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Bergmann J, Oksanen E, Ryde U. Quantum-refinement studies of the bidentate ligand of V‑nitrogenase and the protonation state of CO-inhibited Mo‑nitrogenase. J Inorg Biochem 2021; 219:111426. [PMID: 33756394 DOI: 10.1016/j.jinorgbio.2021.111426] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/19/2021] [Accepted: 03/10/2021] [Indexed: 10/21/2022]
Abstract
Nitrogenase is the only enzyme that can cleave the triple bond in N2, making nitrogen available to plants (although the enzyme itself is strictly microbial). It has been studied extensively with both experimental and computational methods, but many details of the reaction mechanism are still unclear. X-ray crystallography is the main source of structural information for biomacromolecules, but it has problems to discern hydrogen atoms or to distinguish between elements with the same number of electrons. These problems can sometimes be alleviated by introducing quantum chemical calculations in the refinement, providing information about the ideal structure (in the same way as the empirical restraints used in standard crystallographic refinement) and comparing different interpretations of the structure with normal crystallographic and quantum mechanical quality measures. We have performed such quantum-refinement calculations to address two important issues for nitrogenase. First, we show that the bidentate ligand of the active-site FeV cluster in V‑nitrogenase is carbonate, rather than bicarbonate or nitrate. Second, we study the CO-inhibited structure of Mo‑nitrogenase. CO binds to a reduced and protonated state of the enzyme by replacing one of the sulfide ions (S2B) in the active-site FeMo cluster. We examined if it is possible to deduce from the crystal structure the location of the protons. Our results indicates that the crystal structure is best modelled as fully deprotonated.
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Affiliation(s)
- Justin Bergmann
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Esko Oksanen
- European Spallation Source ESS ERIC, Lund, Sweden
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden.
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2
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Cao L, Ryde U. Quantum refinement with multiple conformations: application to the P-cluster in nitrogenase. Acta Crystallogr D Struct Biol 2020; 76:1145-1156. [PMID: 33135685 PMCID: PMC7604908 DOI: 10.1107/s2059798320012917] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 09/21/2020] [Indexed: 11/17/2022] Open
Abstract
X-ray crystallography is the main source of atomistic information on the structure of proteins. Normal crystal structures are obtained as a compromise between the X-ray scattering data and a set of empirical restraints that ensure chemically reasonable bond lengths and angles. However, such restraints are not always available or accurate for nonstandard parts of the structure, for example substrates, inhibitors and metal sites. The method of quantum refinement, in which these empirical restraints are replaced by quantum-mechanical (QM) calculations, has previously been suggested for small but interesting parts of the protein. Here, this approach is extended to allow for multiple conformations in the QM region by performing separate QM calculations for each conformation. This approach is shown to work properly and leads to improved structures in terms of electron-density maps and real-space difference density Z-scores. It is also shown that the quality of the structures can be gauged using QM strain energies. The approach, called ComQumX-2QM, is applied to the P-cluster in two different crystal structures of the enzyme nitrogenase, i.e. an Fe8S7Cys6 cluster, used for electron transfer. One structure is at a very high resolution (1.0 Å) and shows a mixture of two different oxidation states, the fully reduced PN state (Fe82+, 20%) and the doubly oxidized P2+ state (80%). In the original crystal structure the coordinates differed for only two iron ions, but here it is shown that the two states also show differences in other atoms of up to 0.7 Å. The second structure is at a more modest resolution, 2.1 Å, and was originally suggested to show only the one-electron oxidized state, P1+. Here, it is shown that it is rather a 50/50% mixture of the P1+ and P2+ states and that many of the Fe-Fe and Fe-S distances in the original structure were quite inaccurate (by up to 0.8 Å). This shows that the new ComQumX-2QM approach can be used to sort out what is actually seen in crystal structures with dual conformations and to give locally improved coordinates.
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Affiliation(s)
- Lili Cao
- Department of Theoretical Chemistry, Lund University, PO Box 124, 221 00 Lund, Sweden
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, PO Box 124, 221 00 Lund, Sweden
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3
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Cao L, Caldararu O, Ryde U. Does the crystal structure of vanadium nitrogenase contain a reaction intermediate? Evidence from quantum refinement. J Biol Inorg Chem 2020; 25:847-861. [PMID: 32856107 PMCID: PMC7511287 DOI: 10.1007/s00775-020-01813-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 08/14/2020] [Indexed: 12/16/2022]
Abstract
Recently, a crystal structure of V-nitrogenase was presented, showing that one of the µ2 sulphide ions in the active site (S2B) is replaced by a lighter atom, suggested to be NH or NH2, i.e. representing a reaction intermediate. Moreover, a sulphur atom is found 7 Å from the S2B site, suggested to represent a storage site for this ion when it is displaced. We have re-evaluated this structure with quantum refinement, i.e. standard crystallographic refinement in which the empirical restraints (employed to ensure that the final structure makes chemical sense) are replaced by more accurate quantum-mechanical calculations. This allows us to test various interpretations of the structure, employing quantum-mechanical calculations to predict the ideal structure and to use crystallographic measures like the real-space Z-score and electron-density difference maps to decide which structure fits the crystallographic raw data best. We show that the structure contains an OH--bound state, rather than an N2-derived reaction intermediate. Moreover, the structure shows dual conformations in the active site with ~ 14% undissociated S2B ligand, but the storage site seems to be fully occupied, weakening the suggestion that it represents a storage site for the dissociated ligand.
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Affiliation(s)
- Lili Cao
- Department of Theoretical Chemistry, Chemical Centre, Lund University, P. O. Box 124, 221 00, Lund, Sweden
| | - Octav Caldararu
- Department of Theoretical Chemistry, Chemical Centre, Lund University, P. O. Box 124, 221 00, Lund, Sweden
| | - Ulf Ryde
- Department of Theoretical Chemistry, Chemical Centre, Lund University, P. O. Box 124, 221 00, Lund, Sweden.
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4
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Lu Y, Koo J. O 2 sensitivity and H 2 production activity of hydrogenases-A review. Biotechnol Bioeng 2019; 116:3124-3135. [PMID: 31403182 DOI: 10.1002/bit.27136] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 07/23/2019] [Accepted: 08/05/2019] [Indexed: 01/24/2023]
Abstract
Hydrogenases are metalloproteins capable of catalyzing the interconversion between molecular hydrogen and protons and electrons. The iron-sulfur clusters within the enzyme enable rapid relay of electrons which are either consumed or generated at the active site. Their unparalleled catalytic efficiency has attracted attention, especially for potential use in H2 production and/or fuel cell technologies. However, there are limitations to using hydrogenases, especially due to their high O2 sensitivity. The subclass, called [FeFe] hydrogenases, are particularly more vulnerable to O2 but proficient in H2 production. In this review, we provide an overview of mechanistic and protein engineering studies focused on understanding and enhancing O2 tolerance of the enzyme. The emphasis is on ongoing studies that attempt to overcome O2 sensitivity of the enzyme while it catalyzes H2 production in an aerobic environment. We also discuss pioneering attempts to utilize the enzyme in biological H2 production and other industrial processes, as well as our own perspective on future applications.
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Affiliation(s)
- Yuan Lu
- Department of Chemical Engineering, Tsinghua University, Beijing, China
| | - Jamin Koo
- Department of Chemical Engineering, Hongik University, Seoul, Republic of Korea
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5
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Abstract
The advancements of quantum chemical methods and computer power allow detailed mechanistic investigations of metalloenzymes. In particular, both quantum chemical cluster and combined QM/MM approaches have been used, which have been proven to successfully complement experimental studies. This review starts with a brief introduction of nickel-dependent enzymes and then summarizes theoretical studies on the reaction mechanisms of these enzymes, including NiFe hydrogenase, methyl-coenzyme M reductase, nickel CO dehydrogenase, acetyl CoA synthase, acireductone dioxygenase, quercetin 2,4-dioxygenase, urease, lactate racemase, and superoxide dismutase.
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6
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Caldararu O, Manzoni F, Oksanen E, Logan DT, Ryde U. Refinement of protein structures using a combination of quantum-mechanical calculations with neutron and X-ray crystallographic data. Acta Crystallogr D Struct Biol 2019; 75:368-380. [PMID: 30988254 PMCID: PMC6465982 DOI: 10.1107/s205979831900175x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 01/30/2019] [Indexed: 11/20/2022] Open
Abstract
Neutron crystallography is a powerful method to determine the positions of H atoms in macromolecular structures. However, it is sometimes hard to judge what would constitute a chemically reasonable model, and the geometry of H atoms depends more on the surroundings (for example the formation of hydrogen bonds) than heavy atoms, so that the empirical geometry information for the H atoms used to supplement the experimental data is often less accurate. These problems may be reduced by using quantum-mechanical calculations. A method has therefore been developed to combine quantum-mechanical calculations with joint crystallographic refinement against X-ray and neutron data. A first validation of this method is provided by re-refining the structure of the galectin-3 carbohydrate-recognition domain in complex with lactose. The geometry is improved, in particular for water molecules, for which the method leads to better-resolved hydrogen-bonding interactions. The method has also been applied to the active copper site of lytic polysaccharide monooxygenase and shows that the protonation state of the amino-terminal histidine residue can be determined.
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Affiliation(s)
- Octav Caldararu
- Department of Theoretical Chemistry, Lund University, Chemical Centre, PO Box 124, SE-221 00 Lund, Sweden
| | - Francesco Manzoni
- Department of Theoretical Chemistry, Lund University, Chemical Centre, PO Box 124, SE-221 00 Lund, Sweden
- Department of Biochemistry and Structural Biology, Centre for Molecular Protein Science, Lund University, Chemical Centre, PO Box 124, SE-221 00 Lund, Sweden
| | - Esko Oksanen
- Department of Biochemistry and Structural Biology, Centre for Molecular Protein Science, Lund University, Chemical Centre, PO Box 124, SE-221 00 Lund, Sweden
- Instruments Division, European Spallation Source ESS ERIC, PO Box 176, SE-221 00 Lund, Sweden
| | - Derek T. Logan
- Department of Biochemistry and Structural Biology, Centre for Molecular Protein Science, Lund University, Chemical Centre, PO Box 124, SE-221 00 Lund, Sweden
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, PO Box 124, SE-221 00 Lund, Sweden
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7
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Dong G, Phung QM, Pierloot K, Ryde U. Reaction Mechanism of [NiFe] Hydrogenase Studied by Computational Methods. Inorg Chem 2018; 57:15289-15298. [PMID: 30500163 DOI: 10.1021/acs.inorgchem.8b02590] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
[NiFe] hydrogenases catalyze the reversible conversion of molecular hydrogen to protons and electrons. This seemingly simple reaction has attracted much attention because of the prospective use of H2 as a clean fuel. In this paper, we have studied the full reaction mechanism of this enzyme with various computational methods. Geometries were obtained with combined quantum mechanical and molecular mechanics (QM/MM) calculations. To get more accurate energies and obtain a detailed account of the surroundings, we performed big-QM calculations with 819 atoms in the QM region. Moreover, QM/MM thermodynamic cycle perturbation calculations were performed to obtain free energies. Finally, density matrix renormalisation group complete active space self-consistent field calculations were carried out to study the electronic structures of the various states in the reaction mechanism. Our calculations indicate that the Ni-L state is not involved in the reaction mechanism. Instead, the Ni-C state is reduced by one electron and then the bridging hydride ion is transferred to the sulfur atom of Cys546 as a proton and the two electrons transfer to the Ni ion. This step turned out to be rate-determining with an energy barrier of 58 kJ/mol, which is consistent with the experimental rate of 750 ± 90 s-1 (corresponding to ∼52 kJ/mol). The cleavage of the H-H bond is facile with an energy barrier of 33 kJ/mol, according to our calculations. We also find that the reaction energies are sensitive to the size of the QM system, the basis set, and the density functional theory method, in agreement with previous studies.
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Affiliation(s)
- Geng Dong
- Department of Theoretical Chemistry, Chemical Centre , Lund University , P.O. Box 124, SE-221 00 Lund , Sweden
- Department of Biochemistry and Molecular Biology , Shantou University Medical College , Shantou 514041 , Guangdong , PR China
| | - Quan Manh Phung
- Department of Chemistry , KU Leuven , Celestijnenlaan 200F , B-3001 Leuven , Belgium
| | - Kristine Pierloot
- Department of Chemistry , KU Leuven , Celestijnenlaan 200F , B-3001 Leuven , Belgium
| | - Ulf Ryde
- Department of Theoretical Chemistry, Chemical Centre , Lund University , P.O. Box 124, SE-221 00 Lund , Sweden
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8
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Genoni A, Bučinský L, Claiser N, Contreras-García J, Dittrich B, Dominiak PM, Espinosa E, Gatti C, Giannozzi P, Gillet JM, Jayatilaka D, Macchi P, Madsen AØ, Massa L, Matta CF, Merz KM, Nakashima PNH, Ott H, Ryde U, Schwarz K, Sierka M, Grabowsky S. Quantum Crystallography: Current Developments and Future Perspectives. Chemistry 2018; 24:10881-10905. [PMID: 29488652 DOI: 10.1002/chem.201705952] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 02/27/2018] [Indexed: 11/09/2022]
Abstract
Crystallography and quantum mechanics have always been tightly connected because reliable quantum mechanical models are needed to determine crystal structures. Due to this natural synergy, nowadays accurate distributions of electrons in space can be obtained from diffraction and scattering experiments. In the original definition of quantum crystallography (QCr) given by Massa, Karle and Huang, direct extraction of wavefunctions or density matrices from measured intensities of reflections or, conversely, ad hoc quantum mechanical calculations to enhance the accuracy of the crystallographic refinement are implicated. Nevertheless, many other active and emerging research areas involving quantum mechanics and scattering experiments are not covered by the original definition although they enable to observe and explain quantum phenomena as accurately and successfully as the original strategies. Therefore, we give an overview over current research that is related to a broader notion of QCr, and discuss options how QCr can evolve to become a complete and independent domain of natural sciences. The goal of this paper is to initiate discussions around QCr, but not to find a final definition of the field.
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Affiliation(s)
- Alessandro Genoni
- Université de Lorraine, CNRS, Laboratoire LPCT, 1 Boulevard Arago, F-57078, Metz, France
| | - Lukas Bučinský
- Institute of Physical Chemistry and Chemical Physics, Slovak University of Technology, FCHPT SUT, Radlinského 9, SK-812 37, Bratislava, Slovakia
| | - Nicolas Claiser
- Université de Lorraine, CNRS, Laboratoire CRM2, Boulevard des Aiguillettes, BP 70239, F-54506, Vandoeuvre-lès-Nancy, France
| | - Julia Contreras-García
- Sorbonne Universités, UPMC Université Paris 06, CNRS, Laboratoire de Chimie Théorique (LCT), 4 Place Jussieu, F-75252, Paris Cedex 05, France
| | - Birger Dittrich
- Anorganische und Strukturchemie II, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Paulina M Dominiak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, 02-089, Warszawa, Poland
| | - Enrique Espinosa
- Université de Lorraine, CNRS, Laboratoire CRM2, Boulevard des Aiguillettes, BP 70239, F-54506, Vandoeuvre-lès-Nancy, France
| | - Carlo Gatti
- CNR-ISTM Istituto di Scienze e Tecnologie Molecolari, via Golgi 19, Milano, I-20133, Italy.,Istituto Lombardo Accademia di Scienze e Lettere, via Brera 28, 20121, Milano, Italy
| | - Paolo Giannozzi
- Department of Mathematics, Computer Science and Physics, University of Udine, Via delle Scienze 208, I-33100, Udine, Italy
| | - Jean-Michel Gillet
- Structure, Properties and Modeling of Solids Laboratory, CentraleSupelec, Paris-Saclay University, 3 rue Joliot-Curie, 91191, Gif-sur-Yvette, France
| | - Dylan Jayatilaka
- School of Molecular Sciences, University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia
| | - Piero Macchi
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012, Bern, Switzerland
| | - Anders Ø Madsen
- Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen, Denmark
| | - Lou Massa
- Hunter College & the Ph.D. Program of the Graduate Center, City University of New York, New York, USA
| | - Chérif F Matta
- Department of Chemistry and Physics, Mount Saint Vincent University, Halifax, Nova Scotia, B3M 2J6, Canada.,Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, B3H 4J3, Canada.,Department of Chemistry, Saint Mary's University, Halifax, Nova Scotia, B3H 3C3, Canada.,Département de Chimie, Université Laval, Québec, QC G1V 0A6, Canada
| | - Kenneth M Merz
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, 578 South Shaw Lane, East Lansing, Michigan, 48824, USA.,Institute for Cyber Enabled Research, Michigan State University, 567 Wilson Road, Room 1440, East Lansing, Michigan, 48824, USA
| | - Philip N H Nakashima
- Department of Materials Science and Engineering, Monash University, Victoria, 3800, Australia
| | - Holger Ott
- Bruker AXS GmbH, Östliche Rheinbrückenstraße 49, 76187, Karlsruhe, Germany
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-22100, Lund, Sweden
| | - Karlheinz Schwarz
- Technische Universität Wien, Institut für Materialwissenschaften, Getreidemarkt 9, A-1060, Vienna, Austria
| | - Marek Sierka
- Otto Schott Institute of Materials Research, Friedrich Schiller University Jena, Löbdergraben 32, 07743, Jena, Germany
| | - Simon Grabowsky
- Fachbereich 2-Biologie/Chemie, Institut für Anorganische Chemie und Kristallographie, Universität Bremen, Leobener Str. 3, 28359, Bremen, Germany
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9
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Breglia R, Greco C, Fantucci P, De Gioia L, Bruschi M. Theoretical investigation of aerobic and anaerobic oxidative inactivation of the [NiFe]-hydrogenase active site. Phys Chem Chem Phys 2018; 20:1693-1706. [DOI: 10.1039/c7cp06228a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The extraordinary capability of [NiFe]-hydrogenases to catalyse the reversible interconversion of protons and electrons into dihydrogen (H2) has stimulated numerous experimental and theoretical studies addressing the direct utilization of these enzymes in H2 production processes.
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Affiliation(s)
- Raffaella Breglia
- Department of Earth and Environmental Science
- University of Milano Bicocca
- 20126 Milan
- Italy
| | - Claudio Greco
- Department of Earth and Environmental Science
- University of Milano Bicocca
- 20126 Milan
- Italy
| | - Piercarlo Fantucci
- Department of Biotechnology and Biosciences
- University of Milano Bicocca
- 20126 Milan
- Italy
| | - Luca De Gioia
- Department of Biotechnology and Biosciences
- University of Milano Bicocca
- 20126 Milan
- Italy
| | - Maurizio Bruschi
- Department of Earth and Environmental Science
- University of Milano Bicocca
- 20126 Milan
- Italy
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10
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Quantum chemical approaches to [NiFe] hydrogenase. Essays Biochem 2017; 61:293-303. [PMID: 28487405 DOI: 10.1042/ebc20160079] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 02/22/2017] [Accepted: 03/01/2017] [Indexed: 11/17/2022]
Abstract
The mechanism by which [NiFe] hydrogenase catalyses the oxidation of molecular hydrogen is a significant yet challenging topic in bioinorganic chemistry. With far-reaching applications in renewable energy and carbon mitigation, significant effort has been invested in the study of these complexes. In particular, computational approaches offer a unique perspective on how this enzyme functions at an electronic and atomistic level. In this article, we discuss state-of-the art quantum chemical methods and how they have helped deepen our comprehension of [NiFe] hydrogenase. We outline the key strategies that can be used to compute the (i) geometry, (ii) electronic structure, (iii) thermodynamics and (iv) kinetic properties associated with the enzymatic activity of [NiFe] hydrogenase and other bioinorganic complexes.
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11
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Breglia R, Ruiz-Rodriguez MA, Vitriolo A, Gonzàlez-Laredo RF, De Gioia L, Greco C, Bruschi M. Theoretical insights into [NiFe]-hydrogenases oxidation resulting in a slowly reactivating inactive state. J Biol Inorg Chem 2016; 22:137-151. [DOI: 10.1007/s00775-016-1416-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 11/09/2016] [Indexed: 11/28/2022]
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12
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Protonation states of intermediates in the reaction mechanism of [NiFe] hydrogenase studied by computational methods. J Biol Inorg Chem 2016; 21:383-94. [DOI: 10.1007/s00775-016-1348-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 02/23/2016] [Indexed: 10/22/2022]
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13
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Volbeda A, Martin L, Liebgott PP, De Lacey AL, Fontecilla-Camps JC. [NiFe]-hydrogenases revisited: nickel-carboxamido bond formation in a variant with accrued O2-tolerance and a tentative re-interpretation of Ni-SI states. Metallomics 2016; 7:710-8. [PMID: 25780984 DOI: 10.1039/c4mt00309h] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
[NiFe]-hydrogenases are well-studied enzymes capable of oxidizing molecular hydrogen and reducing protons. EPR and FTIR spectroscopic studies have shown that these enzymes can be isolated in several redox states that include paramagnetic oxidized inactive Ni-A and Ni-B species and a reduced Ni-C form. The latter and the diamagnetic respectively more oxidized Ni-SI and more reduced Ni-R forms are generally thought to be involved in the catalytic cycle of [NiFe]-hydrogenases. With the exception of Ni-SI, these different stable states have been well characterized. Here, based on the crystal structure of a partially reduced Desulfovibrio fructosovorans (Df) enzyme and data from the literature we propose that at least one of the Ni-SI sub-states contains an unexpected combination of hydride and sulfenic acid moieties. We have also determined the structure of the less oxygen-sensitive Df [NiFe]-hydrogenase V74C mutant and found that more than half of the active site nickel occupies a novel position, called Ni'. In this new position, the metal ion is coordinated by two cysteine thiolates, a bridging species modeled as SH(-) and a main chain carboxamido N atom. The Ni' coordination is similar to the one found in Ni superoxide dismutase, an enzyme that operates at significantly more positive potentials than [NiFe]-hydrogenases. We propose that the oxygen-tolerance of the V74C variant results from a high potential stabilization of a Ni'(iii) species induced by the change in the metal ion coordination sphere. We also propose that transient Ni'(iii) species can rapidly attract successive electrons from the Fe4S4 proximal cluster accelerating the reduction of oxygen to water and hydroxide. The naturally occurring oxygen-tolerant [NiFe]-hydrogenases have an unusual proximal cluster that has been shown to be exceptionally plastic and capable of undergoing two successive one-electron oxidations. This double oxidation is modulated by the migration of one of the iron atoms in the cluster to the main chain where, as Fe(iii), it forms a bond with a carboxamido N ligand. Like in the Df V74C variant the electrons from the proximal cluster help reducing O2 to H2O and OH(-). In conclusion, in both cases a metal-carboxamido bond may explain, at least partially, the observed oxygen tolerance.
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14
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15
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Vedha SA, Velmurugan G, Venuvanalingam P. Noncovalent interactions between the second coordination sphere and the active site of [NiFeSe] hydrogenase. RSC Adv 2016. [DOI: 10.1039/c6ra11295a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
QM/MM studies on seven truncated models of the oxidized as-isolated state of the [NiFeSe] Hases reveal the influence of the residues in the second coordination sphere on the active site.
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Affiliation(s)
- Swaminathan Angeline Vedha
- Theoretical and Computational Chemistry Laboratory
- School of Chemistry
- Bharathidasan University
- Tiruchirappalli-620 024
- India
| | - Gunasekaran Velmurugan
- Theoretical and Computational Chemistry Laboratory
- School of Chemistry
- Bharathidasan University
- Tiruchirappalli-620 024
- India
| | - Ponnambalam Venuvanalingam
- Theoretical and Computational Chemistry Laboratory
- School of Chemistry
- Bharathidasan University
- Tiruchirappalli-620 024
- India
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16
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Horch M, Lauterbach L, Mroginski MA, Hildebrandt P, Lenz O, Zebger I. Reversible active site sulfoxygenation can explain the oxygen tolerance of a NAD+-reducing [NiFe] hydrogenase and its unusual infrared spectroscopic properties. J Am Chem Soc 2015; 137:2555-64. [PMID: 25647259 DOI: 10.1021/ja511154y] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Oxygen-tolerant [NiFe] hydrogenases are metalloenzymes that represent valuable model systems for sustainable H2 oxidation and production. The soluble NAD(+)-reducing [NiFe] hydrogenase (SH) from Ralstonia eutropha couples the reversible cleavage of H2 with the reduction of NAD(+) and displays a unique O2 tolerance. Here we performed IR spectroscopic investigations on purified SH in various redox states in combination with density functional theory to provide structural insights into the catalytic [NiFe] center. These studies revealed a standard-like coordination of the active site with diatomic CO and cyanide ligands. The long-lasting discrepancy between spectroscopic data obtained in vitro and in vivo could be solved on the basis of reversible cysteine oxygenation in the fully oxidized state of the [NiFe] site. The data are consistent with a model in which the SH detoxifies O2 catalytically by means of an NADH-dependent (per)oxidase reaction involving the intermediary formation of stable cysteine sulfenates. The occurrence of two catalytic activities, hydrogen conversion and oxygen reduction, at the same cofactor may inspire the design of novel biomimetic catalysts performing H2-conversion even in the presence of O2.
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Affiliation(s)
- Marius Horch
- Institut für Chemie, Technische Universität Berlin , Sekr. PC14, Straße des 17, Juni 135, D-10623 Berlin, Germany
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17
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Kaliakin DS, Zaari RR, Varganov SA. Effect of H2 Binding on the Nonadiabatic Transition Probability between Singlet and Triplet States of the [NiFe]-Hydrogenase Active Site. J Phys Chem A 2015; 119:1066-73. [DOI: 10.1021/jp510522z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Danil S. Kaliakin
- Department
of Chemistry, University of Nevada, Reno, 1664 North Virginia Street, Reno, Nevada 89557-0216, United States
- Department
of Chemistry, Siberian Federal University, 79 Svobodnyi Prospect, Krasnoyarsk, Krasnoyarskiy kray 660041, Russia
| | - Ryan R. Zaari
- Department
of Chemistry, University of Nevada, Reno, 1664 North Virginia Street, Reno, Nevada 89557-0216, United States
| | - Sergey A. Varganov
- Department
of Chemistry, University of Nevada, Reno, 1664 North Virginia Street, Reno, Nevada 89557-0216, United States
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18
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Volbeda A, Martin L, Barbier E, Gutiérrez-Sanz O, De Lacey AL, Liebgott PP, Dementin S, Rousset M, Fontecilla-Camps JC. Crystallographic studies of [NiFe]-hydrogenase mutants: towards consensus structures for the elusive unready oxidized states. J Biol Inorg Chem 2015; 20:11-22. [PMID: 25315838 DOI: 10.1007/s00775-014-1203-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 10/01/2014] [Indexed: 01/12/2023]
Abstract
Catalytically inactive oxidized O2-sensitive [NiFe]-hydrogenases are characterized by a mixture of the paramagnetic Ni-A and Ni-B states. Upon O2 exposure, enzymes in a partially reduced state preferentially form the unready Ni-A state. Because partial O2 reduction should generate a peroxide intermediate, this species was previously assigned to the elongated Ni-Fe bridging electron density observed for preparations of [NiFe]-hydrogenases known to contain the Ni-A state. However, this proposition has been challenged based on the stability of this state to UV light exposure and the possibility of generating it anaerobically under either chemical or electrochemical oxidizing conditions. Consequently, we have considered alternative structures for the Ni-A species including oxidation of thiolate ligands to either sulfenate or sulfenic acid. Here, we report both new and revised [NiFe]-hydrogenases structures and conclude, taking into account corresponding characterizations by Fourier transform infrared spectroscopy (FTIR), that the Ni-A species contains oxidized cysteine and bridging hydroxide ligands instead of the peroxide ligand we proposed earlier. Our analysis was rendered difficult by the typical formation of mixtures of unready oxidized states that, furthermore, can be reduced by X-ray induced photoelectrons. The present study could be carried out thanks to the use of Desulfovibrio fructosovorans [NiFe]-hydrogenase mutants with special properties. In addition to the Ni-A state, crystallographic results are also reported for two diamagnetic unready states, allowing the proposal of a revised oxidized inactive Ni-SU model and a new structure characterized by a persulfide ion that is assigned to an Ni-'Sox' species.
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Affiliation(s)
- Anne Volbeda
- University Grenoble Alpes, IBS, 38044, Grenoble, France. .,CEA, IBS, 38044, Grenoble, France. .,CNRS, IBS, 38044, Grenoble, France.
| | - Lydie Martin
- University Grenoble Alpes, IBS, 38044, Grenoble, France.,CEA, IBS, 38044, Grenoble, France.,CNRS, IBS, 38044, Grenoble, France
| | - Elodie Barbier
- University Grenoble Alpes, IBS, 38044, Grenoble, France.,CEA, IBS, 38044, Grenoble, France.,CNRS, IBS, 38044, Grenoble, France.,CEA, MINATEC, 38044, Grenoble, France
| | | | | | - Pierre-Pol Liebgott
- Aix-Marseille Université, CNRS, IMM, 13402, Marseille, France.,Aix-Marseille Université, CNRS/INSU, MIO, 13288, Marseille, France
| | | | - Marc Rousset
- Aix-Marseille Université, CNRS, IMM, 13402, Marseille, France.,Consulate General of France, 205 N Michigan Ave, Chicago, IL, 60601, USA
| | - Juan C Fontecilla-Camps
- University Grenoble Alpes, IBS, 38044, Grenoble, France.,CEA, IBS, 38044, Grenoble, France.,CNRS, IBS, 38044, Grenoble, France
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19
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Schmidt TC, Paasche A, Grebner C, Ansorg K, Becker J, Lee W, Engels B. QM/MM investigations of organic chemistry oriented questions. Top Curr Chem (Cham) 2014; 351:25-101. [PMID: 22392477 DOI: 10.1007/128_2011_309] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
About 35 years after its first suggestion, QM/MM became the standard theoretical approach to investigate enzymatic structures and processes. The success is due to the ability of QM/MM to provide an accurate atomistic picture of enzymes and related processes. This picture can even be turned into a movie if nuclei-dynamics is taken into account to describe enzymatic processes. In the field of organic chemistry, QM/MM methods are used to a much lesser extent although almost all relevant processes happen in condensed matter or are influenced by complicated interactions between substrate and catalyst. There is less importance for theoretical organic chemistry since the influence of nonpolar solvents is rather weak and the effect of polar solvents can often be accurately described by continuum approaches. Catalytic processes (homogeneous and heterogeneous) can often be reduced to truncated model systems, which are so small that pure quantum-mechanical approaches can be employed. However, since QM/MM becomes more and more efficient due to the success in software and hardware developments, it is more and more used in theoretical organic chemistry to study effects which result from the molecular nature of the environment. It is shown by many examples discussed in this review that the influence can be tremendous, even for nonpolar reactions. The importance of environmental effects in theoretical spectroscopy was already known. Due to its benefits, QM/MM can be expected to experience ongoing growth for the next decade.In the present chapter we give an overview of QM/MM developments and their importance in theoretical organic chemistry, and review applications which give impressions of the possibilities and the importance of the relevant effects. Since there is already a bunch of excellent reviews dealing with QM/MM, we will discuss fundamental ingredients and developments of QM/MM very briefly with a focus on very recent progress. For the applications we follow a similar strategy.
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Affiliation(s)
- Thomas C Schmidt
- Institut für Phys. und Theor. Chemie, Emil-Fischer-Strasse 42, Campus Hubland Nord, 97074, Würzburg, Germany
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20
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Delcey MG, Pierloot K, Phung QM, Vancoillie S, Lindh R, Ryde U. Accurate calculations of geometries and singlet–triplet energy differences for active-site models of [NiFe] hydrogenase. Phys Chem Chem Phys 2014; 16:7927-38. [DOI: 10.1039/c4cp00253a] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The relative stability of singlet and triplet state models of [NiFe] hydrogenase have been studied by advanced quantum-mechanical methods.
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Affiliation(s)
- Mickaël G. Delcey
- Department of Chemistry – Ångström
- The Theoretical Chemistry Programme
- Uppsala University
- SE-751 20 Uppsala, Sweden
| | | | - Quan M. Phung
- Department of Chemistry
- University of Leuven
- B-3001 Leuven, Belgium
| | | | - Roland Lindh
- Department of Chemistry – Ångström
- The Theoretical Chemistry Programme
- Uppsala University
- SE-751 20 Uppsala, Sweden
- Uppsala Center for Computational Chemistry – UC3
| | - Ulf Ryde
- Department of Theoretical Chemistry
- Lund University
- Chemical Centre
- SE-221 00 Lund, Sweden
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21
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Sumner S, Söderhjelm P, Ryde U. Effect of Geometry Optimizations on QM-Cluster and QM/MM Studies of Reaction Energies in Proteins. J Chem Theory Comput 2013; 9:4205-14. [DOI: 10.1021/ct400339c] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sophie Sumner
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00
Lund, Sweden
| | - Pär Söderhjelm
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00
Lund, Sweden
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00
Lund, Sweden
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22
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Pelmenschikov V, Kaupp M. Redox-Dependent Structural Transformations of the [4Fe-3S] Proximal Cluster in O2-Tolerant Membrane-Bound [NiFe]-Hydrogenase: A DFT Study. J Am Chem Soc 2013; 135:11809-23. [DOI: 10.1021/ja402159u] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Vladimir Pelmenschikov
- Technische Universität Berlin, Institut für Chemie, Theoretische Chemie, Sekr. C7, Strasse
des 17. Juni 135, 10623 Berlin, Germany
| | - Martin Kaupp
- Technische Universität Berlin, Institut für Chemie, Theoretische Chemie, Sekr. C7, Strasse
des 17. Juni 135, 10623 Berlin, Germany
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23
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Kampa M, Pandelia ME, Lubitz W, van Gastel M, Neese F. A Metal–Metal Bond in the Light-Induced State of [NiFe] Hydrogenases with Relevance to Hydrogen Evolution. J Am Chem Soc 2013; 135:3915-25. [DOI: 10.1021/ja3115899] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mario Kampa
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstrasse 34-36, D-45470 Mülheim
an der Ruhr, Germany
| | - Maria-Eirini Pandelia
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstrasse 34-36, D-45470 Mülheim
an der Ruhr, Germany
| | - Wolfgang Lubitz
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstrasse 34-36, D-45470 Mülheim
an der Ruhr, Germany
| | - Maurice van Gastel
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstrasse 34-36, D-45470 Mülheim
an der Ruhr, Germany
| | - Frank Neese
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstrasse 34-36, D-45470 Mülheim
an der Ruhr, Germany
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24
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Hu L, Söderhjelm P, Ryde U. Accurate Reaction Energies in Proteins Obtained by Combining QM/MM and Large QM Calculations. J Chem Theory Comput 2012; 9:640-9. [PMID: 26589061 DOI: 10.1021/ct3005003] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We here suggest and test a new method to obtain stable energies in proteins for charge-neutral reactions by running large quantum mechanical (QM) calculations on structures obtained by combined QM and molecular mechanics (QM/MM) geometry optimization on several snapshots from molecular dynamics simulations. As a test case, we use a proton transfer between a metal-bound cysteine residue and a second-sphere histidine residue in the active site of [Ni,Fe] hydrogenase, which has been shown to be very sensitive to the surroundings. We include in the QM calculations all residues within 4.5 Å of the active site, two capped residues on each side of the active-site residues, and all charged groups that are buried inside the protein, which for this enzyme includes three iron-sulfur clusters, in total, 930 atoms. These calculations are performed at the BP86/def2-SV(P) level, but the energies are then extrapolated to the B3LYP/def2-TZVP level with a smaller QM system, and zero-point energy, entropy, and thermal effects are added. We test three approaches to model the remaining atoms of the protein solvent, viz., by standard QM/MM approaches using either mechanical or electrostatic embedding or by using a continuum solvation model for the large QM systems. Quite encouragingly, the three approaches give the same results within 14 kJ/mol, and variations in the size of the QM system do not change the energies by more than 8 kJ/mol, provided that the QM/MM junctions are not moved closer to the QM system. The statistical precision for the average over 10 snapshots is 1-3 kJ/mol.
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Affiliation(s)
- LiHong Hu
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden.,School of Computer Science and Information Technology, Northeast Normal University, Changchun, 130024, People's Republic of China
| | - Pär Söderhjelm
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
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25
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Computational study of the electronic structure and magnetic properties of the Ni–C state in [NiFe] hydrogenases including the second coordination sphere. J Biol Inorg Chem 2012; 17:1269-81. [DOI: 10.1007/s00775-012-0941-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Accepted: 09/11/2012] [Indexed: 10/27/2022]
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26
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27
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Affiliation(s)
- LiHong Hu
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
- Faculty of Chemistry, North-east Normal University, Changchun, 130024, P. R. China
| | - Pär Söderhjelm
- Department of Chemistry and Applied Biosciences - Computational Science, ETH Zürich, Via Giuseppe Buffi 13, CH-6900 Lugano, Switzerland
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
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28
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Fuchs MGG, Meyer F, Ryde U. A combined computational and experimental investigation of the [2Fe-2S] cluster in biotin synthase. J Biol Inorg Chem 2010; 15:203-12. [PMID: 19768473 PMCID: PMC2804791 DOI: 10.1007/s00775-009-0585-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2009] [Accepted: 09/04/2009] [Indexed: 11/19/2022]
Abstract
Biotin synthase was the first example of what is now regarded as a distinctive enzyme class within the radical S-adenosylmethionine superfamily, the members of which use Fe/S clusters as the sulphur source in radical sulphur insertion reactions. The crystal structure showed that this enzyme contains a [2Fe-2S] cluster with a highly unusual arginine ligand, besides three normal cysteine ligands. However, the crystal structure is at such a low resolution that neither the exact coordination mode nor the role of this exceptional ligand has been elucidated yet, although it has been shown that it is not essential for enzyme activity. We have used quantum refinement of the crystal structure and combined quantum mechanical and molecular mechanical calculations to explore possible coordination modes and their influences on cluster properties. The investigations show that the protonation state of the arginine ligand has little influence on cluster geometry, so even a positively charged guanidinium moiety would be in close proximity to the iron atom. Nevertheless, the crystallised enzyme most probably contains a deprotonated (neutral) arginine coordinating via the NH group. Furthermore, the Fe...Fe distance seems to be independent of the coordination mode and is in perfect agreement with distances in other structurally characterised [2Fe-2S] clusters. The exceptionally large Fe...Fe distance found in the crystal structure could not be reproduced.
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Affiliation(s)
- Michael G. G. Fuchs
- Institut für Anorganische Chemie, Georg-August-Universität Göttingen, Tammannstrasse 4, 37077 Göttingen, Germany
| | - Franc Meyer
- Institut für Anorganische Chemie, Georg-August-Universität Göttingen, Tammannstrasse 4, 37077 Göttingen, Germany
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, 221 00 Lund, Sweden
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29
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Zhang R, Lev B, Cuervo JE, Noskov SY, Salahub DR. A Guide to QM/MM Methodology and Applications. ADVANCES IN QUANTUM CHEMISTRY 2010. [DOI: 10.1016/s0065-3276(10)59010-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
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30
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Sproviero EM, Newcomer MB, Gascón JA, Batista ER, Brudvig GW, Batista VS. The MoD-QM/MM methodology for structural refinement of photosystem II and other biological macromolecules. PHOTOSYNTHESIS RESEARCH 2009; 102:455-470. [PMID: 19633920 PMCID: PMC2954272 DOI: 10.1007/s11120-009-9467-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2008] [Accepted: 06/25/2009] [Indexed: 05/28/2023]
Abstract
Quantum mechanics/molecular mechanics (QM/MM) hybrid methods are currently the most powerful computational tools for studies of structure/function relations and structural refinement of macrobiomolecules (e.g., proteins and nucleic acids). These methods are highly efficient, since they implement quantum chemistry techniques for modeling only the small part of the system (QM layer) that undergoes chemical modifications, charge transfer, etc., under the influence of the surrounding environment. The rest of the system (MM layer) is described in terms of molecular mechanics force fields, assuming that its influence on the QM layer can be roughly decomposed in terms of electrostatic interactions and steric hindrance. Common limitations of QM/MM methods include inaccuracies in the MM force fields, when polarization effects are not explicitly considered, and the approximate treatment of electrostatic interactions at the boundaries between QM and MM layers. This article reviews recent advances in the development of computational protocols that allow for rigorous modeling of electrostatic interactions in extended systems beyond the common limitations of QM/MM hybrid methods. We focus on the moving-domain QM/MM (MoD-QM/MM) methodology that partitions the system into many molecular domains and obtains the electrostatic and structural properties of the whole system from an iterative self-consistent treatment of the constituent molecular fragments. We illustrate the MoD-QM/MM method as applied to the description of photosystem II as well as in conjunction with the application of spectroscopically constrained QM/MM optimization methods, based on high-resolution spectroscopic data (extended X-ray absorption fine structure spectra, and exchange coupling constants).
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Affiliation(s)
- Eduardo M. Sproviero
- Yale University, Department of Chemistry, P. O. Box 208107, New Haven Connecticut 06520-8107 USA
| | - Michael B. Newcomer
- Yale University, Department of Chemistry, P. O. Box 208107, New Haven Connecticut 06520-8107 USA
| | | | - Enrique R. Batista
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545
| | - Gary W. Brudvig
- Yale University, Department of Chemistry, P. O. Box 208107, New Haven Connecticut 06520-8107 USA
| | - Victor S. Batista
- Yale University, Department of Chemistry, P. O. Box 208107, New Haven Connecticut 06520-8107 USA
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31
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Li X, He X, Wang B, Merz K. Conformational variability of benzamidinium-based inhibitors. J Am Chem Soc 2009; 131:7742-54. [PMID: 19435349 DOI: 10.1021/ja9010833] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Determining the structure of a small molecule bound to a biological receptor (e.g., a protein implicated in a disease state) is a necessary step in structure-based drug design. The preferred conformation of a small molecule can change when bound to a protein, and a detailed knowledge of the preferred conformation(s) of a bound ligand can help in optimizing the affinity of a molecule for its receptor. However, the quality of a protein/ligand complex determined using X-ray crystallography is dependent on the size of the protein, the crystal quality, and the realized resolution. The energy restraints used in traditional X-ray refinement procedures typically use "reduced" (i.e., neglect of electrostatics and dispersion interactions) Engh and Huber force field models that, while quite suitable for modeling proteins, often are less suitable for small molecule structures due to a lack of validated parameters. Through the use of ab initio QM/MM-based X-ray refinement procedures, this shortcoming can be overcome especially in the active site or binding site of a small-molecule inhibitor. Herein, we demonstrate that ab initio QM/MM refinement of an inhibitor/protein complex provides insights into the binding of small molecules beyond what is available using more traditional refinement protocols. In particular, QM/MM refinement studies of benzamidinium derivatives show variable conformational preferences depending on the refinement protocol used and the nature of the active-site region.
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Affiliation(s)
- Xue Li
- Department of Chemistry, Quantum Theory Project, 2328 New Physics Building, P.O. Box 118435, University of Florida, Gainesville, Florida 32611-8435, USA
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Abstract
Combined quantum-mechanics/molecular-mechanics (QM/MM) approaches have become the method of choice for modeling reactions in biomolecular systems. Quantum-mechanical (QM) methods are required for describing chemical reactions and other electronic processes, such as charge transfer or electronic excitation. However, QM methods are restricted to systems of up to a few hundred atoms. However, the size and conformational complexity of biopolymers calls for methods capable of treating up to several 100,000 atoms and allowing for simulations over time scales of tens of nanoseconds. This is achieved by highly efficient, force-field-based molecular mechanics (MM) methods. Thus to model large biomolecules the logical approach is to combine the two techniques and to use a QM method for the chemically active region (e.g., substrates and co-factors in an enzymatic reaction) and an MM treatment for the surroundings (e.g., protein and solvent). The resulting schemes are commonly referred to as combined or hybrid QM/MM methods. They enable the modeling of reactive biomolecular systems at a reasonable computational effort while providing the necessary accuracy.
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Affiliation(s)
- Hans Martin Senn
- Department of Chemistry, WestCHEM and University of Glasgow, Glasgow G12 8QQ, UK.
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33
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Fontecilla-Camps JC. Structure and Function of [NiFe]-Hydrogenases. METAL-CARBON BONDS IN ENZYMES AND COFACTORS 2009. [DOI: 10.1039/9781847559333-00151] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
[NiFe(Se)]-hydrogenases are hetero-dimeric enzymes present in many microorganisms where they catalyze the oxidation of molecular hydrogen or the reduction of protons. Like the other two types of hydrogen-metabolizing enzymes, the [FeFe]- and [Fe]-hydrogenases, [NiFe]-hydrogenases have a Fe(CO)x unit in their active sites that is most likely involved in hydride binding. Because of their complexity, hydrogenases require a maturation machinery that involves several gene products. They include nickel and iron transport, synthesis of CN− (and maybe CO), formation and insertion of a FeCO(CN−)2 unit in the apo form, insertion of nickel and proteolytic cleavage of a C-terminal stretch, a step that ends the maturation process. Because the active site is buried in the structure, electron and proton transfer are required between this site and the molecular surface. The former is mediated by either three or one Fe/S cluster(s) depending on the enzyme. When exposed to oxidizing conditions, such as the presence of O2, [NiFe]-hydrogenases are inactivated. Depending on the redox state of the enzyme, exposure to oxygen results in either a partially reduced oxo species probably a (hydro)peroxo ligand between nickel and iron or a more reduced OH– ligand instead. Under some conditions the thiolates that coordinate the NiFe center can be modified to sulfenates. Understanding this process is of biotechnological interest for H2 production by photosynthetic organisms.
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Affiliation(s)
- Juan C. Fontecilla-Camps
- Laboratoire de Cristallographie et de Cristallogenèse des Proteines, Institut de Biologie Structurale J. P. Ebel (CEA-CNRS-UJF) 41 rue Jules Horowitz F-38027 Grenoble Cédex 1 France
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34
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35
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Kaukonen M, Söderhjelm P, Heimdal J, Ryde U. QM/MM−PBSA Method To Estimate Free Energies for Reactions in Proteins. J Phys Chem B 2008; 112:12537-48. [DOI: 10.1021/jp802648k] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Markus Kaukonen
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Pär Söderhjelm
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Jimmy Heimdal
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
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36
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FTIR spectroelectrochemical characterization of the Ni–Fe–Se hydrogenase from Desulfovibrio vulgaris Hildenborough. J Biol Inorg Chem 2008; 13:1315-20. [DOI: 10.1007/s00775-008-0412-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2008] [Accepted: 08/01/2008] [Indexed: 10/21/2022]
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37
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Ohki Y, Yasumura K, Kuge K, Tanino S, Ando M, Li Z, Tatsumi K. Thiolate-bridged dinuclear iron(tris-carbonyl)-nickel complexes relevant to the active site of [NiFe] hydrogenase. Proc Natl Acad Sci U S A 2008; 105:7652-7. [PMID: 18511566 PMCID: PMC2409409 DOI: 10.1073/pnas.0800538105] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2008] [Indexed: 11/18/2022] Open
Abstract
The reaction of NiBr(2)(EtOH)(4) with a 1:2-3 mixture of FeBr(2)(CO)(4) and Na(SPh) generated a linear trinuclear Fe-Ni-Fe cluster (CO)(3)Fe(mu-SPh)(3)Ni(mu-SPh)(3)Fe(CO)(3), 1, whereas the analogous reaction system FeBr(2)(CO)(4)/Na(S(t)Bu)/NiBr(2)(EtOH)(4) (1:2-3:1) gave rise to a linear tetranuclear Fe-Ni-Ni-Fe cluster [(CO)(3)Fe(mu-S(t)Bu)(3)Ni(mu-Br)](2), 2. By using this tetranuclear cluster 2 as the precursor, we have developed a new synthetic route to a series of thiolate-bridged dinuclear Fe(CO)(3)-Ni complexes, the structures of which mimic [NiFe] hydrogenase active sites. The reactions of 2 with SC(NMe(2))(2) (tmtu), Na{S(CH(2))(2)SMe} and ortho-NaS(C(6)H(4))SR (R = Me, (t)Bu) led to isolation of (CO)(3)Fe(mu-S(t)Bu)(3)NiBr(tmtu), 3, (CO)(3)Fe(S(t)Bu)(mu-S(t)Bu)(2)Ni{S(CH(2))(2)SMe}, 4, and (CO)(3)Fe(S(t)Bu)(mu-S(t)Bu)(2)Ni{S(C(6)H(4))SR}, 5a (R = Me) and 5b (R = (t)Bu), respectively. On the other hand, treatment of 2 with 2-methylthio-phenolate (ortho-O(C(6)H(4))SMe) in methanol resulted in (CO)(3)Fe(mu-S(t)Bu)(3)Ni(MeOH){O(C(6)H(4))SMe}, 6a. The methanol molecule bound to Ni is labile and is readily released under reduced pressure to afford (CO)(3)Fe(S(t)Bu)(mu-S(t)Bu)(2)Ni{O(C(6)H(4))SMe}, 6b, and the coordination geometry of nickel changes from octahedral to square planar. Likewise, the reaction of 2 with NaOAc in methanol followed by crystallization from THF gave (CO)(3)Fe(mu-S(t)Bu)(3)Ni(THF)(OAc), 7. The dinuclear complexes, 3-7, are thermally unstable, and a key to their successful isolation is to carry out the reactions and manipulations at -40 degrees C.
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Affiliation(s)
- Yasuhiro Ohki
- Research Center for Materials Science, Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Kazunari Yasumura
- Research Center for Materials Science, Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Katsuaki Kuge
- Research Center for Materials Science, Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Soichiro Tanino
- Research Center for Materials Science, Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Masaru Ando
- Research Center for Materials Science, Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Zilong Li
- Research Center for Materials Science, Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Kazuyuki Tatsumi
- Research Center for Materials Science, Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
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Kaukonen M, Söderhjelm P, Heimdal J, Ryde U. Proton Transfer at Metal Sites in Proteins Studied by Quantum Mechanical Free-Energy Perturbations. J Chem Theory Comput 2008; 4:985-1001. [DOI: 10.1021/ct700347h] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Markus Kaukonen
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Pär Söderhjelm
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Jimmy Heimdal
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
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39
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Siegbahn PEM, Tye JW, Hall MB. Computational studies of [NiFe] and [FeFe] hydrogenases. Chem Rev 2008; 107:4414-35. [PMID: 17927160 DOI: 10.1021/cr050185y] [Citation(s) in RCA: 361] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Per E M Siegbahn
- Department of Biophysics, Arrhenius Laboratory, Stockholm University, SE-106 91, Stockholm, Sweden.
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40
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Jayapal P, Sundararajan M, Hillier IH, Burton NA. QM/MM studies of Ni–Fe hydrogenases: the effect of enzyme environment on the structure and energies of the inactive and active states. Phys Chem Chem Phys 2008; 10:4249-57. [DOI: 10.1039/b804035d] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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41
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Fontecilla-Camps JC, Volbeda A, Cavazza C, Nicolet Y. Structure/function relationships of [NiFe]- and [FeFe]-hydrogenases. Chem Rev 2007; 107:4273-303. [PMID: 17850165 DOI: 10.1021/cr050195z] [Citation(s) in RCA: 1004] [Impact Index Per Article: 59.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Juan C Fontecilla-Camps
- Laboratoire de Cristallographie et Cristallogenèse des Proteines, Institut de Biologie Structurale J. P. Ebel, CEA, CNRS, Universitè Joseph Fourier, 41 rue J. Horowitz, 38027 Grenoble Cedex 1, France.
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42
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Lubitz W, Reijerse E, van Gastel M. [NiFe] and [FeFe] Hydrogenases Studied by Advanced Magnetic Resonance Techniques. Chem Rev 2007; 107:4331-65. [PMID: 17845059 DOI: 10.1021/cr050186q] [Citation(s) in RCA: 376] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Wolfgang Lubitz
- Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
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Pardo A, De Lacey AL, Fernández VM, Fan Y, Hall MB. Characterization of the active site of catalytically inactive forms of [NiFe] hydrogenases by density functional theory. J Biol Inorg Chem 2007; 12:751-60. [PMID: 17440755 DOI: 10.1007/s00775-007-0227-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2006] [Accepted: 03/06/2007] [Indexed: 11/26/2022]
Abstract
The inactive forms, unready (Ni-A, Ni-SU) and ready (Ni-B), of NiFe hydrogenases are modeled by examining the possibility of hydroxo, oxo, hydroperoxo, peroxo, and sulfenate groups in active-site models and comparing predicted IR frequencies and g tensors with those of the enzyme. The best models for Ni-A and Ni-SU have hydroxo (mu-OH) bridges between Fe and Ni and a terminal sulfenate [Ni-S(=O)Cys] group, although a hydroperoxo model for Ni-A is also quite viable, whereas the best model for Ni-B has only a mu-OH bridge. In addition, a mechanism for the activation of unready hydrogenase is proposed on the basis of the relative stabilities of sulfenate models versus peroxide models.
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Affiliation(s)
- Alejandro Pardo
- Instituto de Catalisis, Consejo Superior de Investigaciones Cientificas, c/ Marie Curie, 2 Campus Cantoblanco, 28049 Madrid, Spain
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45
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Ryde U. Accurate metal-site structures in proteins obtained by combining experimental data and quantum chemistry. Dalton Trans 2006:607-25. [PMID: 17268593 DOI: 10.1039/b614448a] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The use of molecular mechanics calculations to supplement experimental data in standard X-ray crystallography and NMR refinements is discussed and it is shown that structures can be locally improved by the use of quantum chemical calculations. Such calculations can also be used to interpret the structures, e.g. to decide the protonation state of metal-bound ligands. They have shown that metal sites in crystal structures are frequently photoreduced or disordered, which makes the interpretation of the structures hard. Similar methods can be used for EXAFS refinements to obtain a full atomic structure, rather than a set of metal-ligand distances.
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Affiliation(s)
- Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P. O. Box 124, SE-221 00, Lund, Sweden.
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