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Parise A, Ciardullo G, Prejanò M, Lande ADL, Marino T. On the Recognition of Natural Substrate CTP and Endogenous Inhibitor ddhCTP of SARS-CoV-2 RNA-Dependent RNA Polymerase: A Molecular Dynamics Study. J Chem Inf Model 2022; 62:4916-4927. [PMID: 36219674 DOI: 10.1021/acs.jcim.2c01002] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The novel coronavirus SARS-CoV-2 is the causative agent of the COVID-19 outbreak that is affecting the entire planet. As the pandemic is still spreading worldwide, with multiple mutations of the virus, it is of interest and of help to employ computational methods for identifying potential inhibitors of the enzymes responsible for viral replication. Attractive antiviral nucleotide analogue RNA-dependent RNA polymerase (RdRp) chain terminator inhibitors are investigated with this purpose. This study, based on molecular dynamics (MD) simulations, addresses the important aspects of the incorporation of an endogenously synthesized nucleoside triphosphate, ddhCTP, in comparison with the natural nucleobase cytidine triphosphate (CTP) in RdRp. The ddhCTP species is the product of the viperin antiviral protein as part of the innate immune response. The absence of the ribose 3'-OH in ddhCTP could have important implications in its inhibitory mechanism of RdRp. We built an in silico model of the RNA strand embedded in RdRp using experimental methods, starting from the cryo-electron microscopy structure and exploiting the information obtained by spectrometry on the RNA sequence. We determined that the model was stable during the MD simulation time. The obtained results provide deeper insights into the incorporation of nucleoside triphosphates, whose molecular mechanism by the RdRp active site still remains elusive.
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Affiliation(s)
- Angela Parise
- Dipartimento di Chimica e Tecnologie Chimiche, Università Della Calabria, Via Pietro Bucci, 87036 Arcavacata di Rende, CS, Italy.,Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, Orsay 91405, France
| | - Giada Ciardullo
- Dipartimento di Chimica e Tecnologie Chimiche, Università Della Calabria, Via Pietro Bucci, 87036 Arcavacata di Rende, CS, Italy
| | - Mario Prejanò
- Dipartimento di Chimica e Tecnologie Chimiche, Università Della Calabria, Via Pietro Bucci, 87036 Arcavacata di Rende, CS, Italy
| | - Aurélien de la Lande
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, Orsay 91405, France
| | - Tiziana Marino
- Dipartimento di Chimica e Tecnologie Chimiche, Università Della Calabria, Via Pietro Bucci, 87036 Arcavacata di Rende, CS, Italy
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2
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Krachtus D, Smith JC, Imhof P. Quantum Mechanical/Molecular Mechanical Analysis of the Catalytic Mechanism of Phosphoserine Phosphatase. Molecules 2018; 23:E3342. [PMID: 30563005 PMCID: PMC6321591 DOI: 10.3390/molecules23123342] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 12/11/2018] [Accepted: 12/13/2018] [Indexed: 11/25/2022] Open
Abstract
Phosphoserine phosphatase (PSP), a member of the haloacid dehalogenase (HAD) superfamily that comprises the vast majority of phosphotransferases, is likely a steady-state regulator of the level of d-serine in the brain. The proposed catalytic cycle of PSP consists of a two-step mechanism: formation of a phospho-enzyme intermediate by phosphate transfer to Asp11 and its subsequent hydrolysis. Our combined quantum mechanical/molecular mechanical (QM/MM) calculations of the reaction pathways favour a dissociative mechanism of nucleophilic substitution via a trigonal-planar metaphosphate-like configuration for both steps, associated with proton transfer to the leaving group or from the nucleophile. This proton transfer is facilitated by active site residue Asp13 that acts as both a general base and a general acid. Free energy calculation on the reaction pathways further support the structural role of the enzymatic environment and the active site architecture. The choice of a proper reaction coordinate along which to bias the free energy calculations can be guided by a projection of the canonical reaction coordinate obtained from a chain-of-state optimisation onto important internal coordinates.
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Affiliation(s)
- Dieter Krachtus
- Computational Molecular Biophysics Group, Interdisciplinary Center for Scientific Computing (IWR), Im Neuenheimer Feld 368, 69120 Heidelberg, Germany.
| | - Jeremy C Smith
- Computational Molecular Biophysics Group, Interdisciplinary Center for Scientific Computing (IWR), Im Neuenheimer Feld 368, 69120 Heidelberg, Germany.
- University of Tennessee/Oak Ridge National Laboratory, Center for Molecular Biophysics, One Bethel Valley Road, P.O. Box 2008, Oak Ridge, TN 37831-6255, USA.
| | - Petra Imhof
- Freie Universität Berlin, Institute for Theoretical Physics, Arnimallee 14, 14195 Berlin, Germany.
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3
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Mlýnský V, Kührová P, Jurečka P, Šponer J, Otyepka M, Banáš P. Mapping the Chemical Space of the RNA Cleavage and Its Implications for Ribozyme Catalysis. J Phys Chem B 2017; 121:10828-10840. [DOI: 10.1021/acs.jpcb.7b09129] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Vojtěch Mlýnský
- Regional Centre
of Advanced Technologies and Materials, Department of Physical Chemistry,
Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), via
Bonomea 265, 34136 Trieste, Italy
| | - Petra Kührová
- Regional Centre
of Advanced Technologies and Materials, Department of Physical Chemistry,
Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Petr Jurečka
- Regional Centre
of Advanced Technologies and Materials, Department of Physical Chemistry,
Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Jiří Šponer
- Regional Centre
of Advanced Technologies and Materials, Department of Physical Chemistry,
Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolská 135, 612 65 Brno, Czech Republic
| | - Michal Otyepka
- Regional Centre
of Advanced Technologies and Materials, Department of Physical Chemistry,
Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Pavel Banáš
- Regional Centre
of Advanced Technologies and Materials, Department of Physical Chemistry,
Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolská 135, 612 65 Brno, Czech Republic
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4
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Casalino L, Palermo G, Abdurakhmonova N, Rothlisberger U, Magistrato A. Development of Site-Specific Mg(2+)-RNA Force Field Parameters: A Dream or Reality? Guidelines from Combined Molecular Dynamics and Quantum Mechanics Simulations. J Chem Theory Comput 2016; 13:340-352. [PMID: 28001405 DOI: 10.1021/acs.jctc.6b00905] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The vital contribution of Mg2+ ions to RNA biology is challenging to dissect at the experimental level. This calls for the integrative support of atomistic simulations, which at the classical level are plagued by limited accuracy. Indeed, force fields intrinsically neglect nontrivial electronic effects that Mg2+ exerts on its surrounding ligands in varying RNA coordination environments. Here, we present a combined computational study based on classical molecular dynamics (MD) and Density Functional Theory (DFT) calculations, aimed at characterizing (i) the performance of five Mg2+ force field (FF) models in RNA systems and (ii) how charge transfer and polarization affect the binding of Mg2+ ions in different coordination motifs. As a result, a total of ∼2.5 μs MD simulations (100/200 ns for each run) for two prototypical Mg2+-dependent ribozymes showed remarkable differences in terms of populations of inner-sphere coordination site types. Most importantly, complementary DFT calculations unveiled that differences in charge transfer and polarization among recurrent Mg2+-RNA coordination motifs are surprisingly small. In particular, the charge of the Mg2+ ions substantially remains constant through different coordination sites, suggesting that the common philosophy of developing site-specific Mg2+ ion parameters is not in line with the physical origin of the Mg2+-RNA MD simulations inaccuracies. Overall, this study constitutes a guideline for an adept use of current Mg2+ models and provides novel insights for the rational development of next-generation Mg2+ FFs to be employed for atomistic simulations of RNA.
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Affiliation(s)
- Lorenzo Casalino
- International School for Advanced Studies (SISSA) , Trieste, Italy
| | - Giulia Palermo
- Laboratory of Computational Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne , CH-1015 Lausanne, Switzerland
| | - Nodira Abdurakhmonova
- International School for Advanced Studies (SISSA) , Trieste, Italy.,Università degli Studi di Trieste , Trieste, Italy
| | - Ursula Rothlisberger
- Laboratory of Computational Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne , CH-1015 Lausanne, Switzerland
| | - Alessandra Magistrato
- CNR-IOM-Democritos National Simulation Center c/o SISSA , via Bonomea 265, Trieste, Italy
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5
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Batebi H, Imhof P. Phosphodiester hydrolysis computed for cluster models of enzymatic active sites. Theor Chem Acc 2016. [DOI: 10.1007/s00214-016-2020-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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6
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Casalino L, Magistrato A. Structural, dynamical and catalytic interplay between Mg2+ ions and RNA. Vices and virtues of atomistic simulations. Inorganica Chim Acta 2016. [DOI: 10.1016/j.ica.2016.02.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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7
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Casalino L, Palermo G, Rothlisberger U, Magistrato A. Who Activates the Nucleophile in Ribozyme Catalysis? An Answer from the Splicing Mechanism of Group II Introns. J Am Chem Soc 2016; 138:10374-7. [DOI: 10.1021/jacs.6b01363] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Lorenzo Casalino
- International School for Advanced Studies (SISSA), via Bonomea 265, 34136 Trieste, Italy
| | - Giulia Palermo
- Laboratory
of Computational Chemistry and Biochemistry, Institute of Chemical
Sciences and Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Ursula Rothlisberger
- Laboratory
of Computational Chemistry and Biochemistry, Institute of Chemical
Sciences and Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Alessandra Magistrato
- CNR-IOM-Democritos
National Simulation Center c/o SISSA, via Bonomea 265, 34136 Trieste, Italy
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8
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Bekçioğlu-Neff G, Allolio C, Desmukh YS, Hansen MR, Sebastiani D. Dynamical Dimension to the Hofmeister Series: Insights from First-Principles Simulations. Chemphyschem 2016; 17:1166-73. [DOI: 10.1002/cphc.201501150] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Indexed: 11/05/2022]
Affiliation(s)
- Gül Bekçioğlu-Neff
- Institut für Chemie; Martin-Luther-Universität Halle-Wittenberg; Von-Danckelmann-Platz 4 06120 Halle (Saale) Germany
- Physics Department; Freie Universität Berlin; Arnimallee 14 14195 Berlin Germany
| | - Christoph Allolio
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences of the Czech Republic; Flemingovo nám 2 16610 Prague 6 Czech Republic
| | - Yogesh S. Desmukh
- Department of Biobased Materials; Maastricht University; P.O. Box 616 6200MD Maastricht The Netherlands
- Wavin Technology and Innovation; P.O. Box 173 8000 AD Zwolle The Netherlands
| | - Michael Ryan Hansen
- Institut für Physikalische Chemie; Westfälische Wilhelms-Universität Münster; Corrensstrasse 28/30 Münster Germany
| | - Daniel Sebastiani
- Institut für Chemie; Martin-Luther-Universität Halle-Wittenberg; Von-Danckelmann-Platz 4 06120 Halle (Saale) Germany
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9
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Dai Q, Xu JJ, Li HJ, Yi HB. Ion association characteristics in MgCl2and CaCl2aqueous solutions: a density functional theory and molecular dynamics investigation. Mol Phys 2015. [DOI: 10.1080/00268976.2015.1039618] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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10
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Palermo G, Cavalli A, Klein ML, Alfonso-Prieto M, Dal Peraro M, De Vivo M. Catalytic metal ions and enzymatic processing of DNA and RNA. Acc Chem Res 2015; 48:220-8. [PMID: 25590654 DOI: 10.1021/ar500314j] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
CONSPECTUS: Two-metal-ion-dependent nucleases cleave the phosphodiester bonds of nucleic acids via the two-metal-ion (2M) mechanism. Several high-resolution X-ray structures portraying the two-metal-aided catalytic site, together with mutagenesis and kinetics studies, have demonstrated a functional role of the ions for catalysis in numerous metallonucleases. Overall, the experimental data confirm the general mechanistic hypothesis for 2M-aided phosphoryl transfer originally reported by Steitz and Steitz ( Proc. Natl. Acad. Sci. U.S.A. 1993 , 90 ( 14 ), 6498 - 6502 ). This seminal paper proposed that one metal ion favors the formation of the nucleophile, while the nearby second metal ion facilitates leaving group departure during RNA hydrolysis. Both metals were suggested to stabilize the enzymatic transition state. Nevertheless, static X-ray structures alone cannot exhaustively unravel how the two ions execute their functional role along the enzymatic reaction during processing of DNA or RNA strands when moving from reactants to products, passing through metastable intermediates and high-energy transition states. In this Account, we discuss the role of multiscale molecular simulations in further disclosing mechanistic insights of 2M-aided catalysis for two prototypical enzymatic targets for drug discovery, namely, ribonuclease H (RNase H) and type II topoisomerase (topoII). In both examples, first-principles molecular simulations, integrated with structural data, emphasize a cooperative motion of the bimetal motif during catalysis. The coordinated motion of both ions is crucial for maintaining a flexible metal-centered structural architecture exquisitely tailored to accommodate the DNA or RNA sugar-phosphate backbone during phosphodiester bond cleavage. Furthermore, our analysis of RNase H and the N-terminal domain (PAN) of influenza polymerase shows that classical molecular dynamics simulations coupled with enhanced sampling techniques have contributed to describe the modulatory effect of metal ion concentration and metal uptake on the 2M mechanism and efficiency. These aspects all point to the emerging and intriguing role of additional adjacent ions potentially involved in the modulation of phosphoryl transfer reactions and enzymatic turnover in 2M-catalysis, as recently observed experimentally in polymerase η and homing endonuclease I-DmoI. These computational results, integrated with experimental findings, describe and reinforce the nascent concept of a functional and cooperative dynamics of the catalytic metal ions during the 2M-dependent enzymatic processing of DNA and RNA. Encouraged by the insights provided by computational approaches, we foresee further experiments that will feature the functional and joint dynamics of the catalytic metal ions for nucleic acid processing. This could impact the de novo design of artificial metallonucleases and the rational design of potent metal-chelating inhibitors of pharmaceutically relevant enzymes.
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Affiliation(s)
- Giulia Palermo
- Department
of Drug Discovery and Development, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Andrea Cavalli
- Department
of Drug Discovery and Development, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
- Department
of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro
6, I-40126 Bologna, Italy
| | - Michael L. Klein
- Institute
for Computational Molecular Science, Temple University, SERC Building, 1925 North 12th Street, Philadelphia Pennsylvania 19122, United States
| | - Mercedes Alfonso-Prieto
- Institute
for Computational Molecular Science, Temple University, SERC Building, 1925 North 12th Street, Philadelphia Pennsylvania 19122, United States
| | - Matteo Dal Peraro
- Institute
of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne - EPFL, 1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics - SIB, 1015 Lausanne, Switzerland
| | - Marco De Vivo
- Department
of Drug Discovery and Development, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
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11
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Vidossich P, Magistrato A. QM/MM molecular dynamics studies of metal binding proteins. Biomolecules 2014; 4:616-45. [PMID: 25006697 PMCID: PMC4192665 DOI: 10.3390/biom4030616] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 06/05/2014] [Accepted: 06/06/2014] [Indexed: 11/16/2022] Open
Abstract
Mixed quantum-classical (quantum mechanical/molecular mechanical (QM/MM)) simulations have strongly contributed to providing insights into the understanding of several structural and mechanistic aspects of biological molecules. They played a particularly important role in metal binding proteins, where the electronic effects of transition metals have to be explicitly taken into account for the correct representation of the underlying biochemical process. In this review, after a brief description of the basic concepts of the QM/MM method, we provide an overview of its capabilities using selected examples taken from our work. Specifically, we will focus on heme peroxidases, metallo-β-lactamases, α-synuclein and ligase ribozymes to show how this approach is capable of describing the catalytic and/or structural role played by transition (Fe, Zn or Cu) and main group (Mg) metals. Applications will reveal how metal ions influence the formation and reduction of high redox intermediates in catalytic cycles and enhance drug metabolism, amyloidogenic aggregate formation and nucleic acid synthesis. In turn, it will become manifest that the protein frame directs and modulates the properties and reactivity of the metal ions.
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Affiliation(s)
- Pietro Vidossich
- Department of Chemistry, Autonomous University of Barcelona, 08193 Cerdanyola del Vallés, Spain.
| | - Alessandra Magistrato
- CNR-IOM-Democritos National Simulation Center c/o, International School for Advanced Studies (SISSA/ISAS), via Bonomea 265, 34165 Trieste, Italy.
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12
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Rovira C. The description of electronic processes inside proteins from Car-Parrinello molecular dynamics: chemical transformations. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2013. [DOI: 10.1002/wcms.1153] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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13
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Microsolvation of Mg2+, Ca2+: strong influence of formal charges in hydrogen bond networks. J Mol Model 2013; 19:1763-77. [DOI: 10.1007/s00894-012-1716-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Accepted: 11/27/2012] [Indexed: 10/27/2022]
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Rossato L, Rossetto F, Silvestrelli PL. Aqueous solvation of methane from first principles. J Phys Chem B 2012; 116:4552-60. [PMID: 22443455 DOI: 10.1021/jp300774z] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Structural, dynamical, bonding, and electronic properties of water molecules around a soluted methane molecule are studied from first principles. The results are compatible with experiments and qualitatively support the conclusions of recent classical molecular dynamics simulations concerning the controversial issue on the presence of "immobilized" water molecules around hydrophobic groups: the hydrophobic solute slightly reduces (by a less than 2 factor) the mobility of many surrounding water molecules rather than immobilizing just the few ones which are closest to methane, similarly to what was obtained by previous first-principles simulations of soluted methanol. Moreover, the rotational slowing down is compatible with the one predicted on the basis of the excluded volume fraction, which leads to a slower hydrogen bond exchange rate. The analysis of simulations performed at different temperatures suggests that the target temperature of the soluted system must be carefully chosen, in order to avoid artificial slowing-down effects. By generating maximally localized Wannier functions, a detailed description of the polarization effects in both solute and solvent molecules is obtained, which better characterizes the solvation process.
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Affiliation(s)
- Lorenzo Rossato
- Dipartimento di Fisica e Astronomia G. Galilei, Università di Padova, Padova, Italy
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15
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Sgrignani J, Magistrato A. The structural role of Mg2+ ions in a class I RNA polymerase ribozyme: a molecular simulation study. J Phys Chem B 2012; 116:2259-68. [PMID: 22268599 DOI: 10.1021/jp206475d] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
According to the RNA world hypothesis, self-replicating ribozymes, storing the genetic information and being able to perform catalysis, were the constituents of the first living organisms. In particular, RNA polymerase ribozymes, similar to current proteinaceous enzymatic polymerases, may have been able to promote the synthesis of RNA strands in a primitive world. Polymerase catalysis is usually assisted by Mg(2+) ions, but it is not always trivial to find out experimentally the number of Mg(2+) ions placed in the active site as well as the identity and the number of their coordination ligands. Here, we addressed this issue in an artificial class I ligase ribozyme. On the basis of a recently solved crystal structure, we constructed computational models of reactant and product states of this ribozyme, considering monometallic and bimetallic species. Our models were relaxed by force field based molecular dynamics (MD) simulations and mixed quantum-classical (QM/MM) MD. The structural and dynamical properties of these models were consistent with experimental data and were validated by a comparison with the catalytic sites of proteinaceous DNA and RNA polymerases. Consistently with enzymatic polymerases, our results suggest that class I RNA ligases most probably contain two magnesium ions in the active site and they may, therefore, catalyze the junction of two RNA strands via "a two Mg(2+) ions" mechanism.
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Affiliation(s)
- Jacopo Sgrignani
- CNR-IOM-Democritos National Simulation Center C/o International Studies for Advanced Studies (SISSA/ISAS), Via Bonomea 265, 34165, Trieste, Italy
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16
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Yang F, Boero M, Rabu P, Massobrio C. First principles investigation of the atomic structure and magnetic properties of copper hydroxide acetate. CR CHIM 2012. [DOI: 10.1016/j.crci.2011.09.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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17
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Fu CW, Lin TH. Theoretical Study on the Alkaline Hydrolysis of Methyl Thioacetate in Aqueous Solution. J Phys Chem A 2011; 115:13523-33. [DOI: 10.1021/jp204658w] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Chein-Wei Fu
- Institute of Molecular Medicine & Department of Life Science, National Tsing Hua University, Hsinchu, 30013 Taiwan, ROC
| | - Thy-Hou Lin
- Institute of Molecular Medicine & Department of Life Science, National Tsing Hua University, Hsinchu, 30013 Taiwan, ROC
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18
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Boero M. LeuRS Synthetase: A First-Principles Investigation of the Water-Mediated Editing Reaction. J Phys Chem B 2011; 115:12276-86. [DOI: 10.1021/jp2070024] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mauro Boero
- Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504 CNRS-UDS, 23 rue du Loess, BP 43, F-67034 Strasbourg, France
- Research Center for Integrated Science, Japan Advanced Institute of Science and Technology (JAIST), 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
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19
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Qian X. Mechanisms and Energetics for Acid Catalyzed β-d-Glucose Conversion to 5-Hydroxymethylfurfurl. J Phys Chem A 2011; 115:11740-8. [DOI: 10.1021/jp2041982] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xianghong Qian
- Department of Chemical Engineering, University of Arkansas, Fayetteville, Arkansas 72701, United States
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20
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Chval Z, Chvalová D, Leclerc F. Modeling the RNA 2'OH activation: possible roles of metal ion and nucleobase as catalysts in self-cleaving ribozymes. J Phys Chem B 2011; 115:10943-56. [PMID: 21823619 DOI: 10.1021/jp200970d] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The RNA 2'OH activation as taking place in the first chemical step of self-cleaving ribozymes is studied theoretically by DFT and MP2 methods using a continuum solvation model (CPCM). The reaction of proton transfer is studied in the presence of two kinds of catalysts: a fully hydrated metal ion (Mg(2+)) or partially hydrated nucleobase (guanine), taken separately or together leading to three different modes of activation. The metal ion is either directly bound (inner-sphere) or indirectly bound (outer-sphere) to the 2'OH group and a hydroxide ion acts as a general or specific base; the nucleobase is taken in anionic or in neutral enol-tautomeric forms playing itself the role of general base. The presence of a close metal ion (outer-sphere) lowers the pK(a) value of the 2'OH group by several log units in both metal-ion and nuleobase catalysis. The direct metal coordination to the 2'OH group (inner-sphere) further stabilizes the developing negative charge on the nucleophile. The switching from the inner-sphere to the outer-sphere coordination appears to be driven by the energy cost for reorganizing the first coordination shell rather than by the electrostatic repulsion between the ligands. The metal-ion catalysis is more effective with a specific base in the dianionic mechanism. On the other hand, the nucleobase catalysis is more effective in the monoanionic mechanism and in the presence of a metal ion acting as a cofactor through nonspecific electrostatic interactions. The results establish a baseline to study the possible roles of metal and nucleobase catalysts and their environment in more realistic models for self-cleaving ribozymes.
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Affiliation(s)
- Zdeněk Chval
- Department of Laboratory Methods and Information Systems, Faculty of Health and Social Studies, University of South Bohemia, J. Boreckého 27, 370 11 České Budějovice, Czech Republic.
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21
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Park JM, Boero M. Protonation of a hydroxide anion bridging two divalent magnesium cations in water probed by first-principles metadynamics simulation. J Phys Chem B 2010; 114:11102-9. [PMID: 20695500 DOI: 10.1021/jp102991f] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The protonation of a hydroxide anion (OH(-)) located between two magnesium cations (Mg(2+)) in aqueous solution has been investigated by first-principles metadynamics simulation. We observe that the complex Mg(2+)-OH(-)-Mg(2+) is stabilized by the coparticipation of the hydroxide anion to the first hydration shells of both the Mg(2+) cations. Contrary to the cases of OH(-) in pure water, the transfer of protons in the presence of the divalent metal ions turns out to be a slow chemical event. This can be ascribed to the decreased proton affinity of the bridging OH(-). Metadynamics simulation, used to overcome the difficulty of the long time scale required by the protonation of the bridging OH(-), has shown that the system possesses a great stability on the reactant state, characterized by a bioctahedral (6,6) solvation structure around the two Mg(2+) cations. The exploration of the free energy landscape shows that this stable bioctahedral configuration converts into a lower coordinated (5,6) structure, leading to a proton transfer from a water molecule belonging to the first solvation shell of the Mg(2+) ion having the lower coordination to the bridging OH(-); the free energy barrier for the protonation reaction is 11 kcal/mol, meaning that the bridging hydroxide is a weak base. During the proton transfer, the bridging OH(-) reverts to an H(2)O molecule, and this breaks the electrostatic coupling of the two Mg(2+) ions, which depart independently with their own hydration shells, one of which is entirely formed by water molecules. The second one carries the newly created OH(-). Our results show that the flexibility in the metal coordination plays a crucial role in both the protonation process of the bridging OH(-) and the separation of the metal cations, providing useful insight into the nature of proton transfer in binuclear divalent metal ions, with several biological implications, such as, for instance, transesterification of catalytic RNA.
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Affiliation(s)
- Jung Mee Park
- Department of Chemistry, Sungkyunkwan University, Suwon, Gyeonggi, 440-746, Korea.
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Hammerhead ribozymes: true metal or nucleobase catalysis? Where is the catalytic power from? Molecules 2010; 15:5389-407. [PMID: 20714304 PMCID: PMC6257768 DOI: 10.3390/molecules15085389] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Revised: 07/29/2010] [Accepted: 08/04/2010] [Indexed: 11/17/2022] Open
Abstract
The hammerhead ribozyme was first considered as a metalloenzyme despite persistent inconsistencies between structural and functional data. In the last decade, metal ions were confirmed as catalysts in self-splicing ribozymes but displaced by nucleobases in self-cleaving ribozymes. However, a model of catalysis just relying on nucleobases as catalysts does not fully fit some recent data. Gathering and comparing data on metal ions in self-cleaving and self-splicing ribozymes, the roles of divalent metal ions and nucleobases are revisited. Hypothetical models based on cooperation between metal ions and nucleobases are proposed for the catalysis and evolution of this prototype in RNA catalysis.
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Kamiya K, Boero M, Shiraishi K, Oshiyama A, Shigeta Y. Energy Compensation Mechanism for Charge-Separated Protonation States in Aspartate−Histidine Amino Acid Residue Pairs. J Phys Chem B 2010; 114:6567-78. [DOI: 10.1021/jp906148m] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Katsumasa Kamiya
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori, Ako, Hyogo, 678-1297, Japan, CREST, Japan Science and Technology Agency, Sanban-cho, Tokyo 102-0075, Japan, Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504 CNRS and University of Strasbourg, 23, rue du Loess, F-67034 Strasbourg 2, France, Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8571, Japan, Center for Computational
| | - Mauro Boero
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori, Ako, Hyogo, 678-1297, Japan, CREST, Japan Science and Technology Agency, Sanban-cho, Tokyo 102-0075, Japan, Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504 CNRS and University of Strasbourg, 23, rue du Loess, F-67034 Strasbourg 2, France, Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8571, Japan, Center for Computational
| | - Kenji Shiraishi
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori, Ako, Hyogo, 678-1297, Japan, CREST, Japan Science and Technology Agency, Sanban-cho, Tokyo 102-0075, Japan, Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504 CNRS and University of Strasbourg, 23, rue du Loess, F-67034 Strasbourg 2, France, Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8571, Japan, Center for Computational
| | - Atsushi Oshiyama
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori, Ako, Hyogo, 678-1297, Japan, CREST, Japan Science and Technology Agency, Sanban-cho, Tokyo 102-0075, Japan, Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504 CNRS and University of Strasbourg, 23, rue du Loess, F-67034 Strasbourg 2, France, Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8571, Japan, Center for Computational
| | - Yasuteru Shigeta
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori, Ako, Hyogo, 678-1297, Japan, CREST, Japan Science and Technology Agency, Sanban-cho, Tokyo 102-0075, Japan, Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504 CNRS and University of Strasbourg, 23, rue du Loess, F-67034 Strasbourg 2, France, Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8571, Japan, Center for Computational
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Dupureur CM. One is enough: insights into the two-metal ion nuclease mechanism from global analysis and computational studies. Metallomics 2010; 2:609-20. [PMID: 21072352 DOI: 10.1039/c0mt00013b] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Cynthia M Dupureur
- Department of Chemistry & Biochemistry and The Center for Nanoscience, University of Missouri-St. Louis, One University Blvd., St. Louis, MO 63121, USA.
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Reactive Simulations for Biochemical Processes. ADVANCES IN THE ATOMIC-SCALE MODELING OF NANOSYSTEMS AND NANOSTRUCTURED MATERIALS 2010. [DOI: 10.1007/978-3-642-04650-6_3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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26
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Dong H, Nimlos MR, Himmel ME, Johnson DK, Qian X. The effects of water on beta-D-xylose condensation reactions. J Phys Chem A 2009; 113:8577-85. [PMID: 19572686 DOI: 10.1021/jp9025442] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Car-Parrinello-based ab initio molecular dynamics simulations (CPMD) combined with metadynamics (MTD) simulations were used to determine the reaction energetics for the beta-D-xylose condensation reaction to form beta-1,4-linked xylobiose in a dilute acid solution. Protonation of the hydroxyl group on the xylose molecule and the subsequent breaking of the C-O bond were found to be the rate-limiting step during the xylose condensation reaction. Water and water structure was found to play a critical role in these reactions due to the proton's high affinity for water molecules. The reaction free energy and reaction barrier were determined using CPMD-MTD. We found that solvent reorganization due to proton partial desolvation must be taken into account in order to obtain the correct reaction activation energy. Our calculated reaction free energy and reaction activation energy compare well with available experimental results.
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Affiliation(s)
- Haitao Dong
- Department of Mechanical Engineering, Colorado State University, Fort Collins, Colorado 80523, USA
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Silvestrelli PL. Are there immobilized water molecules around hydrophobic groups? Aqueous solvation of methanol from first principles. J Phys Chem B 2009; 113:10728-31. [PMID: 19606832 DOI: 10.1021/jp9044447] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Structural, dynamical, bonding, and electronic properties of water molecules around a soluted methanol molecule are studied from first principles. The results are compatible with experiments and qualitatively support the conclusions of recent classical molecular dynamics simulations concerning the controversial issue on the presence of "immobilized" water molecules around hydrophobic groups: the hydrophobic solute slightly reduces the mobility of many surrounding water molecules rather than immobilizing just the few ones which are closest to the methyl group. By generating maximally localized Wannier functions, a detailed description of the polarization effects in both solute and solvent molecules is obtained, which better elucidates the solvation process.
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Affiliation(s)
- Pier Luigi Silvestrelli
- Dipartimento di Fisica G. Galilei, Universita di Padova, via Marzolo 8, I-35131 Padova, Italy
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Dupureur CM. Roles of metal ions in nucleases. Curr Opin Chem Biol 2008; 12:250-5. [PMID: 18261473 DOI: 10.1016/j.cbpa.2008.01.012] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2007] [Accepted: 01/09/2008] [Indexed: 10/22/2022]
Abstract
The hydrolysis of phosphodiester bonds by metallonucleases is crucial to most aspects of nucleic acid processing. In recent years, studies of the classical restriction endonucleases have given way to the characterization of metallonucleases with widely divergent active site motifs. These developments fuel debates regarding the roles of metal ions in these enzymes. It is fortuitous that the current literature also includes the increased application of a variety of computational techniques to test the roles of metal ions in nucleic acid hydrolysis by these systems. This includes recent proposals and indirect evidence that these enzymes utilize metal ion movement in these reactions.
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Affiliation(s)
- Cynthia M Dupureur
- Department of Chemistry & Biochemistry and the Center for Nanoscience, University of Missouri-St. Louis, MC 27, One University Boulevard, St. Louis, MO 63121, United States.
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Boero M, Park JM, Hagiwara Y, Tateno M. First principles molecular dynamics study of catalytic reactions of biological macromolecular systems: toward analyses with QM/MM hybrid molecular simulations. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2007; 19:365217. [PMID: 21694162 DOI: 10.1088/0953-8984/19/36/365217] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
First principles molecular dynamics simulations performed on a fully solvated RNA model structure allowed us to investigate the mechanism for enzymatic cleavage reactions, in vitro, of RNA enzymes (ribozymes). The concerted action of two metal catalysts turns out to be the most efficient way to promote, on the one hand, the proton abstraction from 2(')-OH that triggers the nucleophilic attack and, on the other hand, the cleavage of the P-O(5(')) bond. In fact, the elimination of one of the two metal cations leads to an increase in the activation energy of the reaction. The simulated pathway shows that an OH(-) in the coordination shell of the Mg(2+) close to O(2(')) promotes the initial proton abstraction and prevents its transfer to the ribozyme. This suggests that, in a real ribozyme, the double-metal-ion reaction mechanism is preferred with respect to single-metal-ion mechanisms either in the presence or in absence of the OH(-) anion. Finally, an insight into the importance of hybrid quantum mechanics/molecular mechanics (QM/MM) schemes is discussed in view of the modelling of a realistic system carrying all the features of a true ribozyme.
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Affiliation(s)
- Mauro Boero
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan. CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan. Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8571, Japan
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Ikeda T, Boero M, Terakura K. Hydration properties of magnesium and calcium ions from constrained first principles molecular dynamics. J Chem Phys 2007; 127:074503. [PMID: 17718616 DOI: 10.1063/1.2768063] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
We studied the solvation structures of the divalent metal cations Mg(2+) and Ca(2+) in ambient water by applying a Car-Parrinello-based constrained molecular dynamics method. By employing the metal-water oxygen coordination number as a reaction coordinate, we could identify distinct aqua complexes characterized by structural variations of the first coordination shell. In particular, our estimated free-energy profile clearly shows that the global minimum for Mg(2+) is represented by a rather stable sixfold coordination in the octahedral arrangement, in agreement with experiments. Conversely, for Ca(2+) the free-energy curve shows several shallow local minima, suggesting that the hydration structure of Ca(2+) is highly variable. Implications for water exchange reactions are also discussed.
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Affiliation(s)
- Takashi Ikeda
- Quantum Beam Science Directorate, Japan Atomic Energy Agency (JAEA), 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
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Kamiya K, Boero M, Tateno M, Shiraishi K, Oshiyama A. Possible Mechanism of Proton Transfer through Peptide Groups in the H-Pathway of the Bovine CytochromecOxidase. J Am Chem Soc 2007; 129:9663-73. [PMID: 17636907 DOI: 10.1021/ja070464y] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The peptide group connecting Tyr440 and Ser441 of the bovine cytochrome c oxidase is involved in a recently proposed proton-transfer path (H-path) where, at variance with other pathways (D- and K-paths), a usual hydrogen-bond network is interrupted, thus making this proton propagation rather unconventional. Our density-functional based molecular dynamics simulations show that, despite this anomaly and provided that a proton can reach a nearby water, a multistep proton-transfer pathway can become a viable pathway for such a reaction: a proton is initially transferred to the carbonyl oxygen of a keto form of the Tyr440-Ser441 peptide group [-CO-NH-], producing an imidic acid [-C(OH)-NH-] as a metastable state; the amide proton of the imidic acid is then transferred, spontaneously to the deprotonated carboxyl group of the Asp51 side chain, leading to the formation of an enol form [-C(OH)=N-] of the Tyr440-Ser441 peptide group. Then a subsequent enol-to-keto tautomerization occurs via a double proton-transfer path realized in the two adjacent Tyr440-Ser441 and Ser441-Asp442 peptide groups. An analysis of this multistep proton-transfer pathway shows that each elementary process occurs through the shortest distance, no permanent conformational changes are induced, thus preserving the X-ray crystal structure, and the reaction path is characterized by a reasonable activation barrier.
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Affiliation(s)
- Katsumasa Kamiya
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8577, Japan
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Abstract
The hammerhead ribozyme is one of the best studied ribozymes, but it still presents challenges for our understanding of RNA catalysis. It catalyzes a transesterification reaction that converts a 5',3' diester to a 2',3' cyclic phosphate diester via an S(N)2 mechanism. Thus, the overall reaction corresponds to that catalyzed by bovine pancreatic ribonuclease. However, an essential distinguishing aspect is that metal ions are not involved in RNase catalysis but appear to be important in ribozymes. Although various techniques have been used to assign specific functions to metals in the hammerhead ribozyme, their number and roles in catalysis is not clear. Two recent theoretical studies on RNA catalysis examined the reaction mechanism of a single-metal-ion model. A two-metal-ion model, which is supported by experiment and based on ab initio and density functional theory calculations, is described here. The proposed mechanism of the reaction has four chemical steps with three intermediates and four transition states along the reaction pathway. Reaction profiles are calculated in the gas phase and in solution. The early steps of the reaction are found to be fast (with low activation barriers), and the last step, corresponding to the departure of the leaving group, is rate limiting. This two-metal-ion model differs from the models proposed previously in that the two metal ions function not only as Lewis acids but also as general acids/bases. Comparison with experiment shows good agreement with thermodynamic and kinetic data. A detailed analysis based on natural bond orbitals (NBOs) and natural energy decomposition (NEDA) provides insights into the role of metal ions and other factors important for catalysis.
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Affiliation(s)
- Fabrice Leclerc
- Laboratoire de Maturation des ARN et Enzymologie Moléculaire, Université Henri Poincaré, Faculté des Sciences, 54506 Vandoeuvre-lès-Nancy, France.
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Ikeda T, Boero M, Terakura K. Hydration of alkali ions from first principles molecular dynamics revisited. J Chem Phys 2007; 126:034501. [PMID: 17249878 DOI: 10.1063/1.2424710] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Structural and dynamical properties of the hydration of Li(+), Na(+), and K(+) in liquid water at ambient conditions were studied by first principles molecular dynamics. Our simulations successfully captured the different hydration behavior shown by the three alkali ions as observed in experiments. The present analyses of the dependence of the self-diffusion coefficient and rotational correlation time of water on the ion concentration suggest that Li(+) (K(+)) is certainly categorized as a structure maker (breaker), whereas Na(+) acts as a weak structure breaker. An analysis of the relevant electronic structures, based on maximally localized Wannier functions, revealed that the dipole moment of H(2)O molecules in the first solvation shell of Na(+) and K(+) decreases by about 0.1 D compared to that in the bulk, due to a contraction of the oxygen lone pair orbital pointing toward the metal ion.
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Affiliation(s)
- Takashi Ikeda
- Synchrotron Radiation Research Unit, Quantum Beam Science Directorate (QuBS), Japan Atomic Energy Agency (JAEA), 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
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Dal Peraro M, Ruggerone P, Raugei S, Gervasio FL, Carloni P. Investigating biological systems using first principles Car-Parrinello molecular dynamics simulations. Curr Opin Struct Biol 2007; 17:149-56. [PMID: 17419051 DOI: 10.1016/j.sbi.2007.03.018] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2006] [Revised: 01/11/2007] [Accepted: 03/20/2007] [Indexed: 11/25/2022]
Abstract
Density functional theory (DFT)-based Car-Parrinello molecular dynamics (CPMD) simulations describe the time evolution of molecular systems without resorting to a predefined potential energy surface. CPMD and hybrid molecular mechanics/CPMD schemes have recently enabled the calculation of redox properties of electron transfer proteins in their complex biological environment. They provided structural and spectroscopic information on novel platinum-based anticancer drugs that target DNA, also setting the basis for the construction of force fields for the metal lesion. Molecular mechanics/CPMD also lead to mechanistic hypotheses for a variety of metalloenzymes. Recent advances that increase the accuracy of DFT and the efficiency of investigating rare events are further expanding the domain of CPMD applications to biomolecules.
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Affiliation(s)
- Matteo Dal Peraro
- Center for Molecular Modeling, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
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Boero M, Ikeda T, Ito E, Terakura K. Hsc70 ATPase: an insight into water dissociation and joint catalytic role of K+ and Mg2+ metal cations in the hydrolysis reaction. J Am Chem Soc 2007; 128:16798-807. [PMID: 17177430 DOI: 10.1021/ja064117k] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Hybrid quantum mechanics/molecular mechanics simulations, coupled to the recently introduced metadynamics method, performed on the adenosine triphosphate (ATP) of the bovine Hsc70 ATPase protein, show which specific water molecule of the solvation shell of the Mg2+ metal cation acts as a trigger in the initial phase of the ATP hydrolysis reaction in ATP synthase. Furthermore, we provide a detailed picture of the reaction mechanism, not accessible to experimental probes, that allows us to address two important issues not yet unraveled: (i) the pathway followed by a proton and a hydroxyl anion, produced upon dissociation of a putative catalytic H2O molecule, that is crucial in the selection of the reaction channel leading to the hydrolysis; (ii) the unique and cooperative role of K+ and Mg2+ metal ions in the reaction, acting as co-catalysts and promoting the release of the inorganic phosphate via an exchange of the OH- hydroxyl anion between their respective solvation shells. This is deeply different from the proton wire mechanism evidenced, for instance, in actin and lowers significantly the free energy barrier of the reaction.
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Affiliation(s)
- Mauro Boero
- Center for Computational Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki 305-8577, Japan.
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36
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Boero M, Gervasio FL, Parrinello M. Charge localisation and hopping in DNA. MOLECULAR SIMULATION 2007. [DOI: 10.1080/08927020601052849] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Komeiji Y, Ishida T, Fedorov DG, Kitaura K. Change in a protein's electronic structure induced by an explicit solvent: Anab initio fragment molecular orbital study of ubiquitin. J Comput Chem 2007; 28:1750-62. [PMID: 17340606 DOI: 10.1002/jcc.20686] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The effect of solvation on the electronic structure of the ubiquitin protein was analyzed using the ab initio fragment molecular orbital (FMO) method. FMO calculations were performed for the protein in vacuo, and the protein was immersed in an explicit solvent shell as thick as 12 A at the HF or MP2 level by using the 6-31G* basis set. The protein's physical properties examined were the net charge, the dipole moment, the internal energy, and the solvent interaction energy. Comparison of the computational results revealed the following changes in the protein upon solvation. First, the positively charged amino acid residues on the protein surface drew electrons from the solvent, while the negatively charged ones transfer electrons to the solvent. Second, the dipole moment of the protein was enhanced as a result of the polarization. Third, the internal energy of the protein was destabilized, but the destabilization was more than compensated for by the generation of a favorable protein-solvent interaction. Finally, the energetic changes were elicited both by the electron correlation effect of the first solvent shell and by the electrostatic effect of more distant solvent molecules. These findings were consistent with the picture of the solvated protein being a polarizable molecule dissolved in a dielectric media.
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Affiliation(s)
- Yuto Komeiji
- Research Institute for Computational Sciences, AIST Tsukuba Central 2, Tsukuba 305-8568, Japan.
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Bresson C, Spezia R, Esnouf S, Solari PL, Coantic S, Den Auwer C. A combined spectroscopic and theoretical approach to investigate structural properties of Co(ii)/Co(iii) tris-cysteinato complexes in aqueous medium. NEW J CHEM 2007. [DOI: 10.1039/b707055a] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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39
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Kamiya K, Boero M, Shiraishi K, Oshiyama A. Enol-to-keto Tautomerism of Peptide Groups. J Phys Chem B 2006; 110:4443-50. [PMID: 16509747 DOI: 10.1021/jp056250p] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Density functional based simulations, performed on polyglycine containing an enol peptide group [-C(OH)N-] which is a structural isomer of a keto form [-CONH-], show that in the enol-to-keto tautomeric reaction, the enol peptide group is less stable than the keto form, and that the enol-to-keto tautomerism is characterized by a cis/trans isomerization of the C-N peptide bond. The rate-limiting step in the cis/trans isomerization is a hydrogen migration from O to N atoms in the peptide group with a transition state consisting of a four-membered ring in the cis configuration. An analysis of the cis/trans isomerization pathway shows that the mechanisms for the cis/trans isomerization are essentially different between the enol and keto forms.
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Affiliation(s)
- Katsumasa Kamiya
- Institute of Physics and Center for Computational Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki 305-8571, Japan.
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