysis have been validated by single-point site-mutagenesis experiments, wherein the target cleavage is abolished for all mutants of R545. In sharp contrast, the cleavage activity is maintained for all mutants of R486. Our work provides mechanistic insights on the catalytic specificity of Ago proteins and could facilitate the design of new gene-editing tools in the long term.
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21
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Nomura Y, Roston D, Montemayor EJ, Cui Q, Butcher SE. Structural and mechanistic basis for preferential deadenylation of U6 snRNA by Usb1. Nucleic Acids Res 2018; 46:11488-11501. [PMID: 30215753 PMCID: PMC6265477 DOI: 10.1093/nar/gky812] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 08/27/2018] [Accepted: 08/29/2018] [Indexed: 01/08/2023] Open
Abstract
Post-transcriptional modification of snRNA is central to spliceosome function. Usb1 is an exoribonuclease that shortens the oligo-uridine tail of U6 snRNA, resulting in a terminal 2',3' cyclic phosphate group in most eukaryotes, including humans. Loss of function mutations in human Usb1 cause the rare disorder poikiloderma with neutropenia (PN), and result in U6 snRNAs with elongated 3' ends that are aberrantly adenylated. Here, we show that human Usb1 removes 3' adenosines with 20-fold greater efficiency than uridines, which explains the presence of adenylated U6 snRNAs in cells lacking Usb1. We determined three high-resolution co-crystal structures of Usb1: wild-type Usb1 bound to the substrate analog adenosine 5'-monophosphate, and an inactive mutant bound to RNAs with a 3' terminal adenosine and uridine. These structures, along with QM/MM MD simulations of the catalytic mechanism, illuminate the molecular basis for preferential deadenylation of U6 snRNA. The extent of Usb1 processing is influenced by the secondary structure of U6 snRNA.
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Affiliation(s)
- Yuichiro Nomura
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Daniel Roston
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
- Department of Chemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Eric J Montemayor
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Qiang Cui
- Department of Chemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Samuel E Butcher
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
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22
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Meuwly M. Reactive molecular dynamics: From small molecules to proteins. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2018. [DOI: 10.1002/wcms.1386] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Markus Meuwly
- Department of Chemistry University of Basel Basel Switzerland
- Department of Chemistry Brown University Providence Rhode Island
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23
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Roston D, Lu X, Fang D, Demapan D, Cui Q. Analysis of Phosphoryl-Transfer Enzymes with QM/MM Free Energy Simulations. Methods Enzymol 2018; 607:53-90. [PMID: 30149869 DOI: 10.1016/bs.mie.2018.05.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We discuss the application of quantum mechanics/molecular mechanics (QM/MM) free energy simulations to the analysis of phosphoryl transfers catalyzed by two enzymes: alkaline phosphatase and myosin. We focus on the nature of the transition state and the issue of mechanochemical coupling, respectively, in the two enzymes. The results illustrate unique insights that emerged from the QM/MM simulations, especially concerning the interpretation of experimental data regarding the nature of enzymatic transition states and coupling between global structural transition and catalysis in the active site. We also highlight a number of technical issues worthy of attention when applying QM/MM free energy simulations, and comment on a number of technical and mechanistic issues that require further studies.
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Affiliation(s)
- Daniel Roston
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, Madison, WI, United States
| | - Xiya Lu
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, Madison, WI, United States
| | - Dong Fang
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, Madison, WI, United States
| | - Darren Demapan
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, Madison, WI, United States
| | - Qiang Cui
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, Madison, WI, United States.
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24
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Petrović D, Szeler K, Kamerlin SCL. Challenges and advances in the computational modeling of biological phosphate hydrolysis. Chem Commun (Camb) 2018; 54:3077-3089. [PMID: 29412205 DOI: 10.1039/c7cc09504j] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Phosphate ester hydrolysis is fundamental to many life processes, and has been the topic of substantial experimental and computational research effort. However, even the simplest of phosphate esters can be hydrolyzed through multiple possible pathways that can be difficult to distinguish between, either experimentally, or computationally. Therefore, the mechanisms of both the enzymatic and non-enzymatic reactions have been historically controversial. In the present contribution, we highlight a number of technical issues involved in reliably modeling these computationally challenging reactions, as well as proposing potential solutions. We also showcase examples of our own work in this area, discussing both the non-enzymatic reaction in aqueous solution, as well as insights obtained from the computational modeling of organophosphate hydrolysis and catalytic promiscuity amongst enzymes that catalyze phosphoryl transfer.
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Affiliation(s)
- Dušan Petrović
- Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden.
| | - Klaudia Szeler
- Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden.
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25
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Brás NF, Fernandes PA, Ramos MJ, Schwartz SD. Mechanistic Insights on Human Phosphoglucomutase Revealed by Transition Path Sampling and Molecular Dynamics Calculations. Chemistry 2018; 24:1978-1987. [PMID: 29131453 DOI: 10.1002/chem.201705090] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Indexed: 12/27/2022]
Abstract
Human α-phosphoglucomutase 1 (α-PGM) catalyzes the isomerization of glucose-1-phosphate into glucose-6-phosphate (G6P) through two sequential phosphoryl transfer steps with a glucose-1,6-bisphosphate (G16P) intermediate. Given that the release of G6P in the gluconeogenesis raises the glucose output levels, α-PGM represents a tempting pharmacological target for type 2 diabetes. Here, we provide the first theoretical study of the catalytic mechanism of human α-PGM. We performed transition-path sampling simulations to unveil the atomic details of the two catalytic chemical steps, which could be key for developing transition state (TS) analogue molecules with inhibitory properties. Our calculations revealed that both steps proceed through a concerted SN 2-like mechanism, with a loose metaphosphate-like TS. Even though experimental data suggests that the two steps are identical, we observed noticeable differences: 1) the transition state ensemble has a well-defined TS region and a late TS for the second step, and 2) larger coordinated protein motions are required to reach the TS of the second step. We have identified key residues (Arg23, Ser117, His118, Lys389), and the Mg2+ ion that contribute in different ways to the reaction coordinate. Accelerated molecular dynamics simulations suggest that the G16P intermediate may reorient without leaving the enzymatic binding pocket, through significant conformational rearrangements of the G16P and of specific loop regions of the human α-PGM.
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Affiliation(s)
- Natércia F Brás
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007, Porto, Portugal.,Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, Arizona, 85721, USA
| | - Pedro A Fernandes
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007, Porto, Portugal
| | - Maria J Ramos
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007, Porto, Portugal
| | - Steven D Schwartz
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, Arizona, 85721, USA
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26
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Purg M, Kamerlin SCL. Empirical Valence Bond Simulations of Organophosphate Hydrolysis: Theory and Practice. Methods Enzymol 2018; 607:3-51. [DOI: 10.1016/bs.mie.2018.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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27
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Wang LP, McKiernan KA, Gomes J, Beauchamp KA, Head-Gordon T, Rice JE, Swope WC, Martínez TJ, Pande VS. Building a More Predictive Protein Force Field: A Systematic and Reproducible Route to AMBER-FB15. J Phys Chem B 2017; 121:4023-4039. [PMID: 28306259 PMCID: PMC9724927 DOI: 10.1021/acs.jpcb.7b02320] [Citation(s) in RCA: 166] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The increasing availability of high-quality experimental data and first-principles calculations creates opportunities for developing more accurate empirical force fields for simulation of proteins. We developed the AMBER-FB15 protein force field by building a high-quality quantum chemical data set consisting of comprehensive potential energy scans and employing the ForceBalance software package for parameter optimization. The optimized potential surface allows for more significant thermodynamic fluctuations away from local minima. In validation studies where simulation results are compared to experimental measurements, AMBER-FB15 in combination with the updated TIP3P-FB water model predicts equilibrium properties with equivalent accuracy, and temperature dependent properties with significantly improved accuracy, in comparison with published models. We also discuss the effect of changing the protein force field and water model on the simulation results.
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Affiliation(s)
- Lee-Ping Wang
- Department of Chemistry, University of California, Davis , Davis, California 95616, United States
| | - Keri A McKiernan
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Joseph Gomes
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Kyle A Beauchamp
- Counsyl, Inc. , South San Francisco, California 94080, United States
| | - Teresa Head-Gordon
- Departments of Chemistry, Bioengineering, Chemical and Biomolecular Engineering, and Kenneth S. Pitzer Center for Theoretical Chemistry, University of California, Berkeley , Berkeley, California 94720, United States
- Chemical Sciences Division, Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Julia E Rice
- IBM Almaden Research Center, IBM Research , San Jose, California 95120, United States
| | - William C Swope
- IBM Almaden Research Center, IBM Research , San Jose, California 95120, United States
| | - Todd J Martínez
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
- PULSE Institute, Stanford University , Stanford, California 94305, United States
- SLAC National Accelerator Laboratory , Menlo Park, California 94025, United States
| | - Vijay S Pande
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
- Departments of Computer Science, Structural Biology, and Program in Biophysics, Stanford University , Stanford, California 94305, United States
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28
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Cui Q. Perspective: Quantum mechanical methods in biochemistry and biophysics. J Chem Phys 2017; 145:140901. [PMID: 27782516 DOI: 10.1063/1.4964410] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
In this perspective article, I discuss several research topics relevant to quantum mechanical (QM) methods in biophysical and biochemical applications. Due to the immense complexity of biological problems, the key is to develop methods that are able to strike the proper balance of computational efficiency and accuracy for the problem of interest. Therefore, in addition to the development of novel ab initio and density functional theory based QM methods for the study of reactive events that involve complex motifs such as transition metal clusters in metalloenzymes, it is equally important to develop inexpensive QM methods and advanced classical or quantal force fields to describe different physicochemical properties of biomolecules and their behaviors in complex environments. Maintaining a solid connection of these more approximate methods with rigorous QM methods is essential to their transferability and robustness. Comparison to diverse experimental observables helps validate computational models and mechanistic hypotheses as well as driving further development of computational methodologies.
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Affiliation(s)
- Qiang Cui
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, USA
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29
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Lu X, Ovchinnikov V, Demapan D, Roston D, Cui Q. Regulation and Plasticity of Catalysis in Enzymes: Insights from Analysis of Mechanochemical Coupling in Myosin. Biochemistry 2017; 56:1482-1497. [PMID: 28225609 DOI: 10.1021/acs.biochem.7b00016] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The mechanism of ATP hydrolysis in the myosin motor domain is analyzed using a combination of DFTB3/CHARMM simulations and enhanced sampling techniques. The motor domain is modeled in the pre-powerstroke state, in the post-rigor state, and as a hybrid based on the post-rigor state with a closed nucleotide-binding pocket. The ATP hydrolysis activity is found to depend on the positioning of nearby water molecules, and a network of polar residues facilitates proton transfer and charge redistribution during hydrolysis. Comparison of the observed hydrolysis pathways and the corresponding free energy profiles leads to detailed models for the mechanism of ATP hydrolysis in the pre-powerstroke state and proposes factors that regulate the hydrolysis activity in different conformational states. In the pre-powerstroke state, the scissile Pγ-O3β bond breaks early in the reaction. Proton transfer from the lytic water to the γ-phosphate through active site residues is an important part of the kinetic bottleneck; several hydrolysis pathways that feature distinct proton transfer routes are found to have similar free energy barriers, suggesting a significant degree of plasticity in the hydrolysis mechanism. Comparison of hydrolysis in the pre-powerstroke state and the closed post-rigor model suggests that optimization of residues beyond the active site for electrostatic stabilization and preorganization is likely important to enzyme design.
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Affiliation(s)
- Xiya Lu
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Victor Ovchinnikov
- Department of Chemistry and Chemical Biology, Harvard University , 12 Oxford Street, Boston, Massachusetts 02138, United States
| | - Darren Demapan
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Daniel Roston
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Qiang Cui
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
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30
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Roston D, Cui Q. Substrate and Transition State Binding in Alkaline Phosphatase Analyzed by Computation of Oxygen Isotope Effects. J Am Chem Soc 2016; 138:11946-57. [PMID: 27541005 PMCID: PMC5705178 DOI: 10.1021/jacs.6b07347] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Enzymes are powerful catalysts, and a thorough understanding of the sources of their catalytic power will facilitate many medical and industrial applications. Here we have studied the catalytic mechanism of alkaline phosphatase (AP), which is one of the most catalytically proficient enzymes known. We have used quantum mechanics calculations and hybrid quantum mechanics/molecular mechanics (QM/MM) simulations to model a variety of isotope effects relevant to the reaction of AP. We have calculated equilibrium isotope effects (EIEs), binding isotope effects (BIEs), and kinetic isotope effects (KIEs) for a range of phosphate mono- and diester substrates. The results agree well with experimental values, but the model for the reaction's transition state (TS) differs from the original interpretation of those experiments. Our model indicates that isotope effects on binding make important contributions to measured KIEs on V/K, which complicated interpretation of the measured values. Our results provide a detailed interpretation of the measured isotope effects and make predictions that can test the proposed model. The model indicates that the substrate is deformed in the ground state (GS) of the reaction and partially resembles the TS. The highly preorganized active site preferentially binds conformations that resemble the TS and not the GS, which induces the substrate to adapt to the enzyme, rather than the other way around-as with classic "induced fit" models. The preferential stabilization of the TS over the GS is what lowers the barrier to the chemical step.
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Affiliation(s)
- Daniel Roston
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin , Madison, Wisconsin 53706, United States
| | - Qiang Cui
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin , Madison, Wisconsin 53706, United States
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31
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Duarte F, Barrozo A, Åqvist J, Williams NH, Kamerlin SCL. The Competing Mechanisms of Phosphate Monoester Dianion Hydrolysis. J Am Chem Soc 2016; 138:10664-73. [PMID: 27471914 PMCID: PMC4999962 DOI: 10.1021/jacs.6b06277] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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Despite the numerous
experimental and theoretical studies on phosphate
monoester hydrolysis, significant questions remain concerning the
mechanistic details of these biologically critical reactions. In the
present work we construct a linear free energy relationship for phosphate
monoester hydrolysis to explore the effect of modulating leaving group
pKa on the competition between solvent-
and substrate-assisted pathways for the hydrolysis of these compounds.
Through detailed comparative electronic-structure studies of methyl
phosphate and a series of substituted aryl phosphate monoesters, we
demonstrate that the preferred mechanism is dependent on the nature
of the leaving group. For good leaving groups, a strong preference
is observed for a more dissociative solvent-assisted pathway. However,
the energy difference between the two pathways gradually reduces as
the leaving group pKa increases and creates
mechanistic ambiguity for reactions involving relatively poor alkoxy
leaving groups. Our calculations show that the transition-state structures
vary smoothly across the range of pKas
studied and that the pathways remain discrete mechanistic alternatives.
Therefore, while not impossible, a biological catalyst would have
to surmount a significantly higher activation barrier to facilitate
a substrate-assisted pathway than for the solvent-assisted pathway
when phosphate is bonded to good leaving groups. For poor leaving
groups, this intrinsic preference disappears.
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Affiliation(s)
- Fernanda Duarte
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University , BMC Box 596, SE-751 24 Uppsala, Sweden
| | - Alexandre Barrozo
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University , BMC Box 596, SE-751 24 Uppsala, Sweden
| | - Johan Åqvist
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University , BMC Box 596, SE-751 24 Uppsala, Sweden
| | - Nicholas H Williams
- Department of Chemistry, Sheffield University , Sheffield S3 7HF, United Kingdom
| | - Shina C L Kamerlin
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University , BMC Box 596, SE-751 24 Uppsala, Sweden
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32
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Roston D, Cui Q. QM/MM Analysis of Transition States and Transition State Analogues in Metalloenzymes. Methods Enzymol 2016; 577:213-50. [PMID: 27498640 DOI: 10.1016/bs.mie.2016.05.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Enzymology is approaching an era where many problems can benefit from computational studies. While ample challenges remain in quantitatively predicting behavior for many enzyme systems, the insights that often come from computations are an important asset for the enzymology community. Here we provide a primer for enzymologists on the types of calculations that are most useful for mechanistic problems in enzymology. In particular, we emphasize the integration of models that range from small active-site motifs to fully solvated enzyme systems for cross-validation and dissection of specific contributions from the enzyme environment. We then use a case study of the enzyme alkaline phosphatase to illustrate specific application of the methods. The case study involves examination of the binding modes of putative transition state analogues (tungstate and vanadate) to the enzyme. The computations predict covalent binding of these ions to the enzymatic nucleophile and that they adopt the trigonal bipyramidal geometry of the expected transition state. By comparing these structures with transition states found through free energy simulations, we assess the degree to which the transition state analogues mimic the true transition states. Technical issues worth treating with care as well as several remaining challenges to quantitative analysis of metalloenzymes are also highlighted during the discussion.
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Affiliation(s)
- D Roston
- Theoretical Chemistry Institute, University of Wisconsin-Madison, Madison, WI, United States.
| | - Q Cui
- Theoretical Chemistry Institute, University of Wisconsin-Madison, Madison, WI, United States.
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33
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Pabis A, Duarte F, Kamerlin SCL. Promiscuity in the Enzymatic Catalysis of Phosphate and Sulfate Transfer. Biochemistry 2016; 55:3061-81. [PMID: 27187273 PMCID: PMC4899807 DOI: 10.1021/acs.biochem.6b00297] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
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The
enzymes that facilitate phosphate and sulfate hydrolysis are
among the most proficient natural catalysts known to date. Interestingly,
a large number of these enzymes are promiscuous catalysts that exhibit
both phosphatase and sulfatase activities in the same active site
and, on top of that, have also been demonstrated to efficiently catalyze
the hydrolysis of other additional substrates with varying degrees
of efficiency. Understanding the factors that underlie such multifunctionality
is crucial both for understanding functional evolution in enzyme superfamilies
and for the development of artificial enzymes. In this Current Topic,
we have primarily focused on the structural and mechanistic basis
for catalytic promiscuity among enzymes that facilitate both phosphoryl
and sulfuryl transfer in the same active site, while comparing this
to how catalytic promiscuity manifests in other promiscuous phosphatases.
We have also drawn on the large number of experimental and computational
studies of selected model systems in the literature to explore the
different features driving the catalytic promiscuity of such enzymes.
Finally, on the basis of this comparative analysis, we probe the plausible
origins and determinants of catalytic promiscuity in enzymes that
catalyze phosphoryl and sulfuryl transfer.
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Affiliation(s)
- Anna Pabis
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University , BMC Box 596, S-751 24 Uppsala, Sweden
| | - Fernanda Duarte
- Chemistry Research Laboratory, University of Oxford , 12 Mansfield Road, Oxford OX1 3TA, U.K.,Physical and Theoretical Chemistry Laboratory, University of Oxford , South Parks Road, Oxford OX1 3QZ, U.K
| | - Shina C L Kamerlin
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University , BMC Box 596, S-751 24 Uppsala, Sweden
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