1
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Field MJ. pDynamo3 Molecular Modeling and Simulation Program. J Chem Inf Model 2022; 62:5849-5854. [PMID: 36449463 DOI: 10.1021/acs.jcim.2c01239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
pDynamo3 is the first formal version of the Dynamo molecular modeling and simulation library that is written in Python 3. It follows from the previous pDynamo versions written in Python 2, the first of which was released in 2007. Both pDynamo and its predecessor, fDynamo, were designed with the aim of providing easy-to-use and flexible frameworks for performing molecular simulations at an atomistic level with a special emphasis on those employing hybrid quantum chemical and molecular mechanical potential methods. Although the use of pDynamo3 is quite similar to that of pDynamo2, it has added significant new capability and also undergone extensive restructuring that will make it much easier to extend with new functionality. The pDynamo3 code is issued under the GNU general public license at https://github.com/pdynamo/pDynamo3 with additional information on the pDynamo website https:www.pdynamo.org.
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Affiliation(s)
- Martin J Field
- Laboratoire de Chimie et Biologie des Métaux, UMR5249, Université Grenoble I, CEA, CNRS, 17 avenue des Martyrs, 38054 Cedex 9, Grenoble, France.,Theory Group, Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042 Cedex 9, Grenoble, France
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2
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Abstract
Density fitting is a standard technique in quantum chemistry as it helps to accelerate certain parts of a calculation, such as the computation of the electron repulsion energy, without significant loss of accuracy. This paper explores the effectiveness of this technique when it is extended to treat interactions with external electrostatic potentials, in particular those that arise from the environment in hybrid quantum chemical/molecular mechanical calculations. It is found that fitted densities are able to well reproduce the energies, forces, and properties obtained using unfitted densities, as long as a suitable operator is employed for the fitting. It is expected that this precision would be improved by the development of basis sets specifically designed to treat these types of interactions and that the use of this approximation could lead to substantial speed-ups in large hybrid potential simulations.
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Affiliation(s)
- Martin J Field
- Laboratoire de Chimie et Biologie des Métaux, UMR5249, Université Grenoble I, CEA, CNRS, 17 avenue des Martyrs, 38054 Cedex 9, Grenoble, France.,Theory Group, Institut Laue-Langevin, 71 avenue des Martyrs CS 20156, 38042 Cedex 9, Grenoble, France
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3
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Queyriaux N, Sun D, Fize J, Pécaut J, Field MJ, Chavarot-Kerlidou M, Artero V. Electrocatalytic Hydrogen Evolution with a Cobalt Complex Bearing Pendant Proton Relays: Acid Strength and Applied Potential Govern Mechanism and Stability. J Am Chem Soc 2019; 142:274-282. [PMID: 31760743 DOI: 10.1021/jacs.9b10407] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
[Co(bapbpy)Cl]+ (bapbpy: 6,6'-bis(2-aminopyridyl)-2,2'-bipyridine) is a polypyridyl cobalt(II) complex bearing both a redox-active bipyridine ligand and pendant proton relays. This compound catalyzes electro-assisted H2 evolution in DMF with distinct mechanisms depending on the strength of the acid used as the proton source (pKa values ranging from 3.4 to 13.5 in DMF) and the applied potential. Electrochemical studies combining cyclic voltammetry and bulk electrolysis measurements enabled one to bring out four distinct catalytic processes. Where applicable, relevant kinetic information were obtained using either foot-of-the-wave analysis (FOWA) or analytical treatment of bulk electrolysis experiments. Among the different catalytic pathways identified in this study, a clear relationship between the catalyst performances and stability was evidenced. These results draw attention to a number of interesting considerations and may help in the development of future adequately designed catalysts.
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Affiliation(s)
- Nicolas Queyriaux
- Univ. Grenoble Alpes , CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux, UMR 5249, 17 rue des Martyrs, 38000 Grenoble , France
| | - Dongyue Sun
- Univ. Grenoble Alpes , CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux, UMR 5249, 17 rue des Martyrs, 38000 Grenoble , France
| | - Jennifer Fize
- Univ. Grenoble Alpes , CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux, UMR 5249, 17 rue des Martyrs, 38000 Grenoble , France
| | - Jacques Pécaut
- Univ. Grenoble Alpes, CEA , CNRS, IRIG, SYMMES, UMR 5819 Equipe Chimie Interface Biologie pour l'Environnement la Santé et la Toxicologie, F-38054 Cedex 9 Grenoble , France
| | - Martin J Field
- Univ. Grenoble Alpes , CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux, UMR 5249, 17 rue des Martyrs, 38000 Grenoble , France
| | - Murielle Chavarot-Kerlidou
- Univ. Grenoble Alpes , CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux, UMR 5249, 17 rue des Martyrs, 38000 Grenoble , France
| | - Vincent Artero
- Univ. Grenoble Alpes , CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux, UMR 5249, 17 rue des Martyrs, 38000 Grenoble , France
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4
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Abstract
Iron-sulfur (FeS) clusters are essential metal cofactors involved in a wide variety of biological functions. Their catalytic efficiency, biosynthesis, and regulation depend on FeS stability in aqueous solution. Here, molecular modeling is used to investigate the hydrolysis of an oxidized (ferric) mononuclear FeS cluster by bare dissociation and water substitution mechanisms in neutral and acidic solution. First, approximate electronic structure descriptions of FeS reactions by density functional theory are validated against high-level wave function CCSD(T) calculations. Solvation contributions are included by an all-atom model with hybrid quantum chemical/molecular mechanical (QM/MM) potentials and enhanced sampling molecular dynamics simulations. The free energy profile obtained for FeS cluster hydrolysis indicates that the hybrid functional M06 together with an implicit solvent correction capture the most important aspects of FeS cluster reactivity in aqueous solution. Then, 20 reaction channels leading to two consecutive Fe-S bond ruptures were explored with this calibrated model. For all protonation states, nucleophilic substitution with concerted bond breaking and forming to iron is the preferred mechanism, both kinetic and thermodynamically. In neutral solution, proton transfer from water to the sulfur leaving group is also concerted. Dissociative reactions show higher barriers and will not be relevant for FeS reactivity when exposed to solvent. These hydrolysis mechanisms may help to explain the stability and catalytic mechanisms of FeS clusters of multiple sizes and proteins.
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Affiliation(s)
- Murilo H Teixeira
- Department of Biochemistry, Instituto de Química , Universidade de São Paulo , Av. Prof. Lineu Prestes 748 , 05508-900 São Paulo , SP , Brazil
| | - Felipe Curtolo
- Department of Biochemistry, Instituto de Química , Universidade de São Paulo , Av. Prof. Lineu Prestes 748 , 05508-900 São Paulo , SP , Brazil
| | - Sofia R G Camilo
- Department of Biochemistry, Instituto de Química , Universidade de São Paulo , Av. Prof. Lineu Prestes 748 , 05508-900 São Paulo , SP , Brazil
| | - Martin J Field
- CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux , Université Grenoble Alpes , 17 rue des Martyrs , 38000 Grenoble , France.,Institut Laue-Langevin , BP 156, 41 Avenue des Martyrs , 38042 Grenoble , Cedex 9, France
| | - Peng Zheng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing , Jiangsu 210023 , China
| | - Hongbin Li
- Department of Chemistry , University of British Columbia , Vancouver , British Columbia V6T 1Z1 , Canada
| | - Guilherme M Arantes
- Department of Biochemistry, Instituto de Química , Universidade de São Paulo , Av. Prof. Lineu Prestes 748 , 05508-900 São Paulo , SP , Brazil
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5
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Zarkadoulas A, Field MJ, Artero V, Mitsopoulou CA. Proton reduction reaction catalyzed by homoleptic nickel bis-1,2-dithiolate complexes: Experimental and theoretical mechanistic investigations. ChemCatChem 2017; 9:2308-2317. [PMID: 28670348 PMCID: PMC5490785 DOI: 10.1002/cctc.201601399] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Indexed: 01/01/2023]
Abstract
A series of homoleptic monoanionic nickel dithiolene complexes [Ni(bdt)2](NBu4), [Ni(tdt)2](NBu4), and [Ni(mnt)2](NBu4) containing the ligands benzene-1,2-dithiolate (bdt2-), toluene-3,4-dithiolate (tdt2-) and maleonitriledithiolate (mnt2-), respectively, have been employed as electrocatalysts in the hydrogen evolution reaction with trifluoroacetic acid as proton source in acetonitrile. All complexes were active catalysts with TONs reaching 113, 158 and 6 for [Ni(bdt)2](NBu4), [Ni(tdt)2](NBu4), and [Ni(mnt)2](NBu4), respectively. Faradaic yield for hydrogen evolution reaction reaches 88 % for 2- , which also displays the minimal overpotential requirement value (467 mV) within the series. Two pathways for H2 evolution can be hypothesized that differ on on the sequence of protonation and reduction steps. DFT calculations are in agreement with experimental data and indicate that protonation at sulfur follows reduction to the dianion. Hydrogen evolves from the direduced-diprotonated form via a highly distorted nickel hydride intermediate. The effects of acid strength and concentration in the hydrogen-evolving mechanism are also discussed.
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Affiliation(s)
- Athanasios Zarkadoulas
- Inorganic Chemistry Laboratory, Chemistry Department, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou 157 71, Greece
| | - Martin J. Field
- DYNAMO/DYNAMOP, Institut de Biologie Structurale, UMR CNRS/Université Grenoble Alpes/CEA 5075, EPN Campus, 6 rue Jules Horowitz F-38000 Grenoble, France
| | - Vincent Artero
- Laboratory of Chemistry and Biology of Metals, Université Grenoble Alpes, CNRS, CEA, 17 rue des Martyrs, F-38000 Grenoble, France
| | - Christiana A. Mitsopoulou
- Inorganic Chemistry Laboratory, Chemistry Department, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou 157 71, Greece
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6
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Garen J, Field MJ, Kneller G, Karplus M, Smith J. Torsional motions of methyl and ammonium groups in the L-alanine crystal : a comparison of molecular dynamics and normal mode calculations. ACTA ACUST UNITED AC 2017. [DOI: 10.1051/jcp/1991882587] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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7
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Shaik MM, Bhattacharjee N, Feliks M, Ng KKS, Field MJ. Norovirus RNA-dependent RNA polymerase: A computational study of metal-binding preferences. Proteins 2017; 85:1435-1445. [PMID: 28383118 DOI: 10.1002/prot.25304] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 03/31/2017] [Accepted: 04/04/2017] [Indexed: 12/21/2022]
Abstract
Norovirus (NV) RNA-dependent RNA polymerase (RdRP) is essential for replicating the genome of the virus, which makes this enzyme a key target for the development of antiviral agents against NV gastroenteritis. In this work, a complex of NV RdRP bound to manganese ions and an RNA primer-template duplex was investigated using X-ray crystallography and hybrid quantum chemical/molecular mechanical simulations. Experimentally, the complex crystallized in a tetragonal crystal form. The nature of the primer/template duplex binding in the resulting structure indicates that the complex is a closed back-tracked state of the enzyme, in which the 3'-end of the primer occupies the position expected for the post-incorporated nucleotide before translocation. Computationally, it is found that the complex can accept a range of divalent metal cations without marked distortions in the active site structure. The highest binding energy is for copper, followed closely by manganese and iron, and then by zinc, nickel, and cobalt. Proteins 2017; 85:1435-1445. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Md Munan Shaik
- Division of Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, 02115.,Department of Pediatrics, Harvard Medical School, 3 Blackfan Street, Boston, Massachusetts, 02115
| | - Nicholus Bhattacharjee
- Dynamo Team/DYNAMOP Group, UMR5075, Université Grenoble I, CEA, CNRS, Institut de Biologie Structurale, 71 Avenue des Martyrs, CS 10090, Grenoble Cedex 9, 38044, France
| | - Mikolaj Feliks
- Dynamo Team/DYNAMOP Group, UMR5075, Université Grenoble I, CEA, CNRS, Institut de Biologie Structurale, 71 Avenue des Martyrs, CS 10090, Grenoble Cedex 9, 38044, France
| | - Kenneth K-S Ng
- Department of Biological Sciences and Alberta Glycomics Centre, University of Calgary, Calgary, Alberta, Canada
| | - Martin J Field
- Dynamo Team/DYNAMOP Group, UMR5075, Université Grenoble I, CEA, CNRS, Institut de Biologie Structurale, 71 Avenue des Martyrs, CS 10090, Grenoble Cedex 9, 38044, France
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8
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Affiliation(s)
- Martin J. Field
- Dynamo Team/DYNAMOP Group,
UMR5075, Université Grenoble I, CEA, CNRS, Institut de Biologie Structurale, 71 Avenue des Martyrs, CS 10090, 38044 Grenoble Cedex 9, France
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9
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Affiliation(s)
- Nicholus Bhattacharjee
- Dynamo
Team/DYNAMOP Group, UMR5075, Université Grenoble I, CEA, CNRS, Institut de Biologie Structurale, 71 Avenue des Martyrs, CS 10090, 38044 Grenoble Cedex 9, France
| | - Mikolaj Feliks
- Dynamo
Team/DYNAMOP Group, UMR5075, Université Grenoble I, CEA, CNRS, Institut de Biologie Structurale, 71 Avenue des Martyrs, CS 10090, 38044 Grenoble Cedex 9, France
| | - Md Munan Shaik
- Division
of Molecular Medicine, Boston Children’s Hospital, Boston, Massachusetts 02115, United States
- Department
of Pediatrics, Harvard Medical School, 3 Blackfan Street, Boston, Massachusetts 02115, United States
| | - Martin J. Field
- Dynamo
Team/DYNAMOP Group, UMR5075, Université Grenoble I, CEA, CNRS, Institut de Biologie Structurale, 71 Avenue des Martyrs, CS 10090, 38044 Grenoble Cedex 9, France
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10
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Bacchi M, Veinberg E, Field MJ, Niklas J, Matsui T, Tiede DM, Poluektov OG, Ikeda‐Saito M, Fontecave M, Artero V. Artificial Hydrogenases Based on Cobaloximes and Heme Oxygenase. Chempluschem 2016; 81:1083-1089. [DOI: 10.1002/cplu.201600218] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 06/06/2016] [Indexed: 11/07/2022]
Affiliation(s)
- Marine Bacchi
- Laboratory of Chemistry and Biology of Metals, UMR 5249 Université Grenoble Alpes, CNRS, CEA 17 rue des Martyrs 38054 Grenoble Cedex 9 France
| | - Elias Veinberg
- DYNAMO/DYNAMOP Institut de Biologie Structurale “Jean-Pierre Ebel”, UMR 5075 Université Grenoble Alpes, CNRS, CEA 41 rue Jules Horowitz 38027 Grenoble Cedex 1 France
| | - Martin J. Field
- DYNAMO/DYNAMOP Institut de Biologie Structurale “Jean-Pierre Ebel”, UMR 5075 Université Grenoble Alpes, CNRS, CEA 41 rue Jules Horowitz 38027 Grenoble Cedex 1 France
| | - Jens Niklas
- Chemical Sciences and Engineering Division Argonne National Laboratory 9700 South Cass Avenue, Lemont, IL 60439 USA
| | - Toshitaka Matsui
- Institute of Multidisciplinary Research for Advanced Materials Tohoku University Katahira, Aoba Sendai 980-8577 Japan
| | - D. M. Tiede
- Chemical Sciences and Engineering Division Argonne National Laboratory 9700 South Cass Avenue, Lemont, IL 60439 USA
| | - Oleg G. Poluektov
- Chemical Sciences and Engineering Division Argonne National Laboratory 9700 South Cass Avenue, Lemont, IL 60439 USA
| | - Masao Ikeda‐Saito
- Institute of Multidisciplinary Research for Advanced Materials Tohoku University Katahira, Aoba Sendai 980-8577 Japan
| | - Marc Fontecave
- Laboratory of Chemistry and Biology of Metals, UMR 5249 Université Grenoble Alpes, CNRS, CEA 17 rue des Martyrs 38054 Grenoble Cedex 9 France
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 Collège de France, CNRS Université Pierre et Marie Curie 11 place Marcellin Berthelot 75005 Paris France
| | - Vincent Artero
- Laboratory of Chemistry and Biology of Metals, UMR 5249 Université Grenoble Alpes, CNRS, CEA 17 rue des Martyrs 38054 Grenoble Cedex 9 France
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11
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Bhattacharjee N, Field MJ, Simorre JP, Arthur M, Bougault CM. Hybrid Potential Simulation of the Acylation of Enterococcus faecium l,d-Transpeptidase by Carbapenems. J Phys Chem B 2016; 120:4767-81. [DOI: 10.1021/acs.jpcb.6b02836] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nicholus Bhattacharjee
- DYNAMO/DYNAMOP,
UMR 5075, Université Grenoble 1, CNRS, CEA, Institut de Biologie
Structurale, 71 Avenue des Martyrs,
CS 10090, 38044 Grenoble Cedex 9, France
| | - Martin J. Field
- DYNAMO/DYNAMOP,
UMR 5075, Université Grenoble 1, CNRS, CEA, Institut de Biologie
Structurale, 71 Avenue des Martyrs,
CS 10090, 38044 Grenoble Cedex 9, France
| | - Jean-Pierre Simorre
- RMN, UMR 5075,
Université Grenoble 1, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des Martyrs, CS 10090, 38044 Grenoble Cedex 9, France
| | - Michel Arthur
- Centre de Recherche
des Cordeliers, Equipe 12, UMR S 872, Université Pierre et
Marie Curie-Paris 6, INSERM, Université Paris Descartes, Sorbonne
Paris Cité, 15 rue de l’Ecole
de Médecine, 75006 Paris, France
| | - Catherine M. Bougault
- RMN, UMR 5075,
Université Grenoble 1, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des Martyrs, CS 10090, 38044 Grenoble Cedex 9, France
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12
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Zarkadoulas A, Field MJ, Papatriantafyllopoulou C, Fize J, Artero V, Mitsopoulou CA. Experimental and Theoretical Insight into Electrocatalytic Hydrogen Evolution with Nickel Bis(aryldithiolene) Complexes as Catalysts. Inorg Chem 2016; 55:432-44. [PMID: 26645557 PMCID: PMC5493980 DOI: 10.1021/acs.inorgchem.5b02000] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A series of neutral and monoanionic nickel dithiolene complexes with p-methoxyphenyl-substituted 1,2-dithiolene ligands have been prepared and characterized with physicochemical methods. Two of the complexes, the monoanion of the symmetric [Ni{S2C2(Ph-p-OCH3)2}2] (3(-)) with NBu4(+) as a counterion and the neutral asymmetric [Ni{S2C2(Ph)(Ph-p-OCH3)}2] (2), have been structurally characterized by single-crystal X-ray crystallography. All complexes have been employed as proton-reducing catalysts in N,N-dimethylformamide with trifluoroacetic acid as the proton source. The complexes are active catalysts with good faradaic yields, reaching 83% for 2 but relatively high overpotential requirements (0.91 and 1.55 V measured at the middle of the catalytic wave for two processes observed depending on the different routes of the mechanism). The similarity of the experimental data regardless of whether the neutral or anionic form of the complexes is used indicates that the neutral form acts as a precatalyst. On the basis of detailed density functional theory calculations, the proposed mechanism reveals two different main routes after protonation of the dianion of the catalyst in accordance with the experimental data, indicating the role of the concentration of the acid and the influence of the methoxy groups. Protonation at sulfur seems be more favorable than that at the metal, which is in marked contrast with the catalytic mechanism proposed for analogous cobalt dithiolene complexes.
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Affiliation(s)
- Athanasios Zarkadoulas
- Inorganic Chemistry Laboratory, Chemistry Department, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou 157 71, Greece
| | - Martin J. Field
- DYNAMO/DYNAMOP, Institut de Biologie Structurale, UMR CNRS/Université Grenoble Alpes/CEA 5075, EPN Campus, 6 rue Jules Horowitz F-38000 Grenoble, France
| | | | - Jennifer Fize
- Laboratory of Chemistry and Biology of Metals, Université Grenoble Alpes, CNRS, CEA, 17 rue des Martyrs, F-38000 Grenoble, France
| | - Vincent Artero
- Laboratory of Chemistry and Biology of Metals, Université Grenoble Alpes, CNRS, CEA, 17 rue des Martyrs, F-38000 Grenoble, France
| | - Christiana A. Mitsopoulou
- Inorganic Chemistry Laboratory, Chemistry Department, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou 157 71, Greece
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13
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Crous W, Field MJ, Naidoo KJ. Simple Link Atom Saccharide Hybrid (SLASH) Treatment for Glycosidic Bonds at the QM/MM Boundary. J Chem Theory Comput 2015; 10:1727-38. [PMID: 26580381 DOI: 10.1021/ct400903n] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We investigated link atom approaches for treating the polar C-O bond with particular reference to the glycosidic bond found in complex carbohydrates. We show that cutting this bond after the oxygen in the QM region and saturating the QM system with a hydrogen link atom leads to greater conformational and configurational accuracy at the boundary compared with cutting the bond before oxygen and saturating the QM system with a halogen link atom to represent the oxygen. Furthermore, we find that balancing the MM atom charges and redistributing the boundary atom charges at the QM/MM boundary minimizes the effect of the link atom, both energetically and structurally. This is illustrated via a series of calculations on a set of carbohydrate and carbohydrate-like model compounds. Finally, we confirm the validity of our model by performing molecular dynamics simulations for a typical disaccharide model compound in water. Our postsimulation conformational and configurational analyses show that the oxygen-to-water hydrogen pair distribution functions and the Φ,Ψ distributions at the glycosidic boundary between the quantum and classical regions compare favorably with results obtained from complete QM and complete MM treatments of the saccharide.
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Affiliation(s)
| | - Martin J Field
- Institut de Biologie Structurale - Jean-Pierre Ebel CEA/CNRS/UJF, 41, rue Jules Horowitz, 38027 Grenoble Cedex 1, France
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14
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Abstract
The pDynamo program has been developed for the simulation of molecular systems using hybrid quantum chemical (QC) and molecular mechanical (MM) potentials. pDynamo is written in a mixture of the computer languages Python and C and is a successor to the previous version of Dynamo, now denoted fDynamo, that was written in Fortran 90 (J. Comput. Chem. 2000, 21, 1088). The current version of Dynamo has a similar range of functionality to the older one but extends it in some significant ways, including the addition of a density functional theory QC capability. This paper gives a general description of pDynamo and outlines some of the advantages and disadvantages that have been encountered in switching computer languages. Some technical aspects of the implementation of pDynamo's algorithms are also discussed and illustrated with the results of example calculations. pDynamo is available on the Web at the address http://www.pdynamo.org and is released under the CeCILL license which is equivalent to the GNU general public license but conforms to the principles of French law.
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Affiliation(s)
- Martin J Field
- Laboratoire de Dynamique Moléculaire Institut de Biologie Structurale - Jean-Pierre Ebel (CEA/CNRS/UJF - UMR 9075), 41 Rue Jules Horowitz, F - 38027 Grenoble, Cedex 01, France
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15
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Affiliation(s)
- Mikolaj Feliks
- Université Grenoble Alpes, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- CEA, IBS, F-38044 Grenoble, France
| | - Martin J. Field
- Université Grenoble Alpes, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- CEA, IBS, F-38044 Grenoble, France
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16
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Affiliation(s)
- Guilherme Menegon Arantes
- Department
of Biochemistry, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-900, São Paulo, SP Brazil
| | - Martin J. Field
- Institut
de Biologie Structurale (IBS), CEA/CNRS/Université Joseph Fourier, 71 Avenue
des Martyrs, CS 10090, 38044 Grenoble Cedex 9, France
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17
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Zheng P, Arantes GM, Field MJ, Li H. Force-induced chemical reactions on the metal centre in a single metalloprotein molecule. Nat Commun 2015; 6:7569. [PMID: 26108369 PMCID: PMC4491811 DOI: 10.1038/ncomms8569] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 05/19/2015] [Indexed: 02/06/2023] Open
Abstract
Metalloproteins play indispensable roles in biology owing to the versatile chemical reactivity of metal centres. However, studying their reactivity in many metalloproteins is challenging, as protein three-dimensional structure encloses labile metal centres, thus limiting their access to reactants and impeding direct measurements. Here we demonstrate the use of single-molecule atomic force microscopy to induce partial unfolding to expose metal centres in metalloproteins to aqueous solution, thus allowing for studying their chemical reactivity in aqueous solution for the first time. As a proof-of-principle, we demonstrate two chemical reactions for the FeS4 centre in rubredoxin: electrophilic protonation and nucleophilic ligand substitution. Our results show that protonation and ligand substitution result in mechanical destabilization of the FeS4 centre. Quantum chemical calculations corroborated experimental results and revealed detailed reaction mechanisms. We anticipate that this novel approach will provide insights into chemical reactivity of metal centres in metalloproteins under biologically more relevant conditions. The investigation of the chemical reactivity of metal centres in metalloproteins in aqueous solution is challenging. Here, the authors demonstrate the use of single molecule force spectroscopy to study the chemical reactivity of the iron-sulfur centre in rubredoxin in aqueous solution.
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Affiliation(s)
- Peng Zheng
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z1.,School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210063, P. R. China
| | - Guilherme M Arantes
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Avenue Lineu Prestes 748, São Paulo SP 05508-900, Brazil
| | - Martin J Field
- Institut de Biologie Structurale (IBS) Jean-Pierre Ebel, CEA/CNRS/Universite Joseph Fourier, 71 Avenue des Martyrs, CS 10090, Grenoble 9 38044, France
| | - Hongbin Li
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z1
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18
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Massin J, Bräutigam M, Kaeffer N, Queyriaux N, Field MJ, Schacher FH, Popp J, Chavarot-Kerlidou M, Dietzek B, Artero V. Dye-sensitized PS-b-P2VP-templated nickel oxide films for photoelectrochemical applications. Interface Focus 2015; 5:20140083. [PMID: 26052420 DOI: 10.1098/rsfs.2014.0083] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Moving from homogeneous water-splitting photocatalytic systems to photoelectrochemical devices requires the preparation and evaluation of novel p-type transparent conductive photoelectrode substrates. We report here on the sensitization of polystyrene-block-poly-(2-vinylpyridine) (PS-b-P2VP) diblock copolymer-templated NiO films with an organic push-pull dye. The potential of these new templated NiO film preparations for photoelectrochemical applications is compared with NiO material templated by F108 triblock copolymers. We conclude that NiO films are promising materials for the construction of dye-sensitized photocathodes to be inserted into photoelectrochemical (PEC) cells. However, a combined effort at the interface between materials science and molecular chemistry, ideally funded within a Global Artificial Photosynthesis Project, is still needed to improve the overall performance of the photoelectrodes and progress towards economically viable PEC devices.
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Affiliation(s)
- Julien Massin
- Laboratoire de Chimie et Biologie des Métaux , University Grenoble Alpes , CNRS, CEA, 17 rue des martyrs, 38000 Grenoble , France
| | - Maximilian Bräutigam
- Leibniz Institute of Photonic Technology (IPHT) Jena e. V. , Albert-Einstein-Strasse 9, Jena 07745 , Germany ; Institute for Physical Chemistry and Abbe Center of Photonics , Friedrich Schiller University Jena , Helmholtzweg 4, Jena 07743 , Germany
| | - Nicolas Kaeffer
- Laboratoire de Chimie et Biologie des Métaux , University Grenoble Alpes , CNRS, CEA, 17 rue des martyrs, 38000 Grenoble , France
| | - Nicolas Queyriaux
- Laboratoire de Chimie et Biologie des Métaux , University Grenoble Alpes , CNRS, CEA, 17 rue des martyrs, 38000 Grenoble , France
| | - Martin J Field
- Institut de Biologie Structurale Jean-Pierre Ebel , University Grenoble Alpes , CNRS, CEA, 71 rue des martyrs, 38000 Grenoble , France
| | - Felix H Schacher
- Institute of Organic Chemistry and Macromolecular Chemistry and Jena Center for Soft Matter (JCSM) , Friedrich-Schiller-University Jena , Lessingstrasse 8, Jena 07743 , Germany
| | - Jürgen Popp
- Leibniz Institute of Photonic Technology (IPHT) Jena e. V. , Albert-Einstein-Strasse 9, Jena 07745 , Germany ; Institute for Physical Chemistry and Abbe Center of Photonics , Friedrich Schiller University Jena , Helmholtzweg 4, Jena 07743 , Germany
| | - Murielle Chavarot-Kerlidou
- Laboratoire de Chimie et Biologie des Métaux , University Grenoble Alpes , CNRS, CEA, 17 rue des martyrs, 38000 Grenoble , France
| | - Benjamin Dietzek
- Leibniz Institute of Photonic Technology (IPHT) Jena e. V. , Albert-Einstein-Strasse 9, Jena 07745 , Germany ; Institute for Physical Chemistry and Abbe Center of Photonics , Friedrich Schiller University Jena , Helmholtzweg 4, Jena 07743 , Germany
| | - Vincent Artero
- Laboratoire de Chimie et Biologie des Métaux , University Grenoble Alpes , CNRS, CEA, 17 rue des martyrs, 38000 Grenoble , France
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19
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Zhang R, Bhattacharjee A, Field MJ, Salahub DR. Multiple proton relay routes in the reaction mechanism of RNAP II: Assessing the effect of structural model. Proteins 2014; 83:268-81. [DOI: 10.1002/prot.24732] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 11/05/2014] [Accepted: 11/06/2014] [Indexed: 12/22/2022]
Affiliation(s)
- Rui Zhang
- Department of Chemistry; Centre for Molecular Simulation, Institute for Quantum Science and Technology, University of Calgary; Calgary Canada
| | - Anirban Bhattacharjee
- Department of Chemistry; Centre for Molecular Simulation, Institute for Quantum Science and Technology, University of Calgary; Calgary Canada
| | - Martin J. Field
- DYNAMOP; Institut de Biologie Structurale, Jean-Pierre Ebel; Grenoble France
| | - Dennis R. Salahub
- Department of Chemistry; Centre for Molecular Simulation, Institute for Quantum Science and Technology, University of Calgary; Calgary Canada
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20
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Bhattacharjee A, Chavarot-Kerlidou M, Dempsey JL, Gray HB, Fujita E, Muckerman JT, Fontecave M, Artero V, Arantes GM, Field MJ. Theoretical modeling of low-energy electronic absorption bands in reduced cobaloximes. Chemphyschem 2014; 15:2951-8. [PMID: 25113847 DOI: 10.1002/cphc.201402398] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 07/08/2014] [Indexed: 11/07/2022]
Abstract
The reduced Co(I) states of cobaloximes are powerful nucleophiles that play an important role in the hydrogen-evolving catalytic activity of these species. In this work we analyze the low-energy electronic absorption bands of two cobaloxime systems experimentally and use a variety of density functional theory and molecular orbital ab initio quantum chemical approaches. Overall we find a reasonable qualitative understanding of the electronic excitation spectra of these compounds but show that obtaining quantitative results remains a challenging task.
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Affiliation(s)
- Anirban Bhattacharjee
- Dynamo Team, DYNAMOP Group, Institut de Biologie Structurale-Jean-Pierre Ebel, UMR 5075, Université Grenoble 1, CNRS, CEA, 71 Avenue des Martyrs, CS 10090, 38044 Grenoble Cedex 9 (France)
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21
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Abstract
The 2013 Nobel Prize in Chemistry was awarded to the authors of the first two publications utilizing the concept of combined quantum mechanical and molecular mechanical (QM/MM) methods. In celebrating this great event in computational chemistry, we review the early development of combined QM/MM techniques and the associated events that took place through the mid-1990s. We also offer some prospects for the future development of quantum mechanical techniques for macromolecular systems.
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Affiliation(s)
- Meiyi Liu
- State Key Laboratory of Theoretical and Computational Chemistry, Theoretical Chemistry Institute, Jilin University, Changchun, Jilin Province (China)
| | - Yingjie Wang
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis MN 55455 (USA)
| | - Yakun Chen
- State Key Laboratory of Theoretical and Computational Chemistry, Theoretical Chemistry Institute, Jilin University, Changchun, Jilin Province (China)
| | - Martin J Field
- Institut de Biologie Structrale, CEA, CNRS, umr5075, Université Joseph Fourier - Grenoble I, 6 rue Jules Horowitz, 38000 Grenoble (France)
| | - Jiali Gao
- State Key Laboratory of Theoretical and Computational Chemistry, Theoretical Chemistry Institute, Jilin University, Changchun, Jilin Province (China)
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis MN 55455 (USA)
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22
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Bacchi M, Berggren G, Niklas J, Veinberg E, Mara MW, Shelby ML, Poluektov OG, Chen LX, Tiede DM, Cavazza C, Field MJ, Fontecave M, Artero V. Cobaloxime-Based Artificial Hydrogenases. Inorg Chem 2014; 53:8071-82. [DOI: 10.1021/ic501014c] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Marine Bacchi
- Laboratory of Chemistry and Biology of
Metals, Université Grenoble Alpes, CNRS, CEA, 17 rue des
Martyrs, F-38000 Grenoble, France
| | - Gustav Berggren
- Laboratory of Chemistry and Biology of
Metals, Université Grenoble Alpes, CNRS, CEA, 17 rue des
Martyrs, F-38000 Grenoble, France
| | - Jens Niklas
- Chemical Sciences and Engineering
Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439, United States
| | - Elias Veinberg
- DYNAMO/DYNAMOP, Institut de Biologie Structurale, UMR
CNRS/Université Grenoble Alpes/CEA 5075, EPN Campus, 6 rue Jules Horowitz F-38000 Grenoble, France
| | - Michael W. Mara
- Department of Chemistry, Northwestern University, 2145 Sheridan
Road, Evanston, Illinois 60208, United States
| | - Megan L. Shelby
- Department of Chemistry, Northwestern University, 2145 Sheridan
Road, Evanston, Illinois 60208, United States
| | - Oleg G. Poluektov
- Chemical Sciences and Engineering
Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439, United States
| | - Lin X. Chen
- Chemical Sciences and Engineering
Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439, United States
- Department of Chemistry, Northwestern University, 2145 Sheridan
Road, Evanston, Illinois 60208, United States
| | - David M. Tiede
- Chemical Sciences and Engineering
Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439, United States
| | - Christine Cavazza
- Laboratory of Chemistry and Biology of
Metals, Université Grenoble Alpes, CNRS, CEA, 17 rue des
Martyrs, F-38000 Grenoble, France
| | - Martin J. Field
- DYNAMO/DYNAMOP, Institut de Biologie Structurale, UMR
CNRS/Université Grenoble Alpes/CEA 5075, EPN Campus, 6 rue Jules Horowitz F-38000 Grenoble, France
| | - Marc Fontecave
- Laboratory of Chemistry and Biology of
Metals, Université Grenoble Alpes, CNRS, CEA, 17 rue des
Martyrs, F-38000 Grenoble, France
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 (Collège
de France, CNRS, Université Pierre et Marie Curie), 11 place Marcellin Berthelot 75005 Paris, France
| | - Vincent Artero
- Laboratory of Chemistry and Biology of
Metals, Université Grenoble Alpes, CNRS, CEA, 17 rue des
Martyrs, F-38000 Grenoble, France
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23
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MacKerell AD, Bashford D, Bellott M, Dunbrack RL, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau FT, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher WE, Roux B, Schlenkrich M, Smith JC, Stote R, Straub J, Watanabe M, Wiórkiewicz-Kuczera J, Yin D, Karplus M. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 2014; 102:3586-616. [PMID: 24889800 DOI: 10.1021/jp973084f] [Citation(s) in RCA: 11569] [Impact Index Per Article: 1156.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
New protein parameters are reported for the all-atom empirical energy function in the CHARMM program. The parameter evaluation was based on a self-consistent approach designed to achieve a balance between the internal (bonding) and interaction (nonbonding) terms of the force field and among the solvent-solvent, solvent-solute, and solute-solute interactions. Optimization of the internal parameters used experimental gas-phase geometries, vibrational spectra, and torsional energy surfaces supplemented with ab initio results. The peptide backbone bonding parameters were optimized with respect to data for N-methylacetamide and the alanine dipeptide. The interaction parameters, particularly the atomic charges, were determined by fitting ab initio interaction energies and geometries of complexes between water and model compounds that represented the backbone and the various side chains. In addition, dipole moments, experimental heats and free energies of vaporization, solvation and sublimation, molecular volumes, and crystal pressures and structures were used in the optimization. The resulting protein parameters were tested by applying them to noncyclic tripeptide crystals, cyclic peptide crystals, and the proteins crambin, bovine pancreatic trypsin inhibitor, and carbonmonoxy myoglobin in vacuo and in crystals. A detailed analysis of the relationship between the alanine dipeptide potential energy surface and calculated protein φ, χ angles was made and used in optimizing the peptide group torsional parameters. The results demonstrate that use of ab initio structural and energetic data by themselves are not sufficient to obtain an adequate backbone representation for peptides and proteins in solution and in crystals. Extensive comparisons between molecular dynamics simulations and experimental data for polypeptides and proteins were performed for both structural and dynamic properties. Energy minimization and dynamics simulations for crystals demonstrate that the latter are needed to obtain meaningful comparisons with experimental crystal structures. The presented parameters, in combination with the previously published CHARMM all-atom parameters for nucleic acids and lipids, provide a consistent set for condensed-phase simulations of a wide variety of molecules of biological interest.
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Affiliation(s)
- A D MacKerell
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, Department of Pharmaceutical Sciences, University of Maryland, School of Pharmacy, Baltimore, Maryland 21201, and Laboratoire de Chimie Biophysique, ISIS, Institut Le Bel, Université Louis Pasteur, 67000 Strasbourg, France
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24
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Bhattacharjee A, Weiss AKH, Artero V, Field MJ, Hofer TS. Electronic Structure and Hydration of Tetramine Cobalt Hydride Complexes. J Phys Chem B 2014; 118:5551-61. [DOI: 10.1021/jp502651s] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Anirban Bhattacharjee
- DYNAMO/DYNAMOP,
Institut de Biologie Structurale (UMR5075, CEA, CNRS, Université Grenoble I), 6 rue Jules Horowitz, 38000 Grenoble, France
| | - Alexander K. H. Weiss
- Department
of Theoretical Chemistry, Institute of General, Inorganic and Theoretical
Chemistry, University of Innsbruck, Inrain 80-82, A-6020 Innsbruck, Austria
| | - Vincent Artero
- Laboratoire
de Chimie et Biologie des Métaux (UMR 5249, CNRS,
CEA, Université Grenoble I), DSV/iRTSV,
CEA-Grenoble, 17 rue des Martyrs, F-38054 Grenoble Cedex 9, France
| | - Martin J. Field
- DYNAMO/DYNAMOP,
Institut de Biologie Structurale (UMR5075, CEA, CNRS, Université Grenoble I), 6 rue Jules Horowitz, 38000 Grenoble, France
| | - Thomas S. Hofer
- Department
of Theoretical Chemistry, Institute of General, Inorganic and Theoretical
Chemistry, University of Innsbruck, Inrain 80-82, A-6020 Innsbruck, Austria
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25
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Wymore T, Field MJ, Langan P, Smith JC, Parks JM. Hydrolysis of DFP and the nerve agent (S)-sarin by DFPase proceeds along two different reaction pathways: implications for engineering bioscavengers. J Phys Chem B 2014; 118:4479-89. [PMID: 24720808 PMCID: PMC4010294 DOI: 10.1021/jp410422c] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
![]()
Organophosphorus
(OP) nerve agents such as (S)-sarin
are among the most highly toxic compounds that have been synthesized.
Engineering enzymes that catalyze the hydrolysis of nerve agents (“bioscavengers”)
is an emerging prophylactic approach to diminish their toxic effects.
Although its native function is not known, diisopropyl fluorophosphatase
(DFPase) from Loligo vulgaris catalyzes
the hydrolysis of OP compounds. Here, we investigate the mechanisms
of diisopropylfluorophosphate (DFP) and (S)-sarin
hydrolysis by DFPase with quantum mechanical/molecular mechanical
umbrella sampling simulations. We find that the mechanism for hydrolysis
of DFP involves nucleophilic attack by Asp229 on phosphorus to form
a pentavalent intermediate. P–F bond dissociation then yields
a phosphoacyl enzyme intermediate in the rate-limiting step. The simulations
suggest that a water molecule, coordinated to the catalytic Ca2+, donates a proton to Asp121 and then attacks the tetrahedral
phosphoacyl intermediate to liberate the diisopropylphosphate product.
In contrast, the calculated free energy barrier for hydrolysis of
(S)-sarin by the same mechanism is highly unfavorable,
primarily because of the instability of the pentavalent phosphoenzyme
species. Instead, simulations suggest that hydrolysis of (S)-sarin proceeds by a mechanism in which Asp229 could activate
an intervening water molecule for nucleophilic attack on the substrate.
These findings may lead to improved strategies for engineering DFPase
and related six-bladed β-propeller folds for more efficient
degradation of OP compounds.
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Affiliation(s)
- Troy Wymore
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831-6309, United States
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26
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Munan Shaik M, Bhattacharjee N, Bhattacharjee A, Field MJ, Zanotti G. Characterization of the divalent metal binding site of bacterial polysaccharide deacetylase using crystallography and quantum chemical calculations. Proteins 2014; 82:1311-8. [DOI: 10.1002/prot.24497] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Revised: 11/18/2013] [Accepted: 12/09/2013] [Indexed: 12/20/2022]
Affiliation(s)
- Md Munan Shaik
- PATBAC, Institut de Biologie Structurale-Jean-Pierre Ebel; Grenoble France
| | | | | | - Martin J. Field
- DYNAMOP, Institut de Biologie Structurale-Jean-Pierre Ebel; Grenoble France
| | - Giuseppe Zanotti
- Department of Biomedical Sciences; University of Padua; Padua Italy
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27
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Abstract
Hybrid quantum chemical/molecular mechanical (QCMM) potentials are very powerful tools for molecular simulation. They are especially useful for studying processes in condensed phase systems, such as chemical reactions that involve a relatively localized change in electronic structure and where the surrounding environment contributes to these changes but can be represented with more computationally efficient functional forms. Despite their utility, however, these potentials are not always straightforward to apply since the extent of significant electronic structure changes occurring in the condensed phase process may not be intuitively obvious. To facilitate their use, we have developed an open-source graphical plug-in, GTKDynamo that links the PyMOL visualization program and the pDynamo QC/MM simulation library. This article describes the implementation of GTKDynamo and its capabilities and illustrates its application to QC/MM simulations.
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Affiliation(s)
- José Fernando R Bachega
- Centro de Biotecnologia Molecular Estrutural, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos–SP, Brazil.
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28
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Bhattacharjee A, Andreiadis ES, Chavarot-Kerlidou M, Fontecave M, Field MJ, Artero V. A Computational Study of the Mechanism of Hydrogen Evolution by Cobalt(Diimine-Dioxime) Catalysts. Chemistry 2013; 19:15166-74. [DOI: 10.1002/chem.201301860] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Indexed: 12/13/2022]
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30
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Arantes GM, Bhattacharjee A, Field MJ. Homolytic Cleavage of FeS Bonds in Rubredoxin under Mechanical Stress. Angew Chem Int Ed Engl 2013; 52:8144-6. [DOI: 10.1002/anie.201303462] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Indexed: 11/07/2022]
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31
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Baggioli A, Crescenzi O, Field MJ, Castiglione F, Raos G. Computational 17O-NMRspectroscopy of organic acids and peracids: comparison of solvation models. Phys Chem Chem Phys 2013; 15:1130-40. [DOI: 10.1039/c2cp43021e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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32
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Canaguier S, Fourmond V, Perotto CU, Fize J, Pécaut J, Fontecave M, Field MJ, Artero V. Catalytic hydrogen production by a Ni–Ru mimic of NiFe hydrogenases involves a proton-coupled electron transfer step. Chem Commun (Camb) 2013; 49:5004-6. [DOI: 10.1039/c3cc40987b] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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33
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Bhattacharjee A, Chavarot-Kerlidou M, Andreiadis ES, Fontecave M, Field MJ, Artero V. Combined Experimental–Theoretical Characterization of the Hydrido-Cobaloxime [HCo(dmgH)2(PnBu3)]. Inorg Chem 2012; 51:7087-93. [DOI: 10.1021/ic2024204] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anirban Bhattacharjee
- Dynamo Team, DYNAMOP Group,
UMR 5075, Université Grenoble 1,
CNRS, CEA; Institut de Biologie Structurale “Jean-Pierre Ebel”,
41 rue Jules Horowitz, 38027 Grenoble Cedex 1, France
| | - Murielle Chavarot-Kerlidou
- Laboratoire de Chimie et Biologie
des Métaux, UMR 5249, Université Grenoble 1, CNRS, CEA DSV/iRTSV; CEA-Grenoble, 17 rue des Martyrs
F-38054 Grenoble Cedex 9, France
| | - Eugen. S. Andreiadis
- Laboratoire de Chimie et Biologie
des Métaux, UMR 5249, Université Grenoble 1, CNRS, CEA DSV/iRTSV; CEA-Grenoble, 17 rue des Martyrs
F-38054 Grenoble Cedex 9, France
| | - Marc Fontecave
- Laboratoire de Chimie et Biologie
des Métaux, UMR 5249, Université Grenoble 1, CNRS, CEA DSV/iRTSV; CEA-Grenoble, 17 rue des Martyrs
F-38054 Grenoble Cedex 9, France
- Collège de France, 11 place Marcellin-Berthelot, 75005 Paris, France
| | - Martin J. Field
- Dynamo Team, DYNAMOP Group,
UMR 5075, Université Grenoble 1,
CNRS, CEA; Institut de Biologie Structurale “Jean-Pierre Ebel”,
41 rue Jules Horowitz, 38027 Grenoble Cedex 1, France
| | - Vincent Artero
- Laboratoire de Chimie et Biologie
des Métaux, UMR 5249, Université Grenoble 1, CNRS, CEA DSV/iRTSV; CEA-Grenoble, 17 rue des Martyrs
F-38054 Grenoble Cedex 9, France
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34
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Nasiri R, Field MJ, Zahedi M, Moosavi-Movahedi AA. Comparative DFT Study To Determine if α-Oxoaldehydes are Precursors for Pentosidine Formation. J Phys Chem A 2012; 116:2986-96. [DOI: 10.1021/jp2104165] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Rasoul Nasiri
- Department of Chemistry, Faculty of Sciences, Shahid Beheshti University, Evin, 19839-63113,
Tehran, Iran
| | - Martin J. Field
- DYNAMO Team,
DYNAMOP Group, Institut de Biologie Structurale—Jean-Pierre Ebel, CNRS-CEA-UJF (UMR5075), Grenoble, France
| | - Mansour Zahedi
- Department of Chemistry, Faculty of Sciences, Shahid Beheshti University, Evin, 19839-63113,
Tehran, Iran
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35
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Affiliation(s)
- Arijit Roy
- Institut de Biologie Structurale (IBS)—Jean-Pierre Ebel, CEA/CNRS/Université Joseph Fourier, 41, rue Jules Horowitz, 38027 Grenoble Cedex 1, France
| | - Martin J. Field
- Institut de Biologie Structurale (IBS)—Jean-Pierre Ebel, CEA/CNRS/Université Joseph Fourier, 41, rue Jules Horowitz, 38027 Grenoble Cedex 1, France
| | - Virgile Adam
- Laboratory of Photochemistry and Spectroscopy, Department of Chemistry, Katholieke Universiteit Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - Dominique Bourgeois
- Institut de Biologie Structurale (IBS)—Jean-Pierre Ebel, CEA/CNRS/Université Joseph Fourier, 41, rue Jules Horowitz, 38027 Grenoble Cedex 1, France
- Pixel Team, IBS/Institut de Recherches en Technologies et Sciences pour le Vivant, iRTSV, Laboratoire de Physiologie Cellulaire et Végétale, CNRS/CEA/INRA/Université Joseph Fourier, 38054 Grenoble, France
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36
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Nasiri R, Field MJ, Zahedi M, Moosavi-Movahedi AA. Cross-Linking Mechanisms of Arginine and Lysine with α,β-Dicarbonyl Compounds in Aqueous Solution. J Phys Chem A 2011; 115:13542-55. [DOI: 10.1021/jp205558d] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Rasoul Nasiri
- Department of Chemistry, Faculty of Sciences, Shahid Beheshti University, Evin, 19839-63113 Tehran, Iran
| | - Martin J. Field
- Laboratoire de Dynamique Moléculaire, Institut de Biologie Structurale-Jean-Pierre Ebel, CNRS-CEA-UJF (UMR5075), Grenoble, France
| | - Mansour Zahedi
- Department of Chemistry, Faculty of Sciences, Shahid Beheshti University, Evin, 19839-63113 Tehran, Iran
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Abstract
Enzymes catalyzing phosphoryl transfer reactions are extremely efficient and are involved in crucial biochemical processes. The mechanisms of these enzymes are complex due to the diversity of substrates that are involved. The reaction can proceed through a pentacoordinated phosphorus species that is either a stable intermediate or a transition state (TS). Because of this, the first X-ray structure of a pentacoordinated phosphorus intermediate in the beta-phosphoglucomutase enzyme aroused great interest but also much controversy. To provide new insights into the nature of that structure, we have determined the reaction path of the phosphorylation step using high-level QM/MM calculations, and have also calculated the geometry of a complex with a transition state analogue (TSA) that has been suggested to be the actual species in the crystal. The protein crystalline environment has been modeled so as to mimic the experimental conditions. We conclude that the pentacoordinated phosphorus formed in this enzyme is not a stable species but a TS, which gives an activation energy for phosphorylation in agreement with kinetic results. We also show that the TSA is a good mimic of the true TS. We have performed a new crystallographic refinement of the original diffraction map of the pentacoordinated phosphorus structure with the MgF(3)(-) TSA. The new fit improves significantly with respect to the original one, which strongly supports that Allen and coworkers wrongly assigned the X-ray structure to a pentavalent phosphorane.
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Affiliation(s)
- Enrique Marcos
- Departament de Química Biològica i Modelització Molecular, Institut de Química Avançada de Catalunya (CSIC), Barcelona, Spain
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Hagiwara Y, Field MJ, Nureki O, Tateno M. Editing mechanism of aminoacyl-tRNA synthetases operates by a hybrid ribozyme/protein catalyst. J Am Chem Soc 2010; 132:2751-8. [PMID: 20136139 DOI: 10.1021/ja9095208] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Aminoacyl-tRNA synthetases (aaRSs) are critical for the translational process, catalyzing the attachment of specific amino acids to their cognate tRNAs. To ensure formation of the correct aminoacyl-tRNA, and thereby enhance the reliability of translation, several aaRSs have an editing capability that hinders formation of misaminoacylated tRNAs. We investigated theoretically the mechanism of the editing reaction for a class I enzyme, leucyl-tRNA synthetase (LeuRS), complexed with a misaminoacylated tRNA(Leu), employing ab initio hybrid quantum mechanical/molecular mechanical potentials in conjunction with molecular dynamics simulations. It is shown that the water molecule that acts as the nucleophile in the editing reaction is activated by a 3'-hydroxyl group at the 3'-end of tRNA(Leu) and that the O2' atom of the leaving group of the substrate is capped by one of the water's hydrogen atoms. Thus, it is shown that editing is a self-cleavage reaction of the tRNA and so it is the tRNA, and not the protein, that drives the reaction. The protein does, however, have an important stabilizing effect on some high-energy intermediates along the reaction path, which is more efficient than the ribozyme would be alone. This indicates that editing is achieved by a novel "hybrid ribozyme/protein catalyst". Analysis of existing experimental data and additional modeling shows that this ribozymal mechanism appears to be widespread, occurring in the ribosome as well as in other aaRSs. It also suggests transitional forms that could have played an important role in the RNA world hypothesis for the origin of life.
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Affiliation(s)
- Yohsuke Hagiwara
- Center for Computational Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba Science City, Ibaraki 305-8577, Japan
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Canaguier S, Vaccaro L, Artero V, Ostermann R, Pécaut J, Field MJ, Fontecave M. Cyclopentadienyl ruthenium-nickel catalysts for biomimetic hydrogen evolution: electrocatalytic properties and mechanistic DFT studies. Chemistry 2010; 15:9350-64. [PMID: 19670195 DOI: 10.1002/chem.200900854] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The new dinuclear nickel-ruthenium complexes [Ni(xbsms)RuCp(L)][PF(6)] (H(2)xbsms = 1,2-bis(4-mercapto-3,3-dimethyl-2-thiabutyl)benzene; Cp(-) = cyclopentadienyl; L = DMSO, CO, PPh(3), and PCy(3)) are reported and are bioinspired mimics of NiFe hydrogenases. These compounds were characterized by X-ray diffraction techniques and display novel structural motifs. Interestingly, [Ni(xbsms)RuCpCO][PF(6)] is stereochemically nonrigid in solution and an isomerization mechanism was derived with the help of density functional theory (DFT) calculations. Because of an increased electron density on the metal centers [Eur. J. Inorg. Chem. 2007, 18, 2613-2626] with respect to the previously described [Ni(xbsms)Ru(CO)(2)Cl(2)] and [Ni(xbsms)Ru(p-cymene)Cl](+) complexes, [Ni(xbsms)RuCp(dmso)][PF(6)] catalyzes hydrogen evolution from Et(3)NH(+) in DMF with an overpotential reduced by 180 mV and thus represents the most efficient NiFe hydrogenase functional mimic. DFT calculations were carried out with several methods to investigate the catalytic cycle and, coupled with electrochemical measurements, allowed a mechanism to be proposed. A terminal or bridging hydride derivative was identified as the active intermediate, with the structure of the bridging form similar to that of the Ni-C active state of NiFe hydrogenases.
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Affiliation(s)
- Sigolène Canaguier
- Laboratoire de Chimie et Biologie des Métaux, Université Joseph Fourier, Grenoble, France
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Vaccaro L, Artero V, Canaguier S, Fontecave M, Field MJ. Mechanism of hydrogen evolution catalyzed by NiFe hydrogenases: insights from a Ni–Ru model compound. Dalton Trans 2010; 39:3043-9. [DOI: 10.1039/b912690b] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Lelimousin M, Adam V, Nienhaus GU, Bourgeois D, Field MJ. Photoconversion of the fluorescent protein EosFP: a hybrid potential simulation study reveals intersystem crossings. J Am Chem Soc 2009; 131:16814-23. [PMID: 19886627 DOI: 10.1021/ja905380y] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fluorescent proteins undergoing green to red photoconversion have proved to be essential tools in cell biology, notably in superlocalization nanoscopy. However, the exact mechanism governing photoconversion, which overall involves irreversible cleavage of the protein backbone and elongation of the chromophore pi-conjugation, remains unclear. In this paper we present a theoretical investigation of the photoconversion reaction in the fluorescent protein EosFP, using excited-state hybrid quantum chemical and molecular mechanical potentials, in conjunction with reaction-path-finding techniques. Our results reveal a mechanism in which the hydroxybenzylidene moiety of the chromophore remains protonated and there is an excited state proton transfer from His62 to Phe61 that promotes peptide bond cleavage. Excitation of the neutral green form of EosFP to the first singlet excited state is followed by two intersystem crossing events, first to a triplet state and then back to the ground state singlet surface. From there, a number of rearrangements occur in the ground state and lead to the red form. Analyses of the structures and energies of the intermediates along the reaction path enable us to identify the critical role of the chromophore environment in promoting photoinduced backbone cleavage. Possible ways in which photoconvertible fluorescent proteins can be engineered to facilitate photoconversion are considered.
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Affiliation(s)
- Mickaël Lelimousin
- CNRS, UMR5075, Institut de Biologie Structurale Jean-Pierre Ebel, 41 rue Jules Horowitz, 38027 Grenoble Cedex 1, France
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Lelimousin M, Noirclerc-Savoye M, Lazareno-Saez C, Paetzold B, Le Vot S, Chazal R, Macheboeuf P, Field MJ, Bourgeois D, Royant A. Intrinsic Dynamics in ECFP and Cerulean Control Fluorescence Quantum Yield. Biochemistry 2009; 48:10038-46. [DOI: 10.1021/bi901093w] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mickaël Lelimousin
- Institut de Biologie Structurale Jean-Pierre Ebel, UMR 5075 CNRS-CEA-Université Joseph Fourier, 41 rue Jules Horowitz, F-38027 Grenoble Cedex 1, France
| | - Marjolaine Noirclerc-Savoye
- Institut de Biologie Structurale Jean-Pierre Ebel, UMR 5075 CNRS-CEA-Université Joseph Fourier, 41 rue Jules Horowitz, F-38027 Grenoble Cedex 1, France
| | - Christelle Lazareno-Saez
- Institut de Biologie Structurale Jean-Pierre Ebel, UMR 5075 CNRS-CEA-Université Joseph Fourier, 41 rue Jules Horowitz, F-38027 Grenoble Cedex 1, France
| | - Bernhard Paetzold
- European Synchrotron Radiation Facility, 6 Rue Jules Horowitz, BP 220, F-38043 Grenoble Cedex, France
| | - Sophie Le Vot
- Institut de Biologie Structurale Jean-Pierre Ebel, UMR 5075 CNRS-CEA-Université Joseph Fourier, 41 rue Jules Horowitz, F-38027 Grenoble Cedex 1, France
| | - Richard Chazal
- Institut de Biologie Structurale Jean-Pierre Ebel, UMR 5075 CNRS-CEA-Université Joseph Fourier, 41 rue Jules Horowitz, F-38027 Grenoble Cedex 1, France
| | - Pauline Macheboeuf
- Institut de Biologie Structurale Jean-Pierre Ebel, UMR 5075 CNRS-CEA-Université Joseph Fourier, 41 rue Jules Horowitz, F-38027 Grenoble Cedex 1, France
| | - Martin J. Field
- Institut de Biologie Structurale Jean-Pierre Ebel, UMR 5075 CNRS-CEA-Université Joseph Fourier, 41 rue Jules Horowitz, F-38027 Grenoble Cedex 1, France
| | - Dominique Bourgeois
- Institut de Biologie Structurale Jean-Pierre Ebel, UMR 5075 CNRS-CEA-Université Joseph Fourier, 41 rue Jules Horowitz, F-38027 Grenoble Cedex 1, France
- European Synchrotron Radiation Facility, 6 Rue Jules Horowitz, BP 220, F-38043 Grenoble Cedex, France
| | - Antoine Royant
- Institut de Biologie Structurale Jean-Pierre Ebel, UMR 5075 CNRS-CEA-Université Joseph Fourier, 41 rue Jules Horowitz, F-38027 Grenoble Cedex 1, France
- European Synchrotron Radiation Facility, 6 Rue Jules Horowitz, BP 220, F-38043 Grenoble Cedex, France
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Affiliation(s)
- Shantanu Roy
- Departement Physik, Universität Basel, Klingelbergstr. 82, 4056 Basel, Switzerland and Laboratoire de Dynamique Moléculaire, Institut de Biologie Structurale—Jean-Pierre Ebel (CEA/CNRS/UJF), 41 rue Jules Horowitz, 38027 Grenoble Cedex 1, France
| | - Stefan Goedecker
- Departement Physik, Universität Basel, Klingelbergstr. 82, 4056 Basel, Switzerland and Laboratoire de Dynamique Moléculaire, Institut de Biologie Structurale—Jean-Pierre Ebel (CEA/CNRS/UJF), 41 rue Jules Horowitz, 38027 Grenoble Cedex 1, France
| | - Martin J. Field
- Departement Physik, Universität Basel, Klingelbergstr. 82, 4056 Basel, Switzerland and Laboratoire de Dynamique Moléculaire, Institut de Biologie Structurale—Jean-Pierre Ebel (CEA/CNRS/UJF), 41 rue Jules Horowitz, 38027 Grenoble Cedex 1, France
| | - Evgeni Penev
- Departement Physik, Universität Basel, Klingelbergstr. 82, 4056 Basel, Switzerland and Laboratoire de Dynamique Moléculaire, Institut de Biologie Structurale—Jean-Pierre Ebel (CEA/CNRS/UJF), 41 rue Jules Horowitz, 38027 Grenoble Cedex 1, France
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Mather A, Chen XM, McGinn S, Field MJ, Sumual S, Mangiafico S, Zhang Y, Kelly DJ, Pollock CA. High glucose induced endothelial cell growth inhibition is associated with an increase in TGFbeta1 secretion and inhibition of Ras prenylation via suppression of the mevalonate pathway. Int J Biochem Cell Biol 2008; 41:561-9. [PMID: 18692592 DOI: 10.1016/j.biocel.2008.07.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2008] [Revised: 06/26/2008] [Accepted: 07/10/2008] [Indexed: 11/29/2022]
Abstract
OBJECTIVE Ras proteins are known to affect cellular growth and function. The influence of the prenylation status of Ras on the observed changes in endothelial cell growth under high glucose conditions has not previously been examined. METHODS Human umbilical vein endothelial cells were exposed to normal or high glucose conditions for 72 h. They were then examined for proliferative and hypertrophic effects, transforming growth factor beta(1) (TGFbeta(1)) release, and phosphorylated p38 expression. The importance of prenylation was explored by the addition of mevalonate, isoprenoids or farnesyltransferase inhibitors to control the high glucose media and by measuring changes induced by high glucose and exogenous TGFbeta(1) in Ras prenylation and farnesyltransferase activity. Kidneys from diabetic rats treated with atorvastatin were also compared to specimens from untreated animals and the expression of the Ras effector p-Akt examined. RESULTS High glucose conditions caused a reduction in cell number. This was reversed in the presence of mevalonate or farnesylpyrophosphate (FPP), suggesting that the cell growth abnormalities observed are due to high glucose induced inhibition of the mevalonate pathway and subsequent prenylation of proteins. Endothelial cells exposed to high glucose increased their secretion of TGFbeta(1) and the phosphorylation of p38 both of which were reversed by concurrent exposure to FPP. A reduction in farnesyltransferase activity was observed after exposure to both high glucose and TGFbeta(1). Exposure to a farnesyltransferase inhibitor in control conditions mimicked the growth response observed with high glucose exposure and prenylated Ras was reduced by exposure to both high glucose and TGFbeta(1). Finally, interruption of the mevalonate pathway with a statin reduced the expression of p-Akt in diabetic rat kidneys. CONCLUSION This study demonstrates that high glucose induced significant alterations in endothelial cell growth by inhibition of the mevalonate pathway, which subsequently mediates the increase in TGFbeta(1) and inhibition of Ras prenylation.
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Affiliation(s)
- A Mather
- Renal Research Laboratory, Kolling Institute, Royal North Shore Hospital, University of Sydney, NSW, Australia
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45
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Fdez. Galván I, Volbeda A, Fontecilla-Camps JC, Field MJ. A QM/MM study of proton transport pathways in a [NiFe] hydrogenase. Proteins 2008; 73:195-203. [DOI: 10.1002/prot.22045] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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46
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Amara P, Fdez Galván I, Fontecilla-Camps JC, Field MJ. The enamine intermediate may not be universal to thiamine catalysis. Angew Chem Int Ed Engl 2008; 46:9019-22. [PMID: 17955561 DOI: 10.1002/anie.200702993] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Patricia Amara
- Laboratoire de Dynamique Moléculaire, Institut de Biologie Structurale Jean-Pierre Ebel, CEA, 41 rue Jules Horowitz, 38027 Grenoble, France.
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Lepsík M, Field MJ. Binding of calcium and other metal ions to the EF-hand loops of calmodulin studied by quantum chemical calculations and molecular dynamics simulations. J Phys Chem B 2007; 111:10012-22. [PMID: 17661504 DOI: 10.1021/jp0716583] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Calcium ion binding by the four EF-hand motifs of the protein calmodulin (CaM) is a central event in Ca2+-based cellular signaling. To understand molecular details of this complex process, isolated Ca2+-binding loops can be studied, by use of both experiments and calculations. In this work, we explore the metal specificity of the four Ca2+-binding loops of CaM using density functional theory (DFT) quantum chemical calculations and molecular dynamics simulations. We study CaM complexes with the physiologically important ions of calcium (Ca2+) and magnesium (Mg2+) and also with two other ions, strontium (Sr2+) and lanthanum (La3+). The former is of interest in the area of radioactive waste bioremediation, whereas the latter is often used as a probe of Ca2+-binding sites. We obtain intrinsic metal ion-loop binding energies as well as their components: vacuum, charge-transfer, solvation, entropy, and deformation terms. A detailed analysis of the results reveals that the total binding energy depends on a delicate balance among these energy components. They, in turn, are determined by the cation's charge and size as well as the amino acid composition and flexibility of the loops and the identity of the metal-chelating residues.
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Affiliation(s)
- Martin Lepsík
- Laboratoire de Dynamique Moléculaire, Institut de Biologie Structurale-Jean-Pierre Ebel, 41 rue Jules Horowitz, 38027 Grenoble Cedex 1, France.
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Blackbeard J, O'Dea KP, Wallace VCJ, Segerdahl A, Pheby T, Takata M, Field MJ, Rice ASC. Quantification of the rat spinal microglial response to peripheral nerve injury as revealed by immunohistochemical image analysis and flow cytometry. J Neurosci Methods 2007; 164:207-17. [PMID: 17553569 PMCID: PMC2726922 DOI: 10.1016/j.jneumeth.2007.04.013] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2007] [Revised: 04/17/2007] [Accepted: 04/22/2007] [Indexed: 12/29/2022]
Abstract
Microgliosis is implicated in the pathophysiology of several neurological disorders, including neuropathic pain. Consequently, perturbation of microgliosis is a mechanistic and drug development target in neuropathic pain, which highlights the requirement for specific, sensitive and reproducible methods of microgliosis measurement. In this study, we used the spinal microgliosis associated with L5 spinal nerve transection and minocycline-induced attenuation thereof to: (1) evaluate novel software based semi-quantitative image analysis paradigms for the assessment of immunohistochemical images. Microgliosis was revealed by immunoreactivity to OX42. Several image analysis paradigms were assessed and compared to a previously validated subjective categorical rating scale. This comparison revealed that grey scale measurement of the proportion of a defined area of spinal cord occupied by OX42 immunoreactive cells is a robust image analysis paradigm. (2) Develop and validate a flow cytometric approach for quantification of spinal microgliosis. The flow cytometric technique reliably quantified microgliosis in spinal cord cell suspensions, using OX42 and ED9 immunoreactivity to identify microglia. The results suggest that image analysis of immunohistochemical revelation of microgliosis reliably detects the spinal microgliosis in response to peripheral nerve injury and pharmacological attenuation thereof. In addition, flow cytometry provides an alternative approach for quantitative analysis of spinal microgliosis elicited by nerve injury.
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Affiliation(s)
- J Blackbeard
- Department of Anaesthetics, Pain Medicine and Intensive Care, Faculty of Medicine, Imperial College London, Chelsea and Westminster Hospital Campus, 369 Fulham Road, London SW10 9NH, UK.
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Abstract
The study of the chemical steps in enzyme-catalyzed reactions represents a challenge for molecular simulation techniques. One concern is how to calculate paths for the reaction. Common techniques include the definition of a reaction coordinate in terms of a small set of (normally) geometrical variables or the determination of minimum energy paths on the potential energy surface of the reacting system. Both have disadvantages, the former because it presupposes knowledge of which variables are likely to be important for reaction and the latter because it provides a static picture and dynamical effects are ignored. In this paper, we employ the transition path sampling method developed by Chandler and co-workers, which overcomes some of these limitations. The reaction that we have chosen is the chorismate-mutase-catalyzed conversion of chorismate into prephenate, which has become something of a test case for simulation studies of enzyme mechanisms. We generated an ensemble of approximately 1000 independent transition paths for the reaction in the enzyme and another approximately 500 for the corresponding reaction in solution. A large variety of analyses of these paths was performed, but we have concentrated on characterizing the transition state ensemble, particularly the flexibility of its structures with respect to other ligands of the enzyme and the time evolution of various geometrical and energetic properties as the reaction proceeds. We have also devised an approximate technique for locating transition state structures along the paths.
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Affiliation(s)
- Ramon Crehuet
- Departament de Química Orgànica Biologica Institut de Investigaciones Químiques i Ambientals de Barcelona, Consejo Superior de Investigaciones Cientificas, Jordi Girona 18, 08034 Barcelona, Catalonia, Spain.
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50
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Puig E, Garcia-Viloca M, Gonzalez-Lafont A, Lluch JM, Field MJ. New insights into the reaction mechanism catalyzed by the glutamate racemase enzyme: pH titration curves and classical molecular dynamics simulations. J Phys Chem B 2007; 111:2385-97. [PMID: 17286428 DOI: 10.1021/jp066350a] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The mechanism of the reactions catalyzed by the pyridoxal-phosphate-independent amino acid racemases and epimerases faces the difficult task of deprotonating a relatively low acidicity proton, the amino acid's alpha-hydrogen, with a relatively poor base, a cysteine. In this work, we propose a mechanism for one of these enzymes, glutamate racemase (MurI), about which many controversies exist, and the roles that its active site residues may play. The titration curves and the pK1/2 values of all of the ionizable residues for different structures leading from reactants to products have been analyzed. From these results a concerted mechanism has been proposed in which the Cys70 residue would deprotonate the alpha-hydrogen of the substrate while, at the same time, being deprotonated by the Asp7 residue. To study the consistency of this mechanism classical molecular dynamics (MD) simulations have been carried out along with pK1/2 calculations on the MD-generated structures.
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Affiliation(s)
- Eduard Puig
- Departament de Química and Institut de Biotecnologia i de Biomedicina, Universitat Autonoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
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