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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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Blanc FEC, Houdusse A, Cecchini M. A weak coupling mechanism for the early steps of the recovery stroke of myosin VI: A free energy simulation and string method analysis. PLoS Comput Biol 2024; 20:e1012005. [PMID: 38662764 PMCID: PMC11086841 DOI: 10.1371/journal.pcbi.1012005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 05/10/2024] [Accepted: 03/15/2024] [Indexed: 05/12/2024] Open
Abstract
Myosin motors use the energy of ATP to produce force and directed movement on actin by a swing of the lever-arm. ATP is hydrolysed during the off-actin re-priming transition termed recovery stroke. To provide an understanding of chemo-mechanical transduction by myosin, it is critical to determine how the reverse swing of the lever-arm and ATP hydrolysis are coupled. Previous studies concluded that the recovery stroke of myosin II is initiated by closure of the Switch II loop in the nucleotide-binding site. Recently, we proposed that the recovery stroke of myosin VI starts with the spontaneous re-priming of the converter domain to a putative pre-transition state (PTS) intermediate that precedes Switch II closing and ATPase activation. Here, we investigate the transition from the pre-recovery, post-rigor (PR) state to PTS in myosin VI using geometric free energy simulations and the string method. First, our calculations rediscover the PTS state agnostically and show that it is accessible from PR via a low free energy transition path. Second, separate path calculations using the string method illuminate the mechanism of the PR to PTS transition with atomic resolution. In this mechanism, the initiating event is a large movement of the converter/lever-arm region that triggers rearrangements in the Relay-SH1 region and the formation of the kink in the Relay helix with no coupling to the active site. Analysis of the free-energy barriers along the path suggests that the converter-initiated mechanism is much faster than the one initiated by Switch II closure, which supports the biological relevance of PTS as a major on-pathway intermediate of the recovery stroke in myosin VI. Our analysis suggests that lever-arm re-priming and ATP hydrolysis are only weakly coupled, so that the myosin recovery stroke is initiated by thermal fluctuations and stabilised by nucleotide consumption via a ratchet-like mechanism.
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Affiliation(s)
- Florian E. C. Blanc
- Institut de Chimie de Strasbourg, UMR7177, CNRS, Université de Strasbourg, Strasbourg, France
- Structural Motility, Institut Curie, CNRS, UMR144, PSL Research University, Paris, France
| | - Anne Houdusse
- Structural Motility, Institut Curie, CNRS, UMR144, PSL Research University, Paris, France
| | - Marco Cecchini
- Institut de Chimie de Strasbourg, UMR7177, CNRS, Université de Strasbourg, Strasbourg, France
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3
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Berta D, Gehrke S, Nyíri K, Vértessy BG, Rosta E. Mechanism-Based Redesign of GAP to Activate Oncogenic Ras. J Am Chem Soc 2023; 145:20302-20310. [PMID: 37682266 PMCID: PMC10515638 DOI: 10.1021/jacs.3c04330] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Indexed: 09/09/2023]
Abstract
Ras GTPases play a crucial role in cell signaling pathways. Mutations of the Ras gene occur in about one third of cancerous cell lines and are often associated with detrimental clinical prognosis. Hot spot residues Gly12, Gly13, and Gln61 cover 97% of oncogenic mutations, which impair the enzymatic activity in Ras. Using QM/MM free energy calculations, we present a two-step mechanism for the GTP hydrolysis catalyzed by the wild-type Ras.GAP complex. We found that the deprotonation of the catalytic water takes place via the Gln61 as a transient Brønsted base. We also determined the reaction profiles for key oncogenic Ras mutants G12D and G12C using QM/MM minimizations, matching the experimentally observed loss of catalytic activity, thereby validating our reaction mechanism. Using the optimized reaction paths, we devised a fast and accurate procedure to design GAP mutants that activate G12D Ras. We replaced GAP residues near the active site and determined the activation barrier for 190 single mutants. We furthermore built a machine learning for ultrafast screening, by fast prediction of the barrier heights, tested both on the single and double mutations. This work demonstrates that fast and accurate screening can be accomplished via QM/MM reaction path optimizations to design protein sequences with increased catalytic activity. Several GAP mutations are predicted to re-enable catalysis in oncogenic G12D, offering a promising avenue to overcome aberrant Ras-driven signal transduction by activating enzymatic activity instead of inhibition. The outlined computational screening protocol is readily applicable for designing ligands and cofactors analogously.
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Affiliation(s)
- Dénes Berta
- Department
of Physics and Astronomy, University College
London, Gower Street, London WC1E
6BT, United Kingdom
| | - Sascha Gehrke
- Department
of Physics and Astronomy, University College
London, Gower Street, London WC1E
6BT, United Kingdom
| | - Kinga Nyíri
- Institute
of Enzymology, Research Centre for Natural Sciences, Magyar tudósok körútja
2, Budapest 1117, Hungary
- Department
of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, Budafoki út 6-8, Budapest 1111, Hungary
| | - Beáta G. Vértessy
- Institute
of Enzymology, Research Centre for Natural Sciences, Magyar tudósok körútja
2, Budapest 1117, Hungary
- Department
of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, Budafoki út 6-8, Budapest 1111, Hungary
| | - Edina Rosta
- Department
of Physics and Astronomy, University College
London, Gower Street, London WC1E
6BT, United Kingdom
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4
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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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5
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Kubař T, Elstner M, Cui Q. Hybrid Quantum Mechanical/Molecular Mechanical Methods For Studying Energy Transduction in Biomolecular Machines. Annu Rev Biophys 2023; 52:525-551. [PMID: 36791746 PMCID: PMC10810093 DOI: 10.1146/annurev-biophys-111622-091140] [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: 02/17/2023]
Abstract
Hybrid quantum mechanical/molecular mechanical (QM/MM) methods have become indispensable tools for the study of biomolecules. In this article, we briefly review the basic methodological details of QM/MM approaches and discuss their applications to various energy transduction problems in biomolecular machines, such as long-range proton transports, fast electron transfers, and mechanochemical coupling. We highlight the particular importance for these applications of balancing computational efficiency and accuracy. Using several recent examples, we illustrate the value and limitations of QM/MM methodologies for both ground and excited states, as well as strategies for calibrating them in specific applications. We conclude with brief comments on several areas that can benefit from further efforts to make QM/MM analyses more quantitative and applicable to increasingly complex biological problems.
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Affiliation(s)
- T Kubař
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany;
| | - M Elstner
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany;
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, Karlsruhe, Germany;
| | - Q Cui
- Department of Chemistry, Boston University, Boston, Massachusetts, USA;
- Department of Physics, Boston University, Boston, Massachusetts, USA
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
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6
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Road-blocker HSP disease mutation disrupts pre-organization for ATP hydrolysis in kinesin through a second sphere control. Proc Natl Acad Sci U S A 2023; 120:e2215170120. [PMID: 36574689 PMCID: PMC9910451 DOI: 10.1073/pnas.2215170120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Kinesin motor proteins perform several essential cellular functions powered by the adenosine triphosphate (ATP) hydrolysis reaction. Several single-point mutations in the kinesin motor protein KIF5A have been implicated to hereditary spastic paraplegia disease (HSP), a lethal neurodegenerative disease in humans. In earlier studies, we have shown that a series of HSP-related mutations can impair the kinesin's long-distance displacement or processivity by modulating the order-disorder transition of the linker connecting the heads to the coiled coil. On the other hand, the reduction of kinesin's ATP hydrolysis reaction rate by a distal asparagine-to-serine mutation is also known to cause HSP disease. However, the molecular mechanism of the ATP hydrolysis reaction in kinesin by this distal mutation is still not fully understood. Using classical molecular dynamics simulations combined with quantum mechanics/molecular mechanics calculations, the pre-organization geometry required for optimal hydrolysis in kinesin motor bound to α/β-tubulin is determined. This optimal geometry has only a single salt-bridge (of the possible two) between Arg203-Glu236, putting a reactive water molecule at a perfect position for hydrolysis. Such geometry is also needed to create the appropriate configuration for proton translocation during ATP hydrolysis. The distal asparagine-to-serine mutation is found to disrupt this optimal geometry. Therefore, the current study along with our previous one demonstrates how two different effects on kinesin dynamics (processivity and ATP hydrolysis), caused by a different set of genotypes, can give rise to the same phenotype leading to HSP disease.
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7
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Yang Z, Hajlasz N, Kulik HJ. Computational Modeling of Conformer Stability in Benenodin-1, a Thermally Actuated Lasso Peptide Switch. J Phys Chem B 2022; 126:3398-3406. [PMID: 35481742 DOI: 10.1021/acs.jpcb.2c00762] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Benenodin-1 is a thermally actuated lasso peptide rotaxane switch with two primary translational isomers that differ in the relative position of the residue Gln15. The conversion from one conformer to the other involves substantial enthalpy-entropy compensation: one conformer is energetically favored and the other is entropically favored. Here, we take a multi-scale quantum mechanical (QM) and classical molecular dynamic (MD) approach to reveal residue-specific sources of these differences in stability. QM reveals that the two benenodin-1 conformers involve distinct hydrogen bonding networks, with the enthalpically favored conformer having more intra-peptide hydrogen bonds between the Gln15 side chain and nearby residues. The evaluation of configurational entropy over the MD-sampled geometries reveals that the entropically favored conformer has enhanced conformational flexibility. By computing the by-residue-sum entropies, we identify the role of Gln15 and neighboring Glu14 in mediating the entropic variation during the switching process. These computational insights help explain the effects of Glu14Ala and Gln15Ala mutations on the conformational population of benenodin-1 observed experimentally.
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Affiliation(s)
- Zhongyue Yang
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Natalia Hajlasz
- 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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8
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Serapian SA, Moroni E, Ferraro M, Colombo G. Atomistic Simulations of the Mechanisms of the Poorly Catalytic Mitochondrial Chaperone Trap1: Insights into the Effects of Structural Asymmetry on Reactivity. ACS Catal 2021. [DOI: 10.1021/acscatal.1c00692] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Stefano A. Serapian
- Department of Chemistry, University of Pavia, Via Torquato Taramelli 12, 27100 Pavia, Italy
| | - Elisabetta Moroni
- ″Giulio Natta” Institute of Chemical and Technological Sciences (SCITEC), Via Mario Bianco 9, 20131 Milan, Italy
| | - Mariarosaria Ferraro
- ″Giulio Natta” Institute of Chemical and Technological Sciences (SCITEC), Via Mario Bianco 9, 20131 Milan, Italy
| | - Giorgio Colombo
- Department of Chemistry, University of Pavia, Via Torquato Taramelli 12, 27100 Pavia, Italy
- ″Giulio Natta” Institute of Chemical and Technological Sciences (SCITEC), Via Mario Bianco 9, 20131 Milan, Italy
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9
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Dutta M, Jana B. Computational modeling of dynein motor proteins at work. Chem Commun (Camb) 2021; 57:272-283. [PMID: 33332489 DOI: 10.1039/d0cc05857b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Along with various experimental methods, a combination of theoretical and computational methods is essential to explore different length-scale and time-scale processes in the biological system. The functional mechanism of a dynein, an ATP-fueled motor protein, working in a multiprotein complex, involves a wide range of length/time-scale events. It generates mechanical force from chemical energy and moves on microtubules towards the minus end direction while performing a large number of biological processes including ciliary beating, intracellular material transport, and cell division. Like in the cases of other conventional motor proteins, a combination of experimental techniques including X-crystallography, cryo-electron microscopy, and single molecular assay have provided a wealth of information about the mechanochemical cycle of a dynein. Dyneins have a large and complex structural architecture and therefore, computational modeling of different aspects of a dynein is extremely challenging. As the process of dynein movement involves varying length and timescales, it demands, like in experiments, a combination of computational methods covering such a wide range of processes for the comprehensive investigation of the mechanochemical cycle. In this review article, we will summarize how the use of state-of-the-art computational methods can provide a detailed molecular understanding of the mechanochemical cycle of the dynein. We implemented all-atom molecular dynamics simulations and hybrid quantum-mechanics/molecular-mechanics simulations to explore the ATP hydrolysis mechanisms at the primary ATPase site (AAA1) of dynein. To investigate the large-scale conformational changes we employed coarse-grained structure-based molecular dynamics simulations to capture the domain motions. Here we explored the conformational changes upon binding of ATP at AAA1, nucleotide state-dependent regulation of the mechanochemical cycle, and inter-head coordination by inter-head tension. Additionally, implementing a phenomenological theoretical model we explore the force-dependent detachment rate of a motorhead from the microtubule and the principle of multi-dynein cooperation during cargo transport.
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Affiliation(s)
- Mandira Dutta
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata - 700032, India.
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10
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Chakraborti A, Baldo AP, Tardiff JC, Schwartz SD. Investigation of the Recovery Stroke and ATP Hydrolysis and Changes Caused Due to the Cardiomyopathic Point Mutations in Human Cardiac β Myosin. J Phys Chem B 2021; 125:6513-6521. [PMID: 34105970 DOI: 10.1021/acs.jpcb.1c03144] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Human cardiac β myosin undergoes the cross-bridge cycle as part of the force-generating mechanism of cardiac muscle. The recovery stroke is considered one of the key steps of the kinetic cycle as it is the conformational rearrangement required to position the active site residues for hydrolysis of ATP and interaction with actin. We explored the free-energy surface of the transition and investigated the effect of the genetic cardiomyopathy causing mutations R453C, I457T, and I467T on this step using metadynamics. This work extends previous studies on Dictyostelium myosin II with engineered mutations. Here, like previously, we generated an unbiased thermodynamic ensemble of reactive trajectories for the chemical step using transition path sampling. Our methodologies were able to predict the changes to the dynamics of the recovery stroke as well as predict the pathway of breakdown of ATP to ADP and HPO42- with the stabilization of the metaphosphate intermediate. We also observed clear differences between the Dictyostelium myosin II and human cardiac β myosin for ATP hydrolysis as well as predict the effect of the mutation I467T on the chemical step.
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Affiliation(s)
- Ananya Chakraborti
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - Anthony P Baldo
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - Jil C Tardiff
- Department of Biomedical Engineering, University of Arizona, Tucson, Arizona 85724, United States
| | - Steven D Schwartz
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
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11
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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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12
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Abstract
QM/MM simulations have become an indispensable tool in many chemical and biochemical investigations. Considering the tremendous degree of success, including recognition by a 2013 Nobel Prize in Chemistry, are there still "burning challenges" in QM/MM methods, especially for biomolecular systems? In this short Perspective, we discuss several issues that we believe greatly impact the robustness and quantitative applicability of QM/MM simulations to many, if not all, biomolecules. We highlight these issues with observations and relevant advances from recent studies in our group and others in the field. Despite such limited scope, we hope the discussions are of general interest and will stimulate additional developments that help push the field forward in meaningful directions.
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Affiliation(s)
- Qiang Cui
- Departments of Chemistry, Physics, and Biomedical Engineering, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Tanmoy Pal
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Luke Xie
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
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13
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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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14
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Baldo AP, Tardiff JC, Schwartz SD. Mechanochemical Function of Myosin II: Investigation into the Recovery Stroke and ATP Hydrolysis. J Phys Chem B 2020; 124:10014-10023. [PMID: 33136401 PMCID: PMC7696650 DOI: 10.1021/acs.jpcb.0c05762] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Myosin regulates muscle function through a complex cycle of conformational rearrangements coupled with the hydrolysis of adenosine triphosphate (ATP). The recovery stroke reorganizes the myosin active site to hydrolyze ATP and cross bridge with the thin filament to produce muscle contraction. Engineered mutations K84M and R704E in Dictyostelium myosin have been designed to specifically inhibit the recovery stroke and have been shown to indirectly affect the ATPase activity of myosin. We investigated these mutagenic perturbations to the recovery stroke and generated thermodynamically correct and unbiased trajectories for native ATP hydrolysis with computationally enhanced sampling methods. Our methodology was able to resolve experimentally observed changes to kinetic and equilibrium dynamics for the recovery stroke with the correct prediction in the severity of these changes. For ATP hydrolysis, the sequential nature along with the stabilization of a metaphosphate intermediate was observed in agreement with previous studies. However, we observed glutamate 459 being utilized as a proton abstractor to prime the attacking water instead of a lytic water, a phenomenon not well categorized in myosin but has in other ATPases. Both rare event methodologies can be extended to human myosin to investigate isoformic differences from Dictyostelium and scan cardiomyopathic mutations to see differential perturbations to kinetics of other conformational changes in myosin such as the power stroke.
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Affiliation(s)
- Anthony P Baldo
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - Jil C Tardiff
- Department of Biomedical Engineering, University of Arizona, Tucson, Arizona 85724, United States
| | - Steven D Schwartz
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
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15
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Mori T, Saito S. Dissecting the Dynamics during Enzyme Catalysis: A Case Study of Pin1 Peptidyl-Prolyl Isomerase. J Chem Theory Comput 2020; 16:3396-3407. [PMID: 32268066 DOI: 10.1021/acs.jctc.9b01279] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Free energy surfaces have played a central role in studying protein conformational changes and enzymatic reactions over decades. Yet, free energy barriers and kinetics are highly dependent on the coordinates chosen to define the surface, and furthermore, the dynamics during the reactions are often overlooked. Our recent study on the Pin1-catalyzed isomerization reaction has indicated that the isomerization transition events remarkably deviate from the free energy path, highlighting the need to understand the reaction dynamics in more detail. To this end, here we investigate the reaction coordinates that describe the transition states of the free energy and transition pathways by minimizing the cross-entropy function. We show that the isomerization transition events can be expressed by the concerted changes in the improper torsion angle ζ and nearby backbone torsional angles of the ligand, whereas the transition state of the free energy surface involves changes in a broad range of coordinates including multiple protein-ligand interactions. The current result supports the previous finding that the isomerization transitions occur quickly from the conformational excited states, which is in sharp contrast to the slow and collective changes suggested from the free energy path. Our results further indicate that the coordinates derived from the transition trajectories are not sufficient for finding the transition states on the free energy surfaces due to the lack of information from conformational excited states.
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Affiliation(s)
- Toshifumi Mori
- Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585, Japan.,School of Physical Sciences, The Graduate University for Advanced Studies, Okazaki, Aichi 444-8585, Japan
| | - Shinji Saito
- Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585, Japan.,School of Physical Sciences, The Graduate University for Advanced Studies, Okazaki, Aichi 444-8585, Japan
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16
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Berta D, Buigues PJ, Badaoui M, Rosta E. Cations in motion: QM/MM studies of the dynamic and electrostatic roles of H + and Mg 2+ ions in enzyme reactions. Curr Opin Struct Biol 2020; 61:198-206. [PMID: 32065923 DOI: 10.1016/j.sbi.2020.01.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 01/04/2020] [Accepted: 01/06/2020] [Indexed: 12/17/2022]
Abstract
Here we discuss current trends in the simulations of enzymatic reactions focusing on phosphate catalysis. The mechanistic details of the proton transfers coupled to the phosphate cleavage is one of the key challenges in QM/MM calculations of these and other enzyme catalyzed reactions. The lack of experimental information offers both an opportunity for computations as well as often unresolved controversies. We discuss the example of small GTPases including the important human Ras protein. The high dimensionality and chemical complexity of these reactions demand carefully chosen computational techniques both in terms of the underlying quantum chemical theory and the sampling of the conformational ensemble. We also point out the important role of Mg2+ ions, and recent advances in their transient involvement in the catalytic mechanisms.
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Affiliation(s)
- Dénes Berta
- Department of Chemistry, King's College London, London, SE1 1DB, United Kingdom
| | - Pedro J Buigues
- Department of Chemistry, King's College London, London, SE1 1DB, United Kingdom
| | - Magd Badaoui
- Department of Chemistry, King's College London, London, SE1 1DB, United Kingdom
| | - Edina Rosta
- Department of Chemistry, King's College London, London, SE1 1DB, United Kingdom.
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17
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Ovchinnikov V, Conti S, Lau EY, Lightstone FC, Karplus M. Microsecond Molecular Dynamics Simulations of Proteins Using a Quasi-Equilibrium Solvation Shell Model. J Chem Theory Comput 2020; 16:1866-1881. [DOI: 10.1021/acs.jctc.9b01072] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Victor Ovchinnikov
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Simone Conti
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Edmond Y. Lau
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94551, United States
| | - Felice C. Lightstone
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94551, United States
| | - Martin Karplus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
- Laboratoire de Chimie Biophysique, ISIS, Université de Strasbourg, 67000 Strasbourg, France
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18
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Manna RN, Dutta M, Jana B. Mechanistic study of the ATP hydrolysis reaction in dynein motor protein. Phys Chem Chem Phys 2019; 22:1534-1542. [PMID: 31872818 DOI: 10.1039/c9cp02194a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Dynein, a large and complex motor protein, harnesses energy from adenosine triphosphate (ATP) hydrolysis to regulate essential cellular activities. The ATP hydrolysis mechanism for the dynein motor is still shrouded in mystery. Herein, molecular dynamics simulations of a dynein motor disclosed that two water molecules are present close to the γ-phosphate of ATP and Glu1742 at the AAA1 site of dynein. We have proposed three possible mechanisms for the ATP hydrolysis. We divulge by using a quantum mechanics/molecular mechanics (QM/MM) study that two water molecules and Glu1742 are crucial for facilitating the ATP hydrolysis reaction in dynein. Moreover, the ATP hydrolysis step is initiated by the activation of lytic water (W1) by Glu1742 through relay proton transfers with the help of auxiliary water (W2) yielding HPO42- and ADP, as a product. In the next step, a proton is shifted back from Glu1742 to generate inorganic phosphate (H2PO4-) via another relay proton transfer event. The overall activation barrier for the Glu1742 assisted ATP hydrolysis is found to be the most favourable pathway compared to other plausible pathways. We also unearthed that ATP hydrolysis in dynein follows a so-called associative-like pathway in its rate-limiting step. Our study ascertained the important indirect roles of the two amino acids (such as Arg2109, Asn1792) and Mg2+ ion in the ATP hydrolysis of dynein. Additionally, multiple sequence alignment of the different organisms of dynein motors has conveyed the evolutionary importance of the Glu1742, Asn1742, and Arg2109 residues, respectively. As similar mechanisms are also prevalent in other motors, and GTPase and ATPase enzymes, the present finding spells out the definitive requirement of a proton relay process through an extended water-chain as one of the key components in an enzymatic ATP hydrolysis reaction.
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Affiliation(s)
- Rabindra Nath Manna
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata-700032, India.
| | - Mandira Dutta
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata-700032, India.
| | - Biman Jana
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata-700032, India.
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19
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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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20
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Structural basis for power stroke vs. Brownian ratchet mechanisms of motor proteins. Proc Natl Acad Sci U S A 2019; 116:19777-19785. [PMID: 31506355 DOI: 10.1073/pnas.1818589116] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Two mechanisms have been proposed for the function of motor proteins: The power stroke and the Brownian ratchet. The former refers to generation of a large downhill free energy gradient over which the motor protein moves nearly irreversibly in making a step, whereas the latter refers to biasing or rectifying the diffusive motion of the motor. Both mechanisms require input of free energy, which generally involves the processing of an ATP (adenosine 5'-triphosphate) molecule. Recent advances in experiments that reveal the details of the stepping motion of motor proteins, together with computer simulations of atomistic structures, have provided greater insights into the mechanisms. Here, we compare the various models of the power stroke and the Brownian ratchet that have been proposed. The 2 mechanisms are not mutually exclusive, and various motor proteins employ them to different extents to perform their biological function. As examples, we discuss linear motor proteins Kinesin-1 and myosin-V, and the rotary motor F1-ATPase, all of which involve a power stroke as the essential element of their stepping mechanism.
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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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Mitchell I, Aradi B, Page AJ. Density functional tight binding-based free energy simulations in the DFTB+ program. J Comput Chem 2018; 39:2452-2458. [DOI: 10.1002/jcc.25583] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 08/14/2018] [Accepted: 08/15/2018] [Indexed: 01/11/2023]
Affiliation(s)
- Izaac Mitchell
- School of Environmental and Life Sciences, University of Newcastle
| | - Bálint Aradi
- Bremen Center for Computational Materials Science, University of Bremen
| | - Alister J. Page
- School of Environmental and Life Sciences, University of Newcastle
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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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Huran AW, Steigemann C, Frauenheim T, Aradi B, Marques MAL. Efficient Automatized Density-Functional Tight-Binding Parametrizations: Application to Group IV Elements. J Chem Theory Comput 2018; 14:2947-2954. [DOI: 10.1021/acs.jctc.7b01269] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ahmad W. Huran
- Institut für Physik, Martin-Luther-Universität Halle-Wittenberg, D-06120 Halle (Saale), Germany
| | - Conrad Steigemann
- Institut für Physik, Martin-Luther-Universität Halle-Wittenberg, D-06120 Halle (Saale), Germany
| | | | - Bálint Aradi
- BCCMS, University of Bremen, 28359 Bremen, Germany
| | - Miguel A. L. Marques
- Institut für Physik, Martin-Luther-Universität Halle-Wittenberg, D-06120 Halle (Saale), Germany
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25
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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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26
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Purg M, Elias M, Kamerlin SCL. Similar Active Sites and Mechanisms Do Not Lead to Cross-Promiscuity in Organophosphate Hydrolysis: Implications for Biotherapeutic Engineering. J Am Chem Soc 2017; 139:17533-17546. [PMID: 29113434 PMCID: PMC5724027 DOI: 10.1021/jacs.7b09384] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Indexed: 01/27/2023]
Abstract
Organophosphate hydrolases are proficient catalysts of the breakdown of neurotoxic organophosphates and have great potential as both biotherapeutics for treating acute organophosphate toxicity and as bioremediation agents. However, proficient organophosphatases such as serum paraoxonase 1 (PON1) and the organophosphate-hydrolyzing lactonase SsoPox are unable to hydrolyze bulkyorganophosphates with challenging leaving groups such as diisopropyl fluorophosphate (DFP) or venomous agent X, creating a major challenge for enzyme design. Curiously, despite their mutually exclusive substrate specificities, PON1 and diisopropyl fluorophosphatase (DFPase) have essentially identical active sites and tertiary structures. In the present work, we use empirical valence bond simulations to probe the catalytic mechanism of DFPase as well as temperature, pH, and mutational effects, demonstrating that DFPase and PON1 also likely utilize identical catalytic mechanisms to hydrolyze their respective substrates. However, detailed examination of both static structures and dynamical simulations demonstrates subtle but significant differences in the electrostatic properties and solvent penetration of the two active sites and, most critically, the role of residues that make no direct contact with either substrate in acting as "specificity switches" between the two enzymes. Specifically, we demonstrate that key residues that are structurally and functionally critical for the paraoxonase activity of PON1 prevent it from being able to hydrolyze DFP with its fluoride leaving group. These insights expand our understanding of the drivers of the evolution of divergent substrate specificity in enzymes with identical active sites and guide the future design of organophosphate hydrolases that hydrolyze compounds with challenging leaving groups.
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Affiliation(s)
- Miha Purg
- Science for Life
Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden
| | - Mikael Elias
- Department of Biochemistry, Molecular Biology and Biophysics &
Biotechnology Institute, University of Minnesota, 1479 Gortner Avenue, St. Paul, Minnesota 55108, United States
| | - 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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27
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Hwang W, Lang MJ, Karplus M. Kinesin motility is driven by subdomain dynamics. eLife 2017; 6:28948. [PMID: 29111975 PMCID: PMC5718755 DOI: 10.7554/elife.28948] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 11/03/2017] [Indexed: 12/13/2022] Open
Abstract
The microtubule (MT)-associated motor protein kinesin utilizes its conserved ATPase head to achieve diverse motility characteristics. Despite considerable knowledge about how its ATPase activity and MT binding are coupled to the motility cycle, the atomic mechanism of the core events remain to be found. To obtain insights into the mechanism, we performed 38.5 microseconds of all-atom molecular dynamics simulations of kinesin-MT complexes in different nucleotide states. Local subdomain dynamics were found to be essential for nucleotide processing. Catalytic water molecules are dynamically organized by the switch domains of the nucleotide binding pocket while ATP is torsionally strained. Hydrolysis products are 'pulled' by switch-I, and a new ATP is 'captured' by a concerted motion of the α0/L5/switch-I trio. The dynamic and wet kinesin-MT interface is tuned for rapid interactions while maintaining specificity. The proposed mechanism provides the flexibility necessary for walking in the crowded cellular environment. Motor proteins called kinesins perform a number of different roles inside cells, including transporting cargo and organizing filaments called microtubules to generate the force needed for a cell to divide. Kinesins move along the microtubules, with different kinesins moving in different ways: some ‘walk’, some jump, and some destroy the microtubule as they travel along it. All kinesins power their movements using the same molecule as fuel – adenosine triphosphate, known as ATP for short. Energy stored in ATP is released by a chemical reaction known as hydrolysis, which uses water to break off specific parts of the ATP molecule. The site to which ATP binds in a kinesin has a similar structure to the ATP binding site of many other proteins that use ATP. However, little was known about the way in which kinesin uses ATP as a fuel, including how ATP binds to kinesin and is hydrolyzed, and how the products of hydrolysis are released. These events are used to power the motor protein. Hwang et al. have used powerful computer simulation methods to examine in detail how ATP interacts with kinesin whilst moving across a microtubule. The simulations suggest that regions (or 'domains') of kinesin near the ATP binding site move around to help in processing ATP. These kinesin domains trap a nearby ATP molecule from the environment and help to deliver water molecules to ATP for hydrolysis. Hwang et al. also found that the domain motion subsequently helps in the release of the hydrolysis products by kinesin. The domains around the ATP pocket vary among the kinesins and these differences may enable kinesins to fine-tune how they use ATP to move. Further investigations will help us understand why different kinesin families behave differently. They will also contribute to exploring how kinesin inhibitors might be used as anti-cancer drugs.
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Affiliation(s)
- Wonmuk Hwang
- Department of Biomedical Engineering, Texas A&M University, College Station, United States.,Department of Materials Science & Engineering, Texas A&M University, College Station, United States.,School of Computational Sciences, Korea Institute for Advanced Study, Seoul, Korea
| | - Matthew J Lang
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, United States.,Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, United States
| | - Martin Karplus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, United States.,Laboratoire de Chimie Biophysique, ISIS, Université de Strasbourg, Strasbourg, France
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28
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Yao J, Wang X, Luo H, Gu P. Understanding the Catalytic Mechanism and the Nature of the Transition State of an Attractive Drug‐Target Enzyme (Shikimate Kinase) by Quantum Mechanical/Molecular Mechanical (QM/MM) Studies. Chemistry 2017; 23:16380-16387. [DOI: 10.1002/chem.201703867] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Indexed: 11/05/2022]
Affiliation(s)
- Jianzhuang Yao
- School of Biological Science and Technology University of Jinan Jinan 250022 P.R. China
| | - Xia Wang
- School of Biological Science and Technology University of Jinan Jinan 250022 P.R. China
| | - Haixia Luo
- Laboratory of Ministry of Education for Conservation and Utilization of Special Biological Resources in the Western China, Life Science School Ningxia University Yinchuan 750021 P.R. China
| | - Pengfei Gu
- School of Biological Science and Technology University of Jinan Jinan 250022 P.R. China
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29
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Bordes I, Castillo R, Moliner V. Theoretical Study of the Phosphoryl Transfer Reaction from ATP to Dha Catalyzed by DhaK from Escherichia coli. J Phys Chem B 2017; 121:8878-8892. [PMID: 28850238 DOI: 10.1021/acs.jpcb.7b04862] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein kinases, representing one of the largest protein families involved in almost all aspects of cell life, have become one of the most important targets for the development of new drugs to be used in, for instance, cancer treatments. In this article an exhaustive theoretical study of the phosphoryl transfer reaction from adenosine triphosphate (ATP) to dihydroxyacetone (Dha) catalyzed by DhaK from Escherichia coli (E. coli) is reported. Two different mechanisms, previously proposed for the phosphoryl transfer from ATP to the hydroxyl side chain of specific serine, threonine, or tyrosine residues, have been explored based on the generation of free energy surfaces (FES) computed with hybrid QM/MM potentials. The results suggest that the substrate-assisted phosphoryl and proton-transfer mechanism is kinetically more favorable than the mechanism where an aspartate would be activating the Dha. Although the details of the mechanisms appear to be dramatically dependent on the level of theory employed in the calculations (PM3/MM, B3LYP:PM3/MM, or B3LYP/MM), the transition states (TSs) for the phosphoryl transfer step appear to be described as a concerted step with different degrees of synchronicity in the breaking and forming bonds process in both explored mechanisms. Residues of the active site belonging to different subunits of the protein, such as Gly78B, Thr79A, Ser80A, Arg178B, and one Mg2+ cation, would be stabilizing the transferred phosphate in the TS. Asp109A would have a structural role by posing the Dha and other residues of the active site in the proper orientation. The information derived from our calculations not only reveals the role of the enzyme and the particular residues of its active site, but it can assist in the rational design of new more specific inhibitors.
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Affiliation(s)
- I Bordes
- Departament de Química Física i Analítica, Universitat Jaume I , 12071 Castellón, Spain
| | - R Castillo
- Departament de Química Física i Analítica, Universitat Jaume I , 12071 Castellón, Spain
| | - V 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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