1
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Suh D, Arattu Thodika AR, Kim S, Nam K, Im W. CHARMM-GUI QM/MM Interfacer for a Quantum Mechanical and Molecular Mechanical (QM/MM) Simulation Setup: 1. Semiempirical Methods. J Chem Theory Comput 2024; 20:5337-5351. [PMID: 38856971 PMCID: PMC11209942 DOI: 10.1021/acs.jctc.4c00439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/17/2024] [Accepted: 05/24/2024] [Indexed: 06/11/2024]
Abstract
Quantum mechanical (QM) treatments, when combined with molecular mechanical (MM) force fields, can effectively handle enzyme-catalyzed reactions without significantly increasing the computational cost. In this context, we present CHARMM-GUI QM/MM Interfacer, a web-based cyberinfrastructure designed to streamline the preparation of various QM/MM simulation inputs with ligand modification. The development of QM/MM Interfacer has been achieved through integration with existing CHARMM-GUI modules, such as PDB Reader and Manipulator, Solution Builder, and Membrane Builder. In addition, new functionalities have been developed to facilitate the one-stop preparation of QM/MM systems and enable interactive and intuitive ligand modifications and QM atom selections. QM/MM Interfacer offers support for a range of semiempirical QM methods, including AM1(+/d), PM3(+/PDDG), MNDO(+/d, +/PDDG), PM6, RM1, and SCC-DFTB, tailored for both AMBER and CHARMM. A nontrivial setup related to ligand modification, link-atom insertion, and charge distribution is automatized through intuitive user interfaces. To illustrate the robustness of QM/MM Interfacer, we conducted QM/MM simulations of three enzyme-substrate systems: dihydrofolate reductase, insulin receptor kinase, and oligosaccharyltransferase. In addition, we have created three tutorial videos about building these systems, which can be found at https://www.charmm-gui.org/demo/qmi. QM/MM Interfacer is expected to be a valuable and accessible web-based tool that simplifies and accelerates the setup process for hybrid QM/MM simulations.
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Affiliation(s)
- Donghyuk Suh
- Department
of Biological Sciences, Chemistry, Bioengineering, and Computer Science
and Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Abdul Raafik Arattu Thodika
- Department
of Chemistry and Biochemistry, The University
of Texas at Arlington, Arlington, Texas 76019-9800, United States
| | - Seonghoon Kim
- Department
of Biological Sciences, Chemistry, Bioengineering, and Computer Science
and Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Kwangho Nam
- Department
of Chemistry and Biochemistry, The University
of Texas at Arlington, Arlington, Texas 76019-9800, United States
| | - Wonpil Im
- Department
of Biological Sciences, Chemistry, Bioengineering, and Computer Science
and Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
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2
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Schwartz R, Zev S, Major DT. Mechanistic docking in terpene synthases using EnzyDock. Methods Enzymol 2024; 699:265-292. [PMID: 38942507 DOI: 10.1016/bs.mie.2024.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
Terpene Synthases (TPS) catalyze the formation of multicyclic, complex terpenes and terpenoids from linear substrates. Molecular docking is an important research tool that can further our understanding of TPS multistep mechanisms and guide enzyme design. Standard docking programs are not well suited to tackle the unique challenges of TPS, like the many chemical steps which form multiple stereo-centers, the weak dispersion interactions between the isoprenoid chain and the hydrophobic region of the active site, description of carbocation intermediates, and finding mechanistically meaningful sets of docked poses. To address these and other unique challenges, we developed the multistate, multiscale docking program EnzyDock and used it to study many TPS and other enzymes. In this review we discuss the unique challenges of TPS, the special features of EnzyDock developed to address these challenges and demonstrate its successful use in ongoing research on the bacterial TPS CotB2.
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Affiliation(s)
- Renana Schwartz
- Department of Chemistry and Institute for Nanotechnology Advanced Materials, Bar Ilan University, Ramat Gan, Israel
| | - Shani Zev
- Department of Chemistry and Institute for Nanotechnology Advanced Materials, Bar Ilan University, Ramat Gan, Israel
| | - Dan T Major
- Department of Chemistry and Institute for Nanotechnology Advanced Materials, Bar Ilan University, Ramat Gan, Israel.
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3
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Nam K, Shao Y, Major DT, Wolf-Watz M. Perspectives on Computational Enzyme Modeling: From Mechanisms to Design and Drug Development. ACS OMEGA 2024; 9:7393-7412. [PMID: 38405524 PMCID: PMC10883025 DOI: 10.1021/acsomega.3c09084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/15/2024] [Accepted: 01/19/2024] [Indexed: 02/27/2024]
Abstract
Understanding enzyme mechanisms is essential for unraveling the complex molecular machinery of life. In this review, we survey the field of computational enzymology, highlighting key principles governing enzyme mechanisms and discussing ongoing challenges and promising advances. Over the years, computer simulations have become indispensable in the study of enzyme mechanisms, with the integration of experimental and computational exploration now established as a holistic approach to gain deep insights into enzymatic catalysis. Numerous studies have demonstrated the power of computer simulations in characterizing reaction pathways, transition states, substrate selectivity, product distribution, and dynamic conformational changes for various enzymes. Nevertheless, significant challenges remain in investigating the mechanisms of complex multistep reactions, large-scale conformational changes, and allosteric regulation. Beyond mechanistic studies, computational enzyme modeling has emerged as an essential tool for computer-aided enzyme design and the rational discovery of covalent drugs for targeted therapies. Overall, enzyme design/engineering and covalent drug development can greatly benefit from our understanding of the detailed mechanisms of enzymes, such as protein dynamics, entropy contributions, and allostery, as revealed by computational studies. Such a convergence of different research approaches is expected to continue, creating synergies in enzyme research. This review, by outlining the ever-expanding field of enzyme research, aims to provide guidance for future research directions and facilitate new developments in this important and evolving field.
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Affiliation(s)
- Kwangho Nam
- Department
of Chemistry and Biochemistry, University
of Texas at Arlington, Arlington, Texas 76019, United States
| | - Yihan Shao
- Department
of Chemistry and Biochemistry, University
of Oklahoma, Norman, Oklahoma 73019-5251, United States
| | - Dan T. Major
- Department
of Chemistry and Institute for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
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4
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Dulko-Smith B, Ojeda-May P, Ådén J, Wolf-Watz M, Nam K. Mechanistic Basis for a Connection between the Catalytic Step and Slow Opening Dynamics of Adenylate Kinase. J Chem Inf Model 2023; 63:1556-1569. [PMID: 36802243 DOI: 10.1021/acs.jcim.2c01629] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Escherichia coli adenylate kinase (AdK) is a small, monomeric enzyme that synchronizes the catalytic step with the enzyme's conformational dynamics to optimize a phosphoryl transfer reaction and the subsequent release of the product. Guided by experimental measurements of low catalytic activity in seven single-point mutation AdK variants (K13Q, R36A, R88A, R123A, R156K, R167A, and D158A), we utilized classical mechanical simulations to probe mutant dynamics linked to product release, and quantum mechanical and molecular mechanical calculations to compute a free energy barrier for the catalytic event. The goal was to establish a mechanistic connection between the two activities. Our calculations of the free energy barriers in AdK variants were in line with those from experiments, and conformational dynamics consistently demonstrated an enhanced tendency toward enzyme opening. This indicates that the catalytic residues in the wild-type AdK serve a dual role in this enzyme's function─one to lower the energy barrier for the phosphoryl transfer reaction and another to delay enzyme opening, maintaining it in a catalytically active, closed conformation for long enough to enable the subsequent chemical step. Our study also discovers that while each catalytic residue individually contributes to facilitating the catalysis, R36, R123, R156, R167, and D158 are organized in a tightly coordinated interaction network and collectively modulate AdK's conformational transitions. Unlike the existing notion of product release being rate-limiting, our results suggest a mechanistic interconnection between the chemical step and the enzyme's conformational dynamics acting as the bottleneck of the catalytic process. Our results also suggest that the enzyme's active site has evolved to optimize the chemical reaction step while slowing down the overall opening dynamics of the enzyme.
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Affiliation(s)
- Beata Dulko-Smith
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas 76019, United States
| | - Pedro Ojeda-May
- High Performance Computing Centre North (HPC2N), Umeå University, Umeå SE-90187, Sweden
| | - Jörgen Ådén
- Department of Chemistry, Umeå University, Umeå SE-90187, Sweden
| | | | - Kwangho Nam
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas 76019, United States
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5
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Ojeda-May P, Mushtaq AU, Rogne P, Verma A, Ovchinnikov V, Grundström C, Dulko-Smith B, Sauer UH, Wolf-Watz M, Nam K. Dynamic Connection between Enzymatic Catalysis and Collective Protein Motions. Biochemistry 2021; 60:2246-2258. [PMID: 34250801 PMCID: PMC8297476 DOI: 10.1021/acs.biochem.1c00221] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
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Enzymes employ a wide range of protein motions to achieve efficient catalysis of
chemical reactions. While the role of collective protein motions in substrate binding,
product release, and regulation of enzymatic activity is generally understood, their
roles in catalytic steps per se remain uncertain. Here, molecular dynamics simulations,
enzyme kinetics, X-ray crystallography, and nuclear magnetic resonance spectroscopy are
combined to elucidate the catalytic mechanism of adenylate kinase and to delineate the
roles of catalytic residues in catalysis and the conformational change in the enzyme.
This study reveals that the motions in the active site, which occur on a time scale of
picoseconds to nanoseconds, link the catalytic reaction to the slow conformational
dynamics of the enzyme by modulating the free energy landscapes of subdomain motions. In
particular, substantial conformational rearrangement occurs in the active site following
the catalytic reaction. This rearrangement not only affects the reaction barrier but
also promotes a more open conformation of the enzyme after the reaction, which then
results in an accelerated opening of the enzyme compared to that of the reactant state.
The results illustrate a linkage between enzymatic catalysis and collective protein
motions, whereby the disparate time scales between the two processes are bridged by a
cascade of intermediate-scale motion of catalytic residues modulating the free energy
landscapes of the catalytic and conformational change processes.
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Affiliation(s)
- Pedro Ojeda-May
- Department of Chemistry, Umeå University, Umeå SE-90187, Sweden.,High Performance Computing Centre North (HPC2N), Umeå University, Umeå SE-90187, Sweden
| | | | - Per Rogne
- Department of Chemistry, Umeå University, Umeå SE-90187, Sweden
| | - Apoorv Verma
- Department of Chemistry, Umeå University, Umeå SE-90187, Sweden
| | - Victor Ovchinnikov
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | | | - Beata Dulko-Smith
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas 76019, United States
| | - Uwe H Sauer
- Department of Chemistry, Umeå University, Umeå SE-90187, Sweden
| | | | - Kwangho Nam
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas 76019, United States
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6
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Nochebuena J, Naseem-Khan S, Cisneros GA. Development and application of quantum mechanics/molecular mechanics methods with advanced polarizable potentials. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL MOLECULAR SCIENCE 2021; 11:e1515. [PMID: 34367343 PMCID: PMC8341087 DOI: 10.1002/wcms.1515] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 12/19/2020] [Indexed: 01/02/2023]
Abstract
Quantum mechanics/molecular mechanics (QM/MM) simulations are a popular approach to study various features of large systems. A common application of QM/MM calculations is in the investigation of reaction mechanisms in condensed-phase and biological systems. The combination of QM and MM methods to represent a system gives rise to several challenges that need to be addressed. The increase in computational speed has allowed the expanded use of more complicated and accurate methods for both QM and MM simulations. Here, we review some approaches that address several common challenges encountered in QM/MM simulations with advanced polarizable potentials, from methods to account for boundary across covalent bonds and long-range effects, to polarization and advanced embedding potentials.
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Affiliation(s)
- Jorge Nochebuena
- Department of Chemistry, University of North Texas, Denton, Texas, USA
| | - Sehr Naseem-Khan
- Department of Chemistry, University of North Texas, Denton, Texas, USA
| | - G Andrés Cisneros
- Department of Chemistry, University of North Texas, Denton, Texas, USA
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7
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Mhashal AR, Major DT. Temperature-Dependent Kinetic Isotope Effects in R67 Dihydrofolate Reductase from Path-Integral Simulations. J Phys Chem B 2021; 125:1369-1377. [PMID: 33522797 PMCID: PMC7883348 DOI: 10.1021/acs.jpcb.0c10318] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/05/2021] [Indexed: 11/28/2022]
Abstract
Calculation of temperature-dependent kinetic isotope effects (KIE) in enzymes presents a significant theoretical challenge. Additionally, it is not trivial to identify enzymes with available experimental accurate intrinsic KIEs in a range of temperatures. In the current work, we present a theoretical study of KIEs in the primitive R67 dihydrofolate reductase (DHFR) enzyme and compare with experimental work. The advantage of R67 DHFR is its significantly lower kinetic complexity compared to more evolved DHFR isoforms. We employ mass-perturbation-based path-integral simulations in conjunction with umbrella sampling and a hybrid quantum mechanics-molecular mechanics Hamiltonian. We obtain temperature-dependent KIEs in good agreement with experiments and ascribe the temperature-dependent KIEs primarily to zero-point energy effects. The active site in the primitive enzyme is found to be poorly preorganized, which allows excessive water access to the active site and results in loosely bound reacting ligands.
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Affiliation(s)
- Anil R. Mhashal
- Department of Chemistry and Institute
for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Dan Thomas Major
- Department of Chemistry and Institute
for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
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8
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Pan X, Nam K, Epifanovsky E, Simmonett AC, Rosta E, Shao Y. A simplified charge projection scheme for long-range electrostatics in ab initio QM/MM calculations. J Chem Phys 2021; 154:024115. [PMID: 33445891 DOI: 10.1063/5.0038120] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
In a previous work [Pan et al., Molecules 23, 2500 (2018)], a charge projection scheme was reported, where outer molecular mechanical (MM) charges [>10 Å from the quantum mechanical (QM) region] were projected onto the electrostatic potential (ESP) grid of the QM region to accurately and efficiently capture long-range electrostatics in ab initio QM/MM calculations. Here, a further simplification to the model is proposed, where the outer MM charges are projected onto inner MM atom positions (instead of ESP grid positions). This enables a representation of the long-range MM electrostatic potential via augmentary charges (AC) on inner MM atoms. Combined with the long-range electrostatic correction function from Cisneros et al. [J. Chem. Phys. 143, 044103 (2015)] to smoothly switch between inner and outer MM regions, this new QM/MM-AC electrostatic model yields accurate and continuous ab initio QM/MM electrostatic energies with a 10 Å cutoff between inner and outer MM regions. This model enables efficient QM/MM cluster calculations with a large number of MM atoms as well as QM/MM calculations with periodic boundary conditions.
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Affiliation(s)
- Xiaoliang Pan
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Pkwy, Norman, Oklahoma 73019, USA
| | - Kwangho Nam
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas 76019, USA
| | - Evgeny Epifanovsky
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Andrew C Simmonett
- National Institutes of Health-National Heart, Lung and Blood Institute, Laboratory of Computational Biology, Bethesda, Maryland 20892, USA
| | - Edina Rosta
- Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
| | - Yihan Shao
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Pkwy, Norman, Oklahoma 73019, USA
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9
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Das S, Shimshi M, Raz K, Nitoker Eliaz N, Mhashal AR, Ansbacher T, Major DT. EnzyDock: Protein–Ligand Docking of Multiple Reactive States along a Reaction Coordinate in Enzymes. J Chem Theory Comput 2019; 15:5116-5134. [DOI: 10.1021/acs.jctc.9b00366] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Susanta Das
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Mor Shimshi
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Keren Raz
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
| | | | - Anil Ranu Mhashal
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Tamar Ansbacher
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
- Hadassah Academic College, 7 Hanevi’im Street, Jerusalem 9101001, Israel
| | - Dan T. Major
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
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10
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Mhashal AR, Pshetitsky Y, Cheatum CM, Kohen A, Major DT. Evolutionary Effects on Bound Substrate pKa in Dihydrofolate Reductase. J Am Chem Soc 2018; 140:16650-16660. [DOI: 10.1021/jacs.8b09089] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Anil R. Mhashal
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Yaron Pshetitsky
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | | | - Amnon Kohen
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - Dan Thomas Major
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 5290002, Israel
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11
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Hudson PS, Han K, Woodcock HL, Brooks BR. Force matching as a stepping stone to QM/MM CB[8] host/guest binding free energies: a SAMPL6 cautionary tale. J Comput Aided Mol Des 2018; 32:983-999. [PMID: 30276502 PMCID: PMC6867086 DOI: 10.1007/s10822-018-0165-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 09/14/2018] [Indexed: 10/28/2022]
Abstract
Use of quantum mechanical/molecular mechanical (QM/MM) methods in binding free energy calculations, particularly in the SAMPL challenge, often fail to achieve improvement over standard additive (MM) force fields. Frequently, the implementation is through use of reference potentials, or the so-called "indirect approach", and inherently relies on sufficient overlap existing between MM and QM/MM configurational spaces. This overlap is generally poor, particularly for the use of free energy perturbation to perform the MM to QM/MM free energy correction at the end states of interest (e.g., bound and unbound states). However, by utilizing MM parameters that best reproduce forces obtained at the desired QM level of theory, it is possible to lessen the configurational disparity between MM and QM/MM. To this end, we sought to use force matching to generate MM parameters for the SAMPL6 CB[8] host-guest binding challenge, classically compute binding free energies, and apply energetic end state corrections to obtain QM/MM binding free energy differences. For the standard set of 11 molecules and the bonus set (including three additional challenge molecules), error statistics, such as the root mean square deviation (RMSE) were moderately poor (5.5 and 5.4 kcal/mol). Correlation statistics, however, were in the top two for both standard and bonus set submissions ([Formula: see text] of 0.42 and 0.26, [Formula: see text] of 0.64 and 0.47 respectively). High RMSE and moderate correlation strongly indicated the presence of systematic error. Identifiable issues were ameliorated for two of the guest molecules, resulting in a reduction of error and pointing to strong prospects for the future use of this methodology.
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Affiliation(s)
- Phillip S Hudson
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20852, USA.
- Department of Chemistry, University of South Florida, Tampa, Florida, 33620, USA.
| | - Kyungreem Han
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20852, USA
| | - H Lee Woodcock
- Department of Chemistry, University of South Florida, Tampa, Florida, 33620, USA
| | - Bernard R Brooks
- Department of Chemistry, University of South Florida, Tampa, Florida, 33620, USA
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12
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Mhashal AR, Pshetitsky Y, Eitan R, Cheatum CM, Kohen A, Major DT. Effect of Asp122 Mutation on the Hydride Transfer in E. coli DHFR Demonstrates the Goldilocks of Enzyme Flexibility. J Phys Chem B 2018; 122:8006-8017. [PMID: 30040418 DOI: 10.1021/acs.jpcb.8b05556] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Dihydrofolate reductase (DHFR) catalyzes the reduction of dihydrofolate (DHF) to tetrahydrofolate (THF) in the presence of NADPH. The key hydride transfer step in the reaction is facilitated by a combination of enzyme active site preorganization and correlated protein motions in the Michaelis-Menten (E:NADPH:DHF) complex. The present theoretical study employs mutagenesis to examine the relation between structural and functional properties of the enzyme. We mutate Asp122 in Escherichia coli DHFR, which is a conserved amino acid in the DHFR family. The consequent effect of the mutation on enzyme catalysis is examined from an energetic, structural and short-time dynamic perspective. Our investigations suggest that the structural and short-time dynamic perturbations caused by Asp122X mutations (X = Asn, Ser, Ala) are along the reaction coordinate and lower the rate of hydride transfer. Importantly, analysis of the correlated and principle component motions in the enzyme suggest that the mutation alters the coupled motions that are present in the wild-type enzyme. In the case of D122N and D122S, the mutations inhibit coupled motion, whereas in the case of D122A, the mutation enhances coupled motion, although all mutations result in similar rate reduction. These results emphasize a Goldilocks principle of enzyme flexibility, that is, enzymes should neither be too rigid nor too flexible.
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Affiliation(s)
- Anil R Mhashal
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry , Bar-Ilan University , Ramat-Gan 52900 , Israel
| | - Yaron Pshetitsky
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry , Bar-Ilan University , Ramat-Gan 52900 , Israel
| | - Reuven Eitan
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry , Bar-Ilan University , Ramat-Gan 52900 , Israel
| | - Christopher M Cheatum
- Department of Chemistry , University of Iowa , Iowa City , Iowa 52242 , United States
| | - Amnon Kohen
- Department of Chemistry , University of Iowa , Iowa City , Iowa 52242 , United States
| | - Dan Thomas Major
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry , Bar-Ilan University , Ramat-Gan 52900 , Israel
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13
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Fritch B, Kosolapov A, Hudson P, Nissley DA, Woodcock HL, Deutsch C, O'Brien EP. Origins of the Mechanochemical Coupling of Peptide Bond Formation to Protein Synthesis. J Am Chem Soc 2018; 140:5077-5087. [PMID: 29577725 DOI: 10.1021/jacs.7b11044] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Mechanical forces acting on the ribosome can alter the speed of protein synthesis, indicating that mechanochemistry can contribute to translation control of gene expression. The naturally occurring sources of these mechanical forces, the mechanism by which they are transmitted 10 nm to the ribosome's catalytic core, and how they influence peptide bond formation rates are largely unknown. Here, we identify a new source of mechanical force acting on the ribosome by using in situ experimental measurements of changes in nascent-chain extension in the exit tunnel in conjunction with all-atom and coarse-grained computer simulations. We demonstrate that when the number of residues composing a nascent chain increases, its unstructured segments outside the ribosome exit tunnel generate piconewtons of force that are fully transmitted to the ribosome's P-site. The route of force transmission is shown to be through the nascent polypetide's backbone, not through the wall of the ribosome's exit tunnel. Utilizing quantum mechanical calculations we find that a consequence of such a pulling force is to decrease the transition state free energy barrier to peptide bond formation, indicating that the elongation of a nascent chain can accelerate translation. Since nascent protein segments can start out as largely unfolded structural ensembles, these results suggest a pulling force is present during protein synthesis that can modulate translation speed. The mechanism of force transmission we have identified and its consequences for peptide bond formation should be relevant regardless of the source of the pulling force.
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Affiliation(s)
- Benjamin Fritch
- Department of Chemistry , Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Andrey Kosolapov
- Department of Physiology , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
| | - Phillip Hudson
- Department of Chemistry , University of South Florida , Tampa , Florida 33620 , United States.,Laboratory of Computational Biology , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Daniel A Nissley
- Department of Chemistry , Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - H Lee Woodcock
- Department of Chemistry , University of South Florida , Tampa , Florida 33620 , United States
| | - Carol Deutsch
- Department of Physiology , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
| | - Edward P O'Brien
- Department of Chemistry , Pennsylvania State University , University Park , Pennsylvania 16802 , United States.,Bioinformatics and Genomics Graduate Program, The Huck Institutes of the Life Sciences , Pennsylvania State University , University Park , Pennsylvania 16802 , United States
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14
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Das S, Nam K, Major DT. Rapid Convergence of Energy and Free Energy Profiles with Quantum Mechanical Size in Quantum Mechanical–Molecular Mechanical Simulations of Proton Transfer in DNA. J Chem Theory Comput 2018; 14:1695-1705. [DOI: 10.1021/acs.jctc.7b00964] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Susanta Das
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Kwangho Nam
- Department of Chemistry, Umeå University, 901 87 Umeå, Sweden
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas 76019-0065, United States
| | - Dan Thomas Major
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 5290002, Israel
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