1
|
Pierce BS, Schmittou AN, York NJ, Madigan RP, Nino PF, Foss FW, Lockart MM. Improved resolution of 3-mercaptopropionate dioxygenase active site provided by ENDOR spectroscopy offers insight into catalytic mechanism. J Biol Chem 2024; 300:105777. [PMID: 38395308 PMCID: PMC10966181 DOI: 10.1016/j.jbc.2024.105777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 02/13/2024] [Accepted: 02/15/2024] [Indexed: 02/25/2024] Open
Abstract
3-mercaptopropionate (3MPA) dioxygenase (MDO) is a mononuclear nonheme iron enzyme that catalyzes the O2-dependent oxidation of thiol-bearing substrates to yield the corresponding sulfinic acid. MDO is a member of the cysteine dioxygenase family of small molecule thiol dioxygenases and thus shares a conserved sequence of active site residues (Serine-155, Histidine-157, and Tyrosine-159), collectively referred to as the SHY-motif. It has been demonstrated that these amino acids directly interact with the mononuclear Fe-site, influencing steady-state catalysis, catalytic efficiency, O2-binding, and substrate coordination. However, the underlying mechanism by which this is accomplished is poorly understood. Here, pulsed electron paramagnetic resonance spectroscopy [1H Mims electron nuclear double resonance spectroscopy] is applied to validate density functional theory computational models for the MDO Fe-site simultaneously coordinated by substrate and nitric oxide (NO), (3MPA/NO)-MDO. The enhanced resolution provided by electron nuclear double resonance spectroscopy allows for direct observation of Fe-bound substrate conformations and H-bond donation from Tyr159 to the Fe-bound NO ligand. Further inclusion of SHY-motif residues within the validated model reveals a distinct channel restricting movement of the Fe-bound NO-ligand. It has been argued that the iron-nitrosyl emulates the structure of potential Fe(III)-superoxide intermediates within the MDO catalytic cycle. While the merit of this assumption remains unconfirmed, the model reported here offers a framework to evaluate oxygen binding at the substrate-bound Fe-site and possible reaction mechanisms. It also underscores the significance of hydrogen bonding interactions within the enzymatic active site.
Collapse
Affiliation(s)
- Brad S Pierce
- Department of Chemistry & Biochemistry, University of Alabama, Tuscaloosa, Alabama, USA.
| | - Allison N Schmittou
- Department of Chemistry & Biochemistry, University of Alabama, Tuscaloosa, Alabama, USA
| | - Nicholas J York
- Department of Chemistry & Biochemistry, University of Alabama, Tuscaloosa, Alabama, USA
| | - Ryan P Madigan
- Department of Chemistry & Biochemistry, The University of Texas at Arlington, Arlington, Texas, USA
| | - Paula F Nino
- Department of Chemistry & Biochemistry, The University of Texas at Arlington, Arlington, Texas, USA
| | - Frank W Foss
- Department of Chemistry & Biochemistry, The University of Texas at Arlington, Arlington, Texas, USA
| | - Molly M Lockart
- Department of Chemistry and Biochemistry, Samford University, Homewood, Alabama, USA.
| |
Collapse
|
2
|
Procacci B, Wrathall SLD, Farmer AL, Shaw DJ, Greetham GM, Parker AW, Rippers Y, Horch M, Lynam JM, Hunt NT. Understanding the [NiFe] Hydrogenase Active Site Environment through Ultrafast Infrared and 2D-IR Spectroscopy of the Subsite Analogue K[CpFe(CO)(CN) 2] in Polar and Protic Solvents. J Phys Chem B 2024; 128:1461-1472. [PMID: 38301127 PMCID: PMC10875664 DOI: 10.1021/acs.jpcb.3c07965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/16/2024] [Accepted: 01/17/2024] [Indexed: 02/03/2024]
Abstract
The [CpFe(CO)(CN)2]- unit is an excellent structural model for the Fe(CO)(CN)2 moiety of the active site found in [NiFe] hydrogenases. Ultrafast infrared (IR) pump-probe and 2D-IR spectroscopy have been used to study K[CpFe(CO)(CN)2] (M1) in a range of protic and polar solvents and as a dry film. Measurements of anharmonicity, intermode vibrational coupling strength, vibrational relaxation time, and solvation dynamics of the CO and CN stretching modes of M1 in H2O, D2O, methanol, dimethyl sulfoxide, and acetonitrile reveal that H-bonding to the CN ligands plays an important role in defining the spectroscopic characteristics and relaxation dynamics of the Fe(CO)(CN)2 unit. Comparisons of the spectroscopic and dynamic data obtained for M1 in solution and in a dry film with those obtained for the enzyme led to the conclusion that the protein backbone forms an important part of the bimetallic active site environment via secondary coordination sphere interactions.
Collapse
Affiliation(s)
- Barbara Procacci
- Department
of Chemistry, York Biomedical Research Institute,
University of York, York YO10 5DD, U.K.
| | - Solomon L. D. Wrathall
- Department
of Chemistry, York Biomedical Research Institute,
University of York, York YO10 5DD, U.K.
| | - Amy L. Farmer
- Department
of Chemistry, York Biomedical Research Institute,
University of York, York YO10 5DD, U.K.
| | - Daniel J. Shaw
- Department
of Chemistry, York Biomedical Research Institute,
University of York, York YO10 5DD, U.K.
| | - Gregory M. Greetham
- STFC
Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0QX, U.K.
| | - Anthony W. Parker
- STFC
Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0QX, U.K.
| | - Yvonne Rippers
- Department
of Physics, Ultrafast Dynamics in Catalysis, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Marius Horch
- Department
of Physics, Ultrafast Dynamics in Catalysis, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Jason M. Lynam
- Department
of Chemistry, York Biomedical Research Institute,
University of York, York YO10 5DD, U.K.
| | - Neil T. Hunt
- Department
of Chemistry, York Biomedical Research Institute,
University of York, York YO10 5DD, U.K.
| |
Collapse
|
3
|
Ravera E, Gigli L, Suturina EA, Calderone V, Fragai M, Parigi G, Luchinat C. A High-Resolution View of the Coordination Environment in a Paramagnetic Metalloprotein from its Magnetic Properties. Angew Chem Int Ed Engl 2021; 60:14960-14966. [PMID: 33595173 DOI: 10.1002/anie.202101149] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Indexed: 12/13/2022]
Abstract
Metalloproteins constitute a significant fraction of the proteome of all organisms and their characterization is critical for both basic sciences and biomedical applications. A large portion of metalloproteins bind paramagnetic metal ions, and paramagnetic NMR spectroscopy has been widely used in their structural characterization. However, the signals of nuclei in the immediate vicinity of the metal center are often broadened beyond detection. In this work, we show that it is possible to determine the coordination environment of the paramagnetic metal in the protein at a resolution inaccessible to other techniques. Taking the structure of a diamagnetic analogue as a starting point, a geometry optimization is carried out by fitting the pseudocontact shifts obtained from first principles quantum chemical calculations to the experimental ones.
Collapse
Affiliation(s)
- Enrico Ravera
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Lucia Gigli
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | | | - Vito Calderone
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Giacomo Parigi
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| |
Collapse
|
4
|
Ravera E, Gigli L, Suturina EA, Calderone V, Fragai M, Parigi G, Luchinat C. A High‐Resolution View of the Coordination Environment in a Paramagnetic Metalloprotein from its Magnetic Properties. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202101149] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Enrico Ravera
- Magnetic Resonance Center (CERM) University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP) Via L. Sacconi 6 50019 Sesto Fiorentino Italy
- Department of Chemistry “Ugo Schiff” University of Florence Via della Lastruccia 3 50019 Sesto Fiorentino Italy
| | - Lucia Gigli
- Magnetic Resonance Center (CERM) University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP) Via L. Sacconi 6 50019 Sesto Fiorentino Italy
- Department of Chemistry “Ugo Schiff” University of Florence Via della Lastruccia 3 50019 Sesto Fiorentino Italy
| | | | - Vito Calderone
- Magnetic Resonance Center (CERM) University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP) Via L. Sacconi 6 50019 Sesto Fiorentino Italy
- Department of Chemistry “Ugo Schiff” University of Florence Via della Lastruccia 3 50019 Sesto Fiorentino Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM) University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP) Via L. Sacconi 6 50019 Sesto Fiorentino Italy
- Department of Chemistry “Ugo Schiff” University of Florence Via della Lastruccia 3 50019 Sesto Fiorentino Italy
| | - Giacomo Parigi
- Magnetic Resonance Center (CERM) University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP) Via L. Sacconi 6 50019 Sesto Fiorentino Italy
- Department of Chemistry “Ugo Schiff” University of Florence Via della Lastruccia 3 50019 Sesto Fiorentino Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM) University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP) Via L. Sacconi 6 50019 Sesto Fiorentino Italy
- Department of Chemistry “Ugo Schiff” University of Florence Via della Lastruccia 3 50019 Sesto Fiorentino Italy
| |
Collapse
|
5
|
Orio M, Pantazis DA. Successes, challenges, and opportunities for quantum chemistry in understanding metalloenzymes for solar fuels research. Chem Commun (Camb) 2021; 57:3952-3974. [DOI: 10.1039/d1cc00705j] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Overview of the rich and diverse contributions of quantum chemistry to understanding the structure and function of the biological archetypes for solar fuel research, photosystem II and hydrogenases.
Collapse
Affiliation(s)
- Maylis Orio
- Aix-Marseille Université
- CNRS
- iSm2
- Marseille
- France
| | - Dimitrios A. Pantazis
- Max-Planck-Institut für Kohlenforschung
- Kaiser-Wilhelm-Platz 1
- 45470 Mülheim an der Ruhr
- Germany
| |
Collapse
|
6
|
York NJ, Lockart MM, Sardar S, Khadka N, Shi W, Stenkamp RE, Zhang J, Kiser PD, Pierce BS. Structure of 3-mercaptopropionic acid dioxygenase with a substrate analog reveals bidentate substrate binding at the iron center. J Biol Chem 2021; 296:100492. [PMID: 33662397 PMCID: PMC8050391 DOI: 10.1016/j.jbc.2021.100492] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/18/2021] [Accepted: 02/26/2021] [Indexed: 12/20/2022] Open
Abstract
Thiol dioxygenases are a subset of nonheme iron oxygenases that catalyze the formation of sulfinic acids from sulfhydryl-containing substrates and dioxygen. Among this class, cysteine dioxygenases (CDOs) and 3-mercaptopropionic acid dioxygenases (3MDOs) are the best characterized, and the mode of substrate binding for CDOs is well understood. However, the manner in which 3-mercaptopropionic acid (3MPA) coordinates to the nonheme iron site in 3MDO remains a matter of debate. A model for bidentate 3MPA coordination at the 3MDO Fe-site has been proposed on the basis of computational docking, whereas steady-state kinetics and EPR spectroscopic measurements suggest a thiolate-only coordination of the substrate. To address this gap in knowledge, we determined the structure of Azobacter vinelandii 3MDO (Av3MDO) in complex with the substrate analog and competitive inhibitor, 3-hydroxypropionic acid (3HPA). The structure together with DFT computational modeling demonstrates that 3HPA and 3MPA associate with iron as chelate complexes with the substrate-carboxylate group forming an additional interaction with Arg168 and the thiol bound at the same position as in CDO. A chloride ligand was bound to iron in the coordination site assigned as the O2-binding site. Supporting HYSCORE spectroscopic experiments were performed on the (3MPA/NO)-bound Av3MDO iron nitrosyl (S = 3/2) site. In combination with spectroscopic simulations and optimized DFT models, this work provides an experimentally verified model of the Av3MDO enzyme-substrate complex, effectively resolving a debate in the literature regarding the preferred substrate-binding denticity. These results elegantly explain the observed 3MDO substrate specificity, but leave unanswered questions regarding the mechanism of substrate-gated reactivity with dioxygen.
Collapse
Affiliation(s)
- Nicholas J York
- Department of Chemistry & Biochemistry, University of Alabama, Tuscaloosa, Alabama, USA
| | - Molly M Lockart
- Department of Chemistry & Biochemistry, University of Alabama, Tuscaloosa, Alabama, USA
| | - Sinjinee Sardar
- Department of Chemistry & Biochemistry, The University of Texas at Arlington, Arlington, Texas, USA
| | - Nimesh Khadka
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Wuxian Shi
- National Synchrotron Light Source-II, Brookhaven National Laboratory, Upton, New York, USA
| | - Ronald E Stenkamp
- Departments of Biological Structure and Biochemistry, University of Washington, Seattle, Washington, USA
| | - Jianye Zhang
- Department of Ophthalmology, School of Medicine, University of California, Irvine, Irvine, California, USA
| | - Philip D Kiser
- Department of Ophthalmology, School of Medicine, University of California, Irvine, Irvine, California, USA; Department of Physiology & Biophysics, School of Medicine, University of California, Irvine, Irvine, California, USA; Research Service, VA Long Beach Healthcare System, Long Beach, California, USA.
| | - Brad S Pierce
- Department of Chemistry & Biochemistry, University of Alabama, Tuscaloosa, Alabama, USA.
| |
Collapse
|
7
|
Vansuch GE, Wu CH, Haja DK, Blair SA, Chica B, Johnson MK, Adams MWW, Dyer RB. Metal-ligand cooperativity in the soluble hydrogenase-1 from Pyrococcus furiosus. Chem Sci 2020; 11:8572-8581. [PMID: 34123117 PMCID: PMC8163435 DOI: 10.1039/d0sc00628a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Metal–ligand cooperativity is an essential feature of bioinorganic catalysis. The design principles of such cooperativity in metalloenzymes are underexplored, but are critical to understand for developing efficient catalysts designed with earth abundant metals for small molecule activation. The simple substrate requirements of reversible proton reduction by the [NiFe]-hydrogenases make them a model bioinorganic system. A highly conserved arginine residue (R355) directly above the exogenous ligand binding position of the [NiFe]-catalytic core is known to be essential for optimal function because mutation to a lysine results in lower catalytic rates. To expand on our studies of soluble hydrogenase-1 from Pyrococcus furiosus (Pf SH1), we investigated the role of R355 by site-directed-mutagenesis to a lysine (R355K) using infrared and electron paramagnetic resonance spectroscopic probes sensitive to active site redox and protonation events. It was found the mutation resulted in an altered ligand binding environment at the [NiFe] centre. A key observation was destabilization of the Nia3+–C state, which contains a bridging hydride. Instead, the tautomeric Nia+–L states were observed. Overall, the results provided insight into complex metal–ligand cooperativity between the active site and protein scaffold that modulates the bridging hydride stability and the proton inventory, which should prove valuable to design principles for efficient bioinspired catalysts. Metal–ligand cooperativity is an essential feature of bioinorganic catalysis.![]()
Collapse
Affiliation(s)
| | - Chang-Hao Wu
- Department of Biochemistry & Molecular Biology, University of Georgia Athens Georgia 30602 USA.,AskGene Pharma Inc. Camarillo CA 93012 USA
| | - Dominik K Haja
- Department of Biochemistry & Molecular Biology, University of Georgia Athens Georgia 30602 USA
| | - Soshawn A Blair
- Department of Chemistry, University of Georgia Athens Georgia 30602 USA
| | - Bryant Chica
- Department of Chemistry, Emory University Atlanta Georgia 30222 USA .,Biosciences Center, National Renewable Energy Laboratory Golden Colorado 80401 USA
| | - Michael K Johnson
- Department of Chemistry, University of Georgia Athens Georgia 30602 USA
| | - Michael W W Adams
- Department of Biochemistry & Molecular Biology, University of Georgia Athens Georgia 30602 USA.,Department of Chemistry, University of Georgia Athens Georgia 30602 USA
| | - R Brian Dyer
- Department of Chemistry, Emory University Atlanta Georgia 30222 USA
| |
Collapse
|
8
|
Gu NX, Oyala PH, Peters JC. H 2 Evolution from a Thiolate-Bound Ni(III) Hydride. J Am Chem Soc 2020; 142:7827-7835. [PMID: 32249575 DOI: 10.1021/jacs.0c00712] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Terminal NiIII hydrides are proposed intermediates in proton reduction catalyzed by both molecular electrocatalysts and metalloenzymes, but well-defined examples of paramagnetic nickel hydride complexes are largely limited to bridging hydrides. Herein, we report the synthesis of an S = 1/2, terminally bound thiolate-NiIII-H complex. This species and its terminal hydride ligand in particular have been thoroughly characterized by vibrational and EPR techniques, including pulse EPR studies. Corresponding DFT calculations suggest appreciable spin leakage onto the thiolate ligand. The hyperfine coupling to the terminal hydride ligand of the thiolate-NiIII-H species is comparable to that of the hydride ligand proposed for the Ni-C hydrogenase intermediate (NiIII-H-FeII). Upon warming, the featured thiolate-NiIII-H species undergoes bimolecular reductive elimination of H2. Associated kinetic studies are discussed and compared with a structurally related FeIII-H species that has also recently been reported to undergo bimolecular H-H coupling.
Collapse
Affiliation(s)
- Nina X Gu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Paul H Oyala
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Jonas C Peters
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| |
Collapse
|
9
|
Affiliation(s)
- Per E. M. Siegbahn
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Rong-Zhen Liao
- Key Laboratory for Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Bioinorganic Chemistry and Materia Media, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, 430074 Wuhan, People’s Republic of China
| |
Collapse
|
10
|
Barrozo A, Orio M. Molecular Electrocatalysts for the Hydrogen Evolution Reaction: Input from Quantum Chemistry. CHEMSUSCHEM 2019; 12:4905-4915. [PMID: 31557393 DOI: 10.1002/cssc.201901828] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 08/22/2019] [Indexed: 06/10/2023]
Abstract
In the pursuit of carbon-free fuels, hydrogen can be considered as an apt energy carrier. The design of molecular electrocatalysts for hydrogen production is important for the development of renewable energy sources that are abundant, inexpensive, and environmentally benign. Over the last 20 years, a large number of electrocatalysts have been developed, and considerable efforts have been directed toward the design of earth-abundant, first-row transition-metal complexes capable of promoting electrocatalytic hydrogen evolution reaction (HER). In this context, numerical approaches have emerged as powerful tools to study the catalytic performances of these complexes. This review covers some of the most significant theoretical mechanistic studies of biomimetic and bioinspired homogeneous HER catalysts. The approaches employed to study the free energy landscapes are discussed and methods used to obtain accurate estimates of relevant observables required to study the HER are presented. Furthermore, the structural and electronic parameters that govern the reactivity, and are necessary to achieve efficient hydrogen production, are discussed in view of future research directions.
Collapse
Affiliation(s)
- Alexandre Barrozo
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, 13397, Marseille, France
| | - Maylis Orio
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, 13397, Marseille, France
| |
Collapse
|
11
|
Slater JW, Marguet SC, Gray ME, Monaco HA, Sotomayor M, Shafaat HS. Power of the Secondary Sphere: Modulating Hydrogenase Activity in Nickel-Substituted Rubredoxin. ACS Catal 2019. [DOI: 10.1021/acscatal.9b01720] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jeffrey W. Slater
- The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Sean C. Marguet
- The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Michelle E. Gray
- The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Haleigh A. Monaco
- The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Marcos Sotomayor
- The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Hannah S. Shafaat
- The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| |
Collapse
|
12
|
Qiu S, Li Q, Xu Y, Shen S, Sun C. Learning from nature: Understanding hydrogenase enzyme using computational approach. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2019. [DOI: 10.1002/wcms.1422] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Siyao Qiu
- Science & Technology Innovation Institute Dongguan University of Technology Dongguan China
| | - Qinye Li
- School of Chemical Engineering Monash University Clayton Victoria Australia
| | - Yongjun Xu
- Science & Technology Innovation Institute Dongguan University of Technology Dongguan China
| | - Shaohua Shen
- International Research Center for Renewable Energy, State Key Laboratory of Multiphase Flow in Power Engineering Xi'an Jiaotong University Shaanxi China
| | - Chenghua Sun
- Department of Chemistry and Biotechnology, and Center for Translational Atomaterials Swinburne University of Technology Hawthorn Victoria Australia
| |
Collapse
|
13
|
New insights into Fe–H$$_{2}$$ and Fe–H$$^{-}$$ bonding of a [NiFe] hydrogenase mimic: a local vibrational mode study. Theor Chem Acc 2019. [DOI: 10.1007/s00214-019-2463-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
14
|
Qiu S, Azofra LM, Macfarlane DR, Sun C. Hydrogen Evolution in [NiFe] Hydrogenases: A Case of Heterolytic Approach between Proton and Hydride. Inorg Chem 2019; 58:2979-2986. [DOI: 10.1021/acs.inorgchem.8b02812] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Siyao Qiu
- Science & Technology Innovation Institute, Dongguan University of Technology, Dongguan 523808, China
- School of Chemistry, Faculty of Science, Monash University, Clayton, VIC 3800, Australia
| | - Luis Miguel Azofra
- KAUST Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Douglas R. Macfarlane
- School of Chemistry, Faculty of Science, Monash University, Clayton, VIC 3800, Australia
- ARC Centre of Excellence for Electromaterials Science (ACES), School of Chemistry, Faculty of Science, Monash University, Clayton, VIC 3800, Australia
| | - Chenghua Sun
- Science & Technology Innovation Institute, Dongguan University of Technology, Dongguan 523808, China
- Department of Chemistry and Biotechnology, Faculty of Science, Engineering and Technology, Swinburne University of Technology, Hawthorn, VIC 3122, Australia
| |
Collapse
|
15
|
Breglia R, Greco C, Fantucci P, De Gioia L, Bruschi M. Reactivation of the Ready and Unready Oxidized States of [NiFe]-Hydrogenases: Mechanistic Insights from DFT Calculations. Inorg Chem 2018; 58:279-293. [PMID: 30576127 DOI: 10.1021/acs.inorgchem.8b02348] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The apparently simple dihydrogen formation from protons and electrons (2H+ + 2e- ⇄ H2) is one of the most challenging reactions in nature. It is catalyzed by metalloenzymes of amazing complexity, called hydrogenases. A better understanding of the chemistry of these enzymes, especially that of the [NiFe]-hydrogenases subgroup, has important implications for production of H2 as alternative sustainable fuel. In this work, reactivation mechanism of the oxidized and inactive Ni-B and Ni-A states of the [NiFe]-hydrogenases active site has been investigated using density functional theory. Results obtained from this study show that one-electron reduction and protonation of the active site promote the removal of the bridging hydroxide ligand contained in Ni-B and Ni-A. However, this process is sufficient to activate only the Ni-B state. H2 binding to the active site is required to convert Ni-A to the active Ni-SIa state. Here, we also propose a reasonable structure for the spectroscopically well-characterized Ni-SIr and Ni-SU species, formed respectively from the one-electron reduction of Ni-B and Ni-A. Ni-SIr, depending on the pH at which the reaction occurs, features a bridging hydroxide ligand or a water molecule terminally coordinated to the Ni atom, whereas in Ni-SU a water molecule is terminally coordinated to the Fe atom, and the Cys64 residue is oxidized to sulfenate. The sulfenate oxygen atom in the Ni-A state affects the stereoelectronic properties of the binuclear cluster by modifying the coordination geometry of Ni, and consequently, by switching the regiochemistry of H2O and H2 binding from the Ni to the Fe atom. This effect is predicted to be at the origin of the different reactivation kinetics of the oxidized and inactive Ni-B and Ni-A states.
Collapse
|
16
|
Qiu S, Azofra LM, MacFarlane DR, Sun C. Hydrogen bonding effect between active site and protein environment on catalysis performance in H 2-producing [NiFe] hydrogenases. Phys Chem Chem Phys 2018; 20:6735-6743. [PMID: 29457815 DOI: 10.1039/c7cp07685a] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The interaction between the active site and the surrounding protein environment plays a fundamental role in the hydrogen evolution reaction (HER) in [NiFe] hydrogenases. Our density functional theory (DFT) findings demonstrate that the reaction Gibbs free energy required for the rate determining step decreases by 7.1 kcal mol-1 when the surrounding protein environment is taken into account, which is chiefly due to free energy decreases for the two H+/e- addition steps (the so-called Ni-SIa to I1, and Ni-C to Ni-R), being the largest thermodynamic impediments of the whole reaction. The variety of hydrogen bonds (H-bonds) between the amino acids and the active site is hypothesised to be the main reason for such stability: H-bonds not only work as electrostatic attractive forces that influence the charge redistribution, but more importantly, they act as an electron 'pull' taking electrons from the active site towards the amino acids. Moreover, the electron 'pull' effect through H-bonds via the S- in cysteine residues shows a larger influence on the energy profile than that via the CN- ligands on Fe.
Collapse
Affiliation(s)
- Siyao Qiu
- School of Chemistry, Faculty of Science, Monash University, Clayton, VIC 3800, Australia.
| | | | | | | |
Collapse
|
17
|
Perotto CU, Sodipo CL, Jones GJ, Tidey JP, Blake AJ, Lewis W, Davies ES, McMaster J, Schröder M. Heterobimetallic [NiFe] Complexes Containing Mixed CO/CN - Ligands: Analogs of the Active Site of the [NiFe] Hydrogenases. Inorg Chem 2018; 57:2558-2569. [PMID: 29465237 DOI: 10.1021/acs.inorgchem.7b02905] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The development of synthetic analogs of the active sites of [NiFe] hydrogenases remains challenging, and, in spite of the number of complexes featuring a [NiFe] center, those featuring CO and CN- ligands at the Fe center are under-represented. We report herein the synthesis of three bimetallic [NiFe] complexes [Ni( N2 S2)Fe(CO)2(CN)2], [Ni( S4)Fe(CO)2(CN)2], and [Ni( N2 S3)Fe(CO)2(CN)2] that each contain a Ni center that bridges through two thiolato S donors to a {Fe(CO)2(CN)2} unit. X-ray crystallographic studies on [Ni( N2 S3)Fe(CO)2(CN)2], supported by DFT calculations, are consistent with a solid-state structure containing distinct molecules in the singlet ( S = 0) and triplet ( S = 1) states. Each cluster exhibits irreversible reduction processes between -1.45 and -1.67 V vs Fc+/Fc and [Ni( N2 S3)Fe(CO)2(CN)2] possesses a reversible oxidation process at 0.17 V vs Fc+/Fc. Spectroelectrochemical infrared (IR) and electron paramagnetic resonance (EPR) studies, supported by density functional theory (DFT) calculations, are consistent with a NiIIIFeII formulation for [Ni( N2 S3)Fe(CO)2(CN)2]+. The singly occupied molecular orbital (SOMO) in [Ni( N2 S3)Fe(CO)2(CN)2]+ is based on Ni 3dz2 and 3p S with the S contributions deriving principally from the apical S-donor. The nature of the SOMO corresponds to that proposed for the Ni-C state of the [NiFe] hydrogenases for which a NiIIIFeII formulation has also been proposed. A comparison of the experimental structures, and the electrochemical and spectroscopic properties of [Ni( N2 S3)Fe(CO)2(CN)2] and its [Ni( N2 S3)] precursor, together with calculations on the oxidized [Ni( N2 S3)Fe(CO)2(CN)2]+ and [Ni( N2 S3)]+ forms suggests that the binding of the {Fe(CO)(CN)2} unit to the {Ni(CysS)4} center at the active site of the [NiFe] hydrogenases suppresses thiolate-based oxidative chemistry involving the bridging thiolate S donors. This is in addition to the role of the Fe center in modulating the redox potential and geometry and supporting a bridging hydride species between the Ni and Fe centers in the Ni-C state.
Collapse
Affiliation(s)
- Carlo U Perotto
- School of Chemistry , University of Nottingham , Nottingham , NG7 2RD , United Kingdom
| | - Charlene L Sodipo
- School of Chemistry , University of Nottingham , Nottingham , NG7 2RD , United Kingdom
| | - Graham J Jones
- School of Chemistry , University of Nottingham , Nottingham , NG7 2RD , United Kingdom
| | - Jeremiah P Tidey
- School of Chemistry , University of Nottingham , Nottingham , NG7 2RD , United Kingdom
| | - Alexander J Blake
- School of Chemistry , University of Nottingham , Nottingham , NG7 2RD , United Kingdom
| | - William Lewis
- School of Chemistry , University of Nottingham , Nottingham , NG7 2RD , United Kingdom
| | - E Stephen Davies
- School of Chemistry , University of Nottingham , Nottingham , NG7 2RD , United Kingdom
| | - Jonathan McMaster
- School of Chemistry , University of Nottingham , Nottingham , NG7 2RD , United Kingdom
| | - Martin Schröder
- The University of Manchester , Oxford Road , Manchester , M13 9PL , United Kingdom
| |
Collapse
|
18
|
Qiu S, Olsen S, MacFarlane DR, Sun C. The oxygen reduction reaction on [NiFe] hydrogenases. Phys Chem Chem Phys 2018; 20:23528-23534. [DOI: 10.1039/c8cp04160a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Oxygen tolerance capacity is critical for hydrogen oxidation/evolution catalysts.
Collapse
Affiliation(s)
- Siyao Qiu
- Science & Technology Innovation Institute
- Dongguan University of Technology
- Dongguan
- China
- School of Chemistry
| | - Seth Olsen
- School of Chemistry
- Faculty of Science
- Monash University
- Clayton
- VIC 3800
| | | | - Chenghua Sun
- Science & Technology Innovation Institute
- Dongguan University of Technology
- Dongguan
- China
- Department of Chemistry and Biotechnology
| |
Collapse
|
19
|
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.
Collapse
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
| |
Collapse
|
20
|
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.
Collapse
|
21
|
Slater JW, Marguet SC, Cirino SL, Maugeri PT, Shafaat HS. Experimental and DFT Investigations Reveal the Influence of the Outer Coordination Sphere on the Vibrational Spectra of Nickel-Substituted Rubredoxin, a Model Hydrogenase Enzyme. Inorg Chem 2017; 56:3926-3938. [PMID: 28323426 DOI: 10.1021/acs.inorgchem.6b02934] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nickel-substituted rubredoxin (NiRd) is a functional enzyme mimic of hydrogenase, highly active for electrocatalytic and solution-phase hydrogen generation. Spectroscopic methods can provide valuable insight into the catalytic mechanism, provided the appropriate technique is used. In this study, we have employed multiwavelength resonance Raman spectroscopy coupled with DFT calculations on an extended active-site model of NiRd to probe the electronic and geometric structures of the resting state of this system. Excellent agreement between experiment and theory is observed, allowing normal mode assignments to be made on the basis of frequency and intensity analyses. Both metal-ligand and ligand-centered vibrational modes are enhanced in the resonance Raman spectra. The latter provide information about the hydrogen bonding network and structural distortions due to perturbations in the secondary coordination sphere. To reproduce the resonance enhancement patterns seen for high-frequency vibrational modes, the secondary coordination sphere must be included in the computational model. The structure and reduction potential of the NiIIIRd state have also been investigated both experimentally and computationally. This work begins to establish a foundation for computational resonance Raman spectroscopy to serve in a predictive fashion for investigating catalytic intermediates of NiRd.
Collapse
Affiliation(s)
- Jeffrey W Slater
- The Ohio State University , 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Sean C Marguet
- The Ohio State University , 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Sabrina L Cirino
- The Ohio State University , 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Pearson T Maugeri
- The Ohio State University , 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Hannah S Shafaat
- The Ohio State University , 100 West 18th Avenue, Columbus, Ohio 43210, United States
| |
Collapse
|
22
|
Dong G, Phung QM, Hallaert SD, Pierloot K, Ryde U. H2binding to the active site of [NiFe] hydrogenase studied by multiconfigurational and coupled-cluster methods. Phys Chem Chem Phys 2017; 19:10590-10601. [DOI: 10.1039/c7cp01331k] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
CCSD(T) and DMRG-CASPT2 calculations show that H2prefers to bind to Ni rather than to Fe in [NiFe] hydrogenase.
Collapse
Affiliation(s)
- Geng Dong
- Department of Theoretical Chemistry
- Lund University
- SE-221 00 Lund
- Sweden
| | - Quan Manh Phung
- Department of Chemistry
- University of Leuven
- B-3001 Leuven
- Belgium
| | | | | | - Ulf Ryde
- Department of Theoretical Chemistry
- Lund University
- SE-221 00 Lund
- Sweden
| |
Collapse
|
23
|
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]
|
24
|
Schilter D, Camara JM, Huynh MT, Hammes-Schiffer S, Rauchfuss TB. Hydrogenase Enzymes and Their Synthetic Models: The Role of Metal Hydrides. Chem Rev 2016; 116:8693-749. [PMID: 27353631 PMCID: PMC5026416 DOI: 10.1021/acs.chemrev.6b00180] [Citation(s) in RCA: 397] [Impact Index Per Article: 49.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydrogenase enzymes efficiently process H2 and protons at organometallic FeFe, NiFe, or Fe active sites. Synthetic modeling of the many H2ase states has provided insight into H2ase structure and mechanism, as well as afforded catalysts for the H2 energy vector. Particularly important are hydride-bearing states, with synthetic hydride analogues now known for each hydrogenase class. These hydrides are typically prepared by protonation of low-valent cores. Examples of FeFe and NiFe hydrides derived from H2 have also been prepared. Such chemistry is more developed than mimicry of the redox-inactive monoFe enzyme, although functional models of the latter are now emerging. Advances in physical and theoretical characterization of H2ase enzymes and synthetic models have proven key to the study of hydrides in particular, and will guide modeling efforts toward more robust and active species optimized for practical applications.
Collapse
Affiliation(s)
- David Schilter
- Center for Multidimensional Carbon Materials, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - James M. Camara
- Department of Chemistry, Yeshiva University, 500 West 185th Street, New York, New York 10033, United States
| | - Mioy T. Huynh
- Department of Chemistry, University of Illinois at Urbana–Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Sharon Hammes-Schiffer
- Department of Chemistry, University of Illinois at Urbana–Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Thomas B. Rauchfuss
- Department of Chemistry, University of Illinois at Urbana–Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| |
Collapse
|
25
|
Qiu S, Azofra LM, MacFarlane DR, Sun C. Unraveling the Role of Ligands in the Hydrogen Evolution Mechanism Catalyzed by [NiFe] Hydrogenases. ACS Catal 2016. [DOI: 10.1021/acscatal.6b01359] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Siyao Qiu
- School
of Chemistry, Faculty of Science, Monash University, Clayton, Victoria 3800, Australia
| | - Luis Miguel Azofra
- School
of Chemistry, Faculty of Science, Monash University, Clayton, Victoria 3800, Australia
- ARC
Centre of Excellence for Electromaterials Science (ACES), School of
Chemistry, Faculty of Science, Monash University, Clayton, Victoria 3800, Australia
| | - Douglas R. MacFarlane
- School
of Chemistry, Faculty of Science, Monash University, Clayton, Victoria 3800, Australia
- ARC
Centre of Excellence for Electromaterials Science (ACES), School of
Chemistry, Faculty of Science, Monash University, Clayton, Victoria 3800, Australia
| | - Chenghua Sun
- School
of Chemistry, Faculty of Science, Monash University, Clayton, Victoria 3800, Australia
- ARC
Centre of Excellence for Electromaterials Science (ACES), School of
Chemistry, Faculty of Science, Monash University, Clayton, Victoria 3800, Australia
| |
Collapse
|
26
|
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]
|
27
|
Chambers GM, Huynh MT, Li Y, Hammes-Schiffer S, Rauchfuss TB, Reijerse E, Lubitz W. Models of the Ni-L and Ni-SIa States of the [NiFe]-Hydrogenase Active Site. Inorg Chem 2016; 55:419-31. [PMID: 26421729 PMCID: PMC4807737 DOI: 10.1021/acs.inorgchem.5b01662] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A new class of synthetic models for the active site of [NiFe]-hydrogenases are described. The Ni(I/II)(SCys)2 and Fe(II)(CN)2CO sites are represented with (RC5H4)Ni(I/II) and Fe(II)(diphos)(CO) modules, where diphos = 1,2-C2H4(PPh2)2(dppe) or cis-1,2-C2H2(PPh2)2(dppv). The two bridging thiolate ligands are represented by CH2(CH2S)2(2-) (pdt(2-)), Me2C(CH2S)2(2-) (Me2pdt(2-)), and (C6H5S)2(2-). The reaction of Fe(pdt)(CO)2(dppe) and [(C5H5)3Ni2]BF4 affords [(C5H5)Ni(pdt)Fe(dppe)(CO)]BF4 ([1a]BF4). Monocarbonyl [1a]BF4 features an S = 0 Ni(II)Fe(II) center with five-coordinated iron, as proposed for the Ni-SIa state of the enzyme. One-electron reduction of [1a](+) affords the S = 1/2 derivative [1a](0), which, according to density functional theory (DFT) calculations and electron paramagnetic resonance and Mössbauer spectroscopies, is best described as a Ni(I)Fe(II) compound. The Ni(I)Fe(II) assignment matches that for the Ni-L state in [NiFe]-hydrogenase, unlike recently reported Ni(II)Fe(I)-based models. Compound [1a](0) reacts with strong acids to liberate 0.5 equiv of H2 and regenerate [1a](+), indicating that H2 evolution is catalyzed by [1a](0). DFT calculations were used to investigate the pathway for H2 evolution and revealed that the mechanism can proceed through two isomers of [1a](0) that differ in the stereochemistry of the Fe(dppe)CO center. Calculations suggest that protonation of [1a](0) (both isomers) affords Ni(III)-H-Fe(II) intermediates, which represent mimics of the Ni-C state of the enzyme.
Collapse
|
28
|
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.
Collapse
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
| |
Collapse
|
29
|
Qiu S, Azofra LM, MacFarlane DR, Sun C. Why is a proton transformed into a hydride by [NiFe] hydrogenases? An intrinsic reactivity analysis based on conceptual DFT. Phys Chem Chem Phys 2016; 18:15369-74. [DOI: 10.1039/c6cp00948d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The hydrogen evolution reaction (HER) catalysed by [NiFe] hydrogenases entails a series of chemical events involving great mechanistic interest.
Collapse
Affiliation(s)
- Siyao Qiu
- School of Chemistry
- Faculty of Science
- Monash University
- Clayton
- Australia
| | | | | | - Chenghua Sun
- School of Chemistry
- Faculty of Science
- Monash University
- Clayton
- Australia
| |
Collapse
|
30
|
Vedha SA, Velmurugan G, Jagadeesan R, Venuvanalingam P. Insights from the computational studies on the oxidized as-isolated state of [NiFeSe] hydrogenase from D. vulgaris Hildenborough. Phys Chem Chem Phys 2015. [PMID: 26205195 DOI: 10.1039/c5cp03071d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A density functional theory study of the active site structure and features of the oxygen tolerant [NiFeSe] Hase in the oxidized as-isolated state of the enzyme D. vulgaris Hildenborough (DvH) is reported here. The three conformers reported to be present in the X-ray structure (PDB ID: ) have been studied. The novel bidentate interchalcogen ligand (S-Se) in Conf-I of the [NiFeSe] Hase reported for the first time in hydrogenases (Hase) is found to be of donor-acceptor type with an uneven η(2) L → M σ-bond. The symmetry mismatch at the sp orbital of Se and at the dz(2) orbital of Ni has been identified to be the reason for the inability of Conf-II to convert to Conf-I. NBO analysis shows that the sulfinate ligand peculiar to the state stabilizes the active site through n →π* interactions. The results reveal that the isolated oxidized state of the [NiFeSe] Hase is significantly different from the well-known [NiFe] Hase.
Collapse
Affiliation(s)
- Swaminathan Angeline Vedha
- Theoretical and Computational Chemistry Laboratory, School of Chemistry, Bharathidasan University, Tiruchirappalli-620 024, India.
| | | | | | | |
Collapse
|
31
|
Dinda S, Genest A, Rösch N. O2 Activation and Catalytic Alcohol Oxidation by Re Complexes with Redox-Active Ligands: A DFT Study of Mechanism. ACS Catal 2015. [DOI: 10.1021/acscatal.5b00509] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Shrabani Dinda
- Institute of High Performance Computing, Agency for Science, Technology
and Research, 1 Fusionopolis Way, #16-16
Connexis, Singapore 138632, Singapore
| | - Alexander Genest
- Institute of High Performance Computing, Agency for Science, Technology
and Research, 1 Fusionopolis Way, #16-16
Connexis, Singapore 138632, Singapore
| | - Notker Rösch
- Institute of High Performance Computing, Agency for Science, Technology
and Research, 1 Fusionopolis Way, #16-16
Connexis, Singapore 138632, Singapore
- Department Chemie and Catalysis Research
Center, Technische Universität München, 85747 Garching, Germany
| |
Collapse
|
32
|
Murphy BJ, Hidalgo R, Roessler MM, Evans RM, Ash PA, Myers WK, Vincent KA, Armstrong FA. Discovery of Dark pH-Dependent H(+) Migration in a [NiFe]-Hydrogenase and Its Mechanistic Relevance: Mobilizing the Hydrido Ligand of the Ni-C Intermediate. J Am Chem Soc 2015; 137:8484-9. [PMID: 26103582 PMCID: PMC4500644 DOI: 10.1021/jacs.5b03182] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Despite extensive studies on [NiFe]-hydrogenases,
the mechanism
by which these enzymes produce and activate H2 so efficiently
remains unclear. A well-known EPR-active state produced under H2 and known as Ni-C is assigned as a NiIII–FeII species with a hydrido ligand in the bridging position between
the two metals. It has long been known that low-temperature photolysis
of Ni-C yields distinctive EPR-active states, collectively termed
Ni-L, that are attributed to migration of the bridging-H species as
a proton; however, Ni-L has mainly been regarded as an artifact with
no mechanistic relevance. It is now demonstrated, based on EPR and
infrared spectroscopic studies, that the Ni-C to Ni-L interconversion
in Hydrogenase-1 (Hyd-1) from Escherichia coli is a pH-dependent process that proceeds readily in the dark—proton
migration from Ni-C being favored as the pH is increased. The persistence
of Ni-L in Hyd-1 must relate to unassigned differences in proton affinities
of metal and adjacent amino acid sites, although the unusually high
reduction potentials of the adjacent Fe–S centers in this O2-tolerant hydrogenase might also be a contributory factor,
impeding elementary electron transfer off the [NiFe] site after proton
departure. The results provide compelling evidence that Ni-L is a
true, albeit elusive, catalytic intermediate of [NiFe]-hydrogenases.
Collapse
Affiliation(s)
- Bonnie J Murphy
- †Department of Chemistry and ‡Centre for Advanced Electron Spin Resonance, University of Oxford, Oxford OX1 3QR, United Kingdom
| | - Ricardo Hidalgo
- †Department of Chemistry and ‡Centre for Advanced Electron Spin Resonance, University of Oxford, Oxford OX1 3QR, United Kingdom
| | - Maxie M Roessler
- †Department of Chemistry and ‡Centre for Advanced Electron Spin Resonance, University of Oxford, Oxford OX1 3QR, United Kingdom
| | - Rhiannon M Evans
- †Department of Chemistry and ‡Centre for Advanced Electron Spin Resonance, University of Oxford, Oxford OX1 3QR, United Kingdom
| | - Philip A Ash
- †Department of Chemistry and ‡Centre for Advanced Electron Spin Resonance, University of Oxford, Oxford OX1 3QR, United Kingdom
| | - William K Myers
- †Department of Chemistry and ‡Centre for Advanced Electron Spin Resonance, University of Oxford, Oxford OX1 3QR, United Kingdom
| | - Kylie A Vincent
- †Department of Chemistry and ‡Centre for Advanced Electron Spin Resonance, University of Oxford, Oxford OX1 3QR, United Kingdom
| | - Fraser A Armstrong
- †Department of Chemistry and ‡Centre for Advanced Electron Spin Resonance, University of Oxford, Oxford OX1 3QR, United Kingdom
| |
Collapse
|
33
|
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
| |
Collapse
|
34
|
Peters JW, Schut GJ, Boyd ES, Mulder DW, Shepard EM, Broderick JB, King PW, Adams MWW. [FeFe]- and [NiFe]-hydrogenase diversity, mechanism, and maturation. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1853:1350-69. [PMID: 25461840 DOI: 10.1016/j.bbamcr.2014.11.021] [Citation(s) in RCA: 273] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 11/10/2014] [Accepted: 11/16/2014] [Indexed: 11/29/2022]
Abstract
The [FeFe]- and [NiFe]-hydrogenases catalyze the formal interconversion between hydrogen and protons and electrons, possess characteristic non-protein ligands at their catalytic sites and thus share common mechanistic features. Despite the similarities between these two types of hydrogenases, they clearly have distinct evolutionary origins and likely emerged from different selective pressures. [FeFe]-hydrogenases are widely distributed in fermentative anaerobic microorganisms and likely evolved under selective pressure to couple hydrogen production to the recycling of electron carriers that accumulate during anaerobic metabolism. In contrast, many [NiFe]-hydrogenases catalyze hydrogen oxidation as part of energy metabolism and were likely key enzymes in early life and arguably represent the predecessors of modern respiratory metabolism. Although the reversible combination of protons and electrons to generate hydrogen gas is the simplest of chemical reactions, the [FeFe]- and [NiFe]-hydrogenases have distinct mechanisms and differ in the fundamental chemistry associated with proton transfer and control of electron flow that also help to define catalytic bias. A unifying feature of these enzymes is that hydrogen activation itself has been restricted to one solution involving diatomic ligands (carbon monoxide and cyanide) bound to an Fe ion. On the other hand, and quite remarkably, the biosynthetic mechanisms to produce these ligands are exclusive to each type of enzyme. Furthermore, these mechanisms represent two independent solutions to the formation of complex bioinorganic active sites for catalyzing the simplest of chemical reactions, reversible hydrogen oxidation. As such, the [FeFe]- and [NiFe]-hydrogenases are arguably the most profound case of convergent evolution. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases.
Collapse
Affiliation(s)
- John W Peters
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Gerrit J Schut
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Eric S Boyd
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - David W Mulder
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Eric M Shepard
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Joan B Broderick
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Paul W King
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| |
Collapse
|
35
|
Smith DMA, Raugei S, Squier TC. Modulation of active site electronic structure by the protein matrix to control [NiFe] hydrogenase reactivity. Phys Chem Chem Phys 2014; 16:24026-33. [PMID: 25285653 DOI: 10.1039/c4cp03518f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Control of the reactivity of the nickel center of the [NiFe] hydrogenase and other metalloproteins commonly involves outer coordination sphere ligands that act to modify the geometry and physical properties of the active site metal centers. We carried out a combined set of classical molecular dynamics and quantum/classical mechanics calculations to provide quantitative estimates of how dynamic fluctuations of the active site within the protein matrix modulate the electronic structure at the catalytic center. Specifically we focused on the dynamics of the inner and outer coordination spheres of the cysteinate-bound Ni-Fe cluster in the catalytically active Ni-C state. There are correlated movements of the cysteinate ligands and the surrounding hydrogen-bonding network, which modulate the electron affinity at the active site and the proton affinity of a terminal cysteinate. On the basis of these findings, we hypothesize a coupling between protein dynamics and electron and proton transfer reactions critical to dihydrogen production.
Collapse
Affiliation(s)
- Dayle M A Smith
- Pacific Northwest National Laboratory, P.O. Box 999, MSIN J4-33, Richland, Washington 99352, USA.
| | | | | |
Collapse
|
36
|
Vedha SA, Solomon RV, Venuvanalingam P. Atomic partitioning of M-H2 bonds in [NiFe] hydrogenase--a test case of concurrent binding. Phys Chem Chem Phys 2014; 16:10698-707. [PMID: 24756140 DOI: 10.1039/c4cp00526k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The possibility of simultaneous addition of η(2)-H2 to both the metals (Ni and Fe) in the active site of the as isolated state of the enzyme (Ni-SI) is examined here by an atom-by-atom electronic energy partitioning based on the QTAIM method. Results show that the 4LS state prefers H2 removal than addition. Destabilization of the atomic basins of the thiolate bridges and decrease of the electrophilicity of the Fe and Ni, resulting in poor back donation to the CO ligand, are the bottlenecks that hamper dihydrogen activation simultaneously. The study helps to understand why such states are seldom accessed in the activation of dihydrogen. Moreover, Ni has been found to be the natural choice for the dihydrogen binding.
Collapse
Affiliation(s)
- Swaminathan Angeline Vedha
- Theoretical & Computational Chemistry Laboratory, School of Chemistry, Bharathidasan University, Tiruchirappalli 24, India.
| | | | | |
Collapse
|
37
|
Affiliation(s)
- Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Hideaki Ogata
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Olaf Rüdiger
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Edward Reijerse
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| |
Collapse
|
38
|
Bruschi M, Tiberti M, Guerra A, De Gioia L. Disclosure of Key Stereoelectronic Factors for Efficient H2 Binding and Cleavage in the Active Site of [NiFe]-Hydrogenases. J Am Chem Soc 2014; 136:1803-14. [DOI: 10.1021/ja408511y] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Maurizio Bruschi
- Department
of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza
della Scienza 1, 20126-Milan, Italy
| | - Matteo Tiberti
- Department
of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza
della Scienza 2, 20126-Milan, Italy
| | - Alessandro Guerra
- Department
of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza
della Scienza 2, 20126-Milan, Italy
| | - Luca De Gioia
- Department
of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza
della Scienza 2, 20126-Milan, Italy
| |
Collapse
|
39
|
Abstract
AbstractEnzymes that naturally contain an organometallic complex are highly rare. Hydrogenases commonly include iron carbonyl(s) at the active site and play central roles in the hydrogen metabolism of microorganisms. [NiFe]-hydrogenases that harbor an Ni-Fe(CN)2CO complex at the active site most widely exist among organisms, compared with the other two types, [FeFe]- and [Fe]-hydrogenases. Since the first crystal structure report in 1995, structural information of the Ni-Fe cluster with various redox/substrate-bound states has been obtained, although details of the reaction mechanisms are poorly understood. While the subunit composition, physiological function, and spectroscopic/biochemical properties of [NiFe]-hydrogenases are diverse, structural information of only a limited group of the enzymes is available so far. In this paper, structural aspects of [NiFe]-hydrogenases are reviewed and recent progresses in understanding the mechanism of an O2-tolerant property of limited members and active site assembling of [NiFe]-hydrogenases are described.
Collapse
|
40
|
Krämer T, Kampa M, Lubitz W, van Gastel M, Neese F. Theoretical Spectroscopy of the NiIIIntermediate States in the Catalytic Cycle and the Activation of [NiFe] Hydrogenases. Chembiochem 2013; 14:1898-905. [DOI: 10.1002/cbic.201300104] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Indexed: 11/05/2022]
|
41
|
Roemelt M, Neese F. Excited States of Large Open-Shell Molecules: An Efficient, General, and Spin-Adapted Approach Based on a Restricted Open-Shell Ground State Wave function. J Phys Chem A 2013; 117:3069-83. [DOI: 10.1021/jp3126126] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Michael Roemelt
- 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
| |
Collapse
|
42
|
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
| |
Collapse
|