1
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Fatima S, Olshansky L. Conformational control over proton-coupled electron transfer in metalloenzymes. Nat Rev Chem 2024:10.1038/s41570-024-00646-7. [PMID: 39223400 DOI: 10.1038/s41570-024-00646-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/29/2024] [Indexed: 09/04/2024]
Abstract
From the reduction of dinitrogen to the oxidation of water, the chemical transformations catalysed by metalloenzymes underlie global geochemical and biochemical cycles. These reactions represent some of the most kinetically and thermodynamically challenging processes known and require the complex choreography of the fundamental building blocks of nature, electrons and protons, to be carried out with utmost precision and accuracy. The rate-determining step of catalysis in many metalloenzymes consists of a protein structural rearrangement, suggesting that nature has evolved to leverage macroscopic changes in protein molecular structure to control subatomic changes in metallocofactor electronic structure. The proton-coupled electron transfer mechanisms operative in nitrogenase, photosystem II and ribonucleotide reductase exemplify this interplay between molecular and electronic structural control. We present the culmination of decades of study on each of these systems and clarify what is known regarding the interplay between structural changes and functional outcomes in these metalloenzyme linchpins.
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Affiliation(s)
- Saman Fatima
- Department of Chemistry, College of Liberal Arts and Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Lisa Olshansky
- Department of Chemistry, College of Liberal Arts and Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Materials Research Laboratory, The Grainger College of Engineering, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- The Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL, USA.
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2
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Warmack RA, Rees DC. Nitrogenase beyond the Resting State: A Structural Perspective. Molecules 2023; 28:7952. [PMID: 38138444 PMCID: PMC10745740 DOI: 10.3390/molecules28247952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 12/24/2023] Open
Abstract
Nitrogenases have the remarkable ability to catalyze the reduction of dinitrogen to ammonia under physiological conditions. How does this happen? The current view of the nitrogenase mechanism focuses on the role of hydrides, the binding of dinitrogen in a reductive elimination process coupled to loss of dihydrogen, and the binding of substrates to a binuclear site on the active site cofactor. This review focuses on recent experimental characterizations of turnover relevant forms of the enzyme determined by cryo-electron microscopy and other approaches, and comparison of these forms to the resting state enzyme and the broader family of iron sulfur clusters. Emerging themes include the following: (i) The obligatory coupling of protein and electron transfers does not occur in synthetic and small-molecule iron-sulfur clusters. The coupling of these processes in nitrogenase suggests that they may involve unique features of the cofactor, such as hydride formation on the trigonal prismatic arrangement of irons, protonation of belt sulfurs, and/or protonation of the interstitial carbon. (ii) Both the active site cofactor and protein are dynamic under turnover conditions; the changes are such that more highly reduced forms may differ in key ways from the resting-state structure. Homocitrate appears to play a key role in coupling cofactor and protein dynamics. (iii) Structural asymmetries are observed in nitrogenase under turnover-relevant conditions by cryo-electron microscopy, although the mechanistic relevance of these states (such as half-of-sites reactivity) remains to be established.
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Affiliation(s)
- Rebeccah A. Warmack
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Douglas C. Rees
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA
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3
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Westhead O, Spry M, Bagger A, Shen Z, Yadegari H, Favero S, Tort R, Titirici M, Ryan MP, Jervis R, Katayama Y, Aguadero A, Regoutz A, Grimaud A, Stephens IEL. The role of ion solvation in lithium mediated nitrogen reduction. JOURNAL OF MATERIALS CHEMISTRY. A 2023; 11:12746-12758. [PMID: 37346742 PMCID: PMC10281334 DOI: 10.1039/d2ta07686a] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 01/13/2023] [Accepted: 11/15/2022] [Indexed: 06/23/2023]
Abstract
Since its verification in 2019, there have been numerous high-profile papers reporting improved efficiency of lithium-mediated electrochemical nitrogen reduction to make ammonia. However, the literature lacks any coherent investigation systematically linking bulk electrolyte properties to electrochemical performance and Solid Electrolyte Interphase (SEI) properties. In this study, we discover that the salt concentration has a remarkable effect on electrolyte stability: at concentrations of 0.6 M LiClO4 and above the electrode potential is stable for at least 12 hours at an applied current density of -2 mA cm-2 at ambient temperature and pressure. Conversely, at the lower concentrations explored in prior studies, the potential required to maintain a given N2 reduction current increased by 8 V within a period of 1 hour under the same conditions. The behaviour is linked more coordination of the salt anion and cation with increasing salt concentration in the electrolyte observed via Raman spectroscopy. Time of flight secondary ion mass spectrometry and X-ray photoelectron spectroscopy reveal a more inorganic, and therefore more stable, SEI layer is formed with increasing salt concentration. A drop in faradaic efficiency for nitrogen reduction is seen at concentrations higher than 0.6 M LiClO4, which is attributed to a combination of a decrease in nitrogen solubility and diffusivity as well as increased SEI conductivity as measured by electrochemical impedance spectroscopy.
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Affiliation(s)
- O Westhead
- Department of Materials, Imperial College London UK
- Solid-State Chemistry and Energy Laboratory, UMR8260, CNRS, Collège de France France
| | - M Spry
- Department of Materials, Imperial College London UK
| | - A Bagger
- Department of Chemistry, University of Copenhagen Denmark
- Department of Chemical Engineering, Imperial College London UK
| | - Z Shen
- Department of Materials, Imperial College London UK
| | - H Yadegari
- Department of Materials, Imperial College London UK
| | - S Favero
- Department of Chemical Engineering, Imperial College London UK
| | - R Tort
- Department of Chemical Engineering, Imperial College London UK
| | - M Titirici
- Department of Chemical Engineering, Imperial College London UK
- The Faraday Institution, Quad One, Harwell Science and Innovation Campus Didcot OX11 0RA UK
| | - M P Ryan
- Department of Materials, Imperial College London UK
- The Faraday Institution, Quad One, Harwell Science and Innovation Campus Didcot OX11 0RA UK
| | - R Jervis
- The Faraday Institution, Quad One, Harwell Science and Innovation Campus Didcot OX11 0RA UK
- Eletrochemical Innovation Lab, Department of Chemical Engineering, University College London UK
| | | | - A Aguadero
- Department of Materials, Imperial College London UK
- The Faraday Institution, Quad One, Harwell Science and Innovation Campus Didcot OX11 0RA UK
- Instituto de Ciencia de Materiales de Madrid ICMM-CSIC Spain
| | - A Regoutz
- Department of Chemistry, University College London UK
| | - A Grimaud
- Solid-State Chemistry and Energy Laboratory, UMR8260, CNRS, Collège de France France
- Réseau sur le Stockage Electrochimique de l'Energie (RS2E), CNRS FR 3459 80039 Amiens Cedex 1 France
- Department of Chemistry, Merkert Chemistry Center, Boston College Chestnut Hill MA USA
| | - I E L Stephens
- Department of Materials, Imperial College London UK
- The Faraday Institution, Quad One, Harwell Science and Innovation Campus Didcot OX11 0RA UK
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4
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Near ambient N2 fixation on solid electrodes versus enzymes and homogeneous catalysts. Nat Rev Chem 2023; 7:184-201. [PMID: 37117902 DOI: 10.1038/s41570-023-00462-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/31/2022] [Indexed: 02/04/2023]
Abstract
The Mo/Fe nitrogenase enzyme is unique in its ability to efficiently reduce dinitrogen to ammonia at atmospheric pressures and room temperature. Should an artificial electrolytic device achieve the same feat, it would revolutionize fertilizer production and even provide an energy-dense, truly carbon-free fuel. This Review provides a coherent comparison of recent progress made in dinitrogen fixation on solid electrodes, homogeneous catalysts and nitrogenases. Specific emphasis is placed on systems for which there is unequivocal evidence that dinitrogen reduction has taken place. By establishing the cross-cutting themes and synergies between these systems, we identify viable avenues for future research.
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5
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Threatt SD, Rees DC. Biological nitrogen fixation in theory, practice, and reality: a perspective on the molybdenum nitrogenase system. FEBS Lett 2023; 597:45-58. [PMID: 36344435 PMCID: PMC10100503 DOI: 10.1002/1873-3468.14534] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/30/2022] [Accepted: 10/31/2022] [Indexed: 11/09/2022]
Abstract
Nitrogenase is the sole enzyme responsible for the ATP-dependent conversion of atmospheric dinitrogen into the bioavailable form of ammonia (NH3 ), making this protein essential for the maintenance of the nitrogen cycle and thus life itself. Despite the widespread use of the Haber-Bosch process to industrially produce NH3 , biological nitrogen fixation still accounts for half of the bioavailable nitrogen on Earth. An important feature of nitrogenase is that it operates under physiological conditions, where the equilibrium strongly favours ammonia production. This biological, multielectron reduction is a complex catalytic reaction that has perplexed scientists for decades. In this review, we explore the current understanding of the molybdenum nitrogenase system based on experimental and computational research, as well as the limitations of the crystallographic, spectroscopic, and computational techniques employed. Finally, essential outstanding questions regarding the nitrogenase system will be highlighted alongside suggestions for future experimental and computational work to elucidate this essential yet elusive process.
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Affiliation(s)
- Stephanie D Threatt
- Division of Chemistry and Chemical Engineering, Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, USA
| | - Douglas C Rees
- Division of Chemistry and Chemical Engineering, Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, USA
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6
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Westhead O, Jervis R, Stephens IEL. Is lithium the key for nitrogen electroreduction? Science 2021; 372:1149-1150. [PMID: 34112680 DOI: 10.1126/science.abi8329] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Olivia Westhead
- Department of Materials, Imperial College London, London, UK
| | - Rhodri Jervis
- Electrochemical Innovation Laboratory, Department of Chemical Engineering, University College London, London, UK
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7
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Jasniewski AJ, Lee CC, Ribbe MW, Hu Y. Reactivity, Mechanism, and Assembly of the Alternative Nitrogenases. Chem Rev 2020; 120:5107-5157. [PMID: 32129988 PMCID: PMC7491575 DOI: 10.1021/acs.chemrev.9b00704] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Biological nitrogen fixation is catalyzed by the enzyme nitrogenase, which facilitates the cleavage of the relatively inert triple bond of N2. Nitrogenase is most commonly associated with the molybdenum-iron cofactor called FeMoco or the M-cluster, and it has been the subject of extensive structural and spectroscopic characterization over the past 60 years. In the late 1980s and early 1990s, two "alternative nitrogenase" systems were discovered, isolated, and found to incorporate V or Fe in place of Mo. These systems are regulated by separate gene clusters; however, there is a high degree of structural and functional similarity between each nitrogenase. Limited studies with the V- and Fe-nitrogenases initially demonstrated that these enzymes were analogously active as the Mo-nitrogenase, but more recent investigations have found capabilities that are unique to the alternative systems. In this review, we will discuss the reactivity, biosynthetic, and mechanistic proposals for the alternative nitrogenases as well as their electronic and structural properties in comparison to the well-characterized Mo-dependent system. Studies over the past 10 years have been particularly fruitful, though key aspects about V- and Fe-nitrogenases remain unexplored.
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Affiliation(s)
- Andrew J Jasniewski
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900, United States
| | - Chi Chung Lee
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900, United States
| | - Markus W Ribbe
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900, United States
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States
| | - Yilin Hu
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900, United States
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8
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Affiliation(s)
- Oliver Einsle
- Institute for Biochemistry, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Douglas C. Rees
- Division of Chemistry and Chemical Engineering, Howard Hughes Medical Institute, California Institute of Technology, Pasadena California 91125, United States
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9
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Abstract
![]()
Nitrogenase
is the only enzyme that can cleave the strong triple
bond in N2. The active site contains a complicated MoFe7S9C cluster. It is believed that it needs to accept
four protons and electrons, forming the E4 state, before
it can bind N2. However, there is no consensus on the atomic
structure of the E4 state. Experimental studies indicate
that it should contain two hydride ions bridging two pairs of Fe ions,
and it has been suggested that both hydride ions as well as the two
protons bind on the same face of the cluster. On the other hand, density
functional theory (DFT) studies have indicated that it is energetically
more favorable with either three hydride ions or with a triply protonated
carbide ion, depending on the DFT functional. We have performed a
systematic combined quantum mechanical and molecular mechanical (QM/MM)
study of possible E4 states with two bridging hydride ions.
Our calculations suggest that the most favorable structure has hydride
ions bridging the Fe2/6 and Fe3/7 ion pairs. In fact, such structures
are 14 kJ/mol more stable than structures with three hydride ions,
showing that pure DFT functionals give energetically most favorable
structures in agreement with experiments. An important reason for
this finding is that we have identified a new type of broken-symmetry
state that involves only two Fe ions with minority spin, in contrast
to the previously studied states with three Fe ions with minority
spin. The energetically best structures have the two hydride ions
on different faces of the FeMo cluster, whereas better agreement with
ENDOR data is obtained if they are on the same face; such structures
are only 6–22 kJ/mol less stable.
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Affiliation(s)
- Lili Cao
- 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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10
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Dance I. Computational Investigations of the Chemical Mechanism of the Enzyme Nitrogenase. Chembiochem 2020; 21:1671-1709. [DOI: 10.1002/cbic.201900636] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Indexed: 12/15/2022]
Affiliation(s)
- Ian Dance
- School of Chemistry UNSW Sydney Sydney 2052 Australia
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11
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Van Stappen C, Thorhallsson AT, Decamps L, Bjornsson R, DeBeer S. Resolving the structure of the E 1 state of Mo nitrogenase through Mo and Fe K-edge EXAFS and QM/MM calculations. Chem Sci 2019; 10:9807-9821. [PMID: 32055350 PMCID: PMC6984330 DOI: 10.1039/c9sc02187f] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 09/03/2019] [Indexed: 11/21/2022] Open
Abstract
Biological nitrogen fixation is predominately accomplished through Mo nitrogenase, which utilizes a complex MoFe7S9C catalytic cluster to reduce N2 to NH3. This cluster requires the accumulation of three to four reducing equivalents prior to binding N2; however, despite decades of research, the intermediate states formed prior to N2 binding are still poorly understood. Herein, we use Mo and Fe K-edge X-ray absorption spectroscopy and QM/MM calculations to investigate the nature of the E1 state, which is formed following the addition of the first reducing equivalent to Mo nitrogenase. By analyzing the extended X-ray absorption fine structure (EXAFS) region, we provide structural insight into the changes that occur in the metal clusters of the protein when forming the E1 state, and use these metrics to assess a variety of possible models of the E1 state. The combination of our experimental and theoretical results supports that formation of E1 involves an Fe-centered reduction combined with the protonation of a belt-sulfide of the cluster. Hence, these results provide critical experiment and computational insight into the mechanism of this important enzyme.
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Affiliation(s)
- Casey Van Stappen
- Max-Planck Institute for Chemical Energy Conversion , Stiftstrasse 34-36 , 45470 Mülheim an der Ruhr , NRW , Germany . ;
| | - Albert Thor Thorhallsson
- Max-Planck Institute for Chemical Energy Conversion , Stiftstrasse 34-36 , 45470 Mülheim an der Ruhr , NRW , Germany . ;
| | - Laure Decamps
- Max-Planck Institute for Chemical Energy Conversion , Stiftstrasse 34-36 , 45470 Mülheim an der Ruhr , NRW , Germany . ;
| | - Ragnar Bjornsson
- Max-Planck Institute for Chemical Energy Conversion , Stiftstrasse 34-36 , 45470 Mülheim an der Ruhr , NRW , Germany . ;
| | - Serena DeBeer
- Max-Planck Institute for Chemical Energy Conversion , Stiftstrasse 34-36 , 45470 Mülheim an der Ruhr , NRW , Germany . ;
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12
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Zacarias S, Temporão A, Barrio MD, Fourmond V, Léger C, Matias PM, Pereira IAC. A Hydrophilic Channel Is Involved in Oxidative Inactivation of a [NiFeSe] Hydrogenase. ACS Catal 2019. [DOI: 10.1021/acscatal.9b02347] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Sónia Zacarias
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Adriana Temporão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Melisa del Barrio
- Aix Marseille Univ., CNRS, Bioénergétique et Ingénierie des Protéines, UMR 7281 Marseille, France
| | - Vincent Fourmond
- Aix Marseille Univ., CNRS, Bioénergétique et Ingénierie des Protéines, UMR 7281 Marseille, France
| | - Christophe Léger
- Aix Marseille Univ., CNRS, Bioénergétique et Ingénierie des Protéines, UMR 7281 Marseille, France
| | - Pedro M. Matias
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2780-901 Oeiras, Portugal
| | - Inês A. C. Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
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13
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Survey of the Geometric and Electronic Structures of the Key Hydrogenated Forms of FeMo-co, the Active Site of the Enzyme Nitrogenase: Principles of the Mechanistically Significant Coordination Chemistry. INORGANICS 2019. [DOI: 10.3390/inorganics7010008] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The enzyme nitrogenase naturally hydrogenates N2 to NH3, achieved through the accumulation of H atoms on FeMo-co, the Fe7MoS9C(homocitrate) cluster that is the catalytically active site. Four intermediates, E1H1, E2H2, E3H3, and E4H4, carry these hydrogen atoms. I report density functional calculations of the numerous possibilities for the geometric and electronic structures of these poly-hydrogenated forms of FeMo-co. This survey involves more than 100 structures, including those with bound H2, and assesses their relative energies and most likely electronic states. Twelve locations for bound H atoms in the active domain of FeMo-co, including Fe–H–Fe and Fe–H–S bridges, are studied. A significant result is that transverse Fe–H–Fe bridges (transverse to the pseudo-threefold axis of FeMo-co and shared with triply-bridging S) are not possible geometrically unless the S is hydrogenated to become doubly-bridging. The favourable Fe–H–Fe bridges are shared with doubly-bridging S. ENDOR data for an E4H4 intermediate trapped at low temperature, and interpretations in terms of the geometrical and electronic structure of E4H4, are assessed in conjunction with the calculated possibilities. The results reported here yield a set of 24 principles for the mechanistically significant coordination chemistry of H and H2 on FeMo-co, in the stages prior to N2 binding.
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14
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Dance I. What is the role of the isolated small water pool near FeMo‐co, the active site of nitrogenase? FEBS J 2018; 285:2972-2986. [DOI: 10.1111/febs.14519] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 05/02/2018] [Accepted: 05/22/2018] [Indexed: 01/14/2023]
Affiliation(s)
- Ian Dance
- School of Chemistry UNSW Sydney NSW Australia
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15
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Davydov R, Khadka N, Yang ZY, Fielding AJ, Lukoyanov D, Dean DR, Seefeldt LC, Hoffman BM. Exploring Electron/Proton Transfer and Conformational Changes in the Nitrogenase MoFe Protein and FeMo-cofactor Through Cryoreduction/EPR Measurements. Isr J Chem 2016; 56:841-851. [PMID: 27777444 DOI: 10.1002/ijch.201600026] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We combine cryoreduction/annealing/EPR measurements of nitrogenase MoFe protein with results of earlier investigations to provide a detailed view of the electron/proton transfer events and conformational changes that occur during early stages of [e-/H+] accumulation by the MoFe protein. This includes reduction of (i) the non-catalytic state of the iron-molybdenum cofactor (FeMo-co) active site that is generated by chemical oxidation of the resting-state cofactor (S = 3/2)) within resting MoFe (E0), and (ii) the catalytic state that has accumulated n =1 [e-/H+] above the resting-state level, denoted E1(1H) (S ≥ 1) in the Lowe-Thorneley kinetic scheme. FeMo-co does not undergo a major change of conformation during reduction of oxidized FeMo-co. In contrast, FeMo-co undergoes substantial conformational changes during the reduction of E0 to E1(1H), and of E1(1H) to E2(2H) (n = 2; S = 3/2). The experimental results further suggest that the E1(1H) → E2(2H) step involves coupled delivery of a proton and electron (PCET) to FeMo-co of E1(H) to generate a non-equilibrium S = ½ form E2(2H)*. This subsequently undergoes conformational relaxation and attendant change in FeMo-co spin state, to generate the equilibrium E2(2H) (S = 3/2) state. Unexpectedly, these experiments also reveal conformational coupling between FeMo-co and P-cluster, and between Fe protein binding and FeMo-co, which might play a role in gated ET from reduced Fe protein to FeMo-co.
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Affiliation(s)
- Roman Davydov
- Department of Chemistry, Northwestern University, Evanston, IL 60208
| | - Nimesh Khadka
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322
| | - Zhi-Yong Yang
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322
| | - Andrew J Fielding
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322
| | - Dmitriy Lukoyanov
- Department of Chemistry, Northwestern University, Evanston, IL 60208
| | - Dennis R Dean
- Department of Biochemistry, Virginia Tech, 110 Fralin Hall, Blacksburg, VA 24061
| | - Lance C Seefeldt
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University, Evanston, IL 60208
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16
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Maiuri M, Delfino I, Cerullo G, Manzoni C, Pelmenschikov V, Guo Y, Wang H, Gee LB, Dapper CH, Newton WE, Cramer SP. Low frequency dynamics of the nitrogenase MoFe protein via femtosecond pump probe spectroscopy - Observation of a candidate promoting vibration. J Inorg Biochem 2015; 153:128-135. [PMID: 26343576 DOI: 10.1016/j.jinorgbio.2015.07.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 06/18/2015] [Accepted: 07/09/2015] [Indexed: 11/28/2022]
Abstract
We have used femtosecond pump-probe spectroscopy (FPPS) to study the FeMo-cofactor within the nitrogenase (N2ase) MoFe protein from Azotobacter vinelandii. A sub-20-fs visible laser pulse was used to pump the sample to an excited electronic state, and a second sub-10-fs pulse was used to probe changes in transmission as a function of probe wavelength and delay time. The excited protein relaxes to the ground state with a ~1.2ps time constant. With the short laser pulse we coherently excited the vibrational modes associated with the FeMo-cofactor active site, which are then observed in the time domain. Superimposed on the relaxation dynamics, we distinguished a variety of oscillation frequencies with the strongest band peaks at ~84, 116, 189, and 226cm(-1). Comparison with data from nuclear resonance vibrational spectroscopy (NRVS) shows that the latter pair of signals comes predominantly from the FeMo-cofactor. The frequencies obtained from the FPPS experiment were interpreted with normal mode calculations using both an empirical force field (EFF) and density functional theory (DFT). The FPPS data were also compared with the first reported resonance Raman (RR) spectrum of the N2ase MoFe protein. This approach allows us to outline and assign vibrational modes having relevance to the catalytic activity of N2ase. In particular, the 226cm(-1) band is assigned as a potential 'promoting vibration' in the H-atom transfer (or proton-coupled electron transfer) processes that are an essential feature of N2ase catalysis. The results demonstrate that high-quality room-temperature solution data can be obtained on the MoFe protein by the FPPS technique and that these data provide added insight to the motions and possible operation of this protein and its catalytic prosthetic group.
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Affiliation(s)
- Margherita Maiuri
- IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Ines Delfino
- Dipartimento di Scienze Ecologiche e Biologiche, Università della Tuscia, Largo dell'Università, I-01100 Viterbo, Italy
| | - Giulio Cerullo
- IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Cristian Manzoni
- IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Vladimir Pelmenschikov
- Institut für Chemie, Technische Universität Berlin, Strasse des 17 Juni 135, 10623 Berlin, Germany
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15213, United States
| | - Hongxin Wang
- Department of Chemistry, University of California, Davis, CA 95616, United States
| | - Leland B Gee
- Department of Chemistry, University of California, Davis, CA 95616, United States
| | - Christie H Dapper
- Department of Biochemistry, Virginia Polytechnic Institute & State University, Blacksburg, VA 24061, United States
| | - William E Newton
- Department of Biochemistry, Virginia Polytechnic Institute & State University, Blacksburg, VA 24061, United States
| | - Stephen P Cramer
- Department of Chemistry, University of California, Davis, CA 95616, United States; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States.
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17
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Gee LB, Leontyev I, Stuchebrukhov A, Scott AD, Pelmenschikov V, Cramer SP. Docking and migration of carbon monoxide in nitrogenase: the case for gated pockets from infrared spectroscopy and molecular dynamics. Biochemistry 2015; 54:3314-9. [PMID: 25919807 DOI: 10.1021/acs.biochem.5b00216] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Evidence of a CO docking site near the FeMo cofactor in nitrogenase has been obtained by Fourier transform infrared spectroscopy-monitored low-temperature photolysis. We investigated the possible migration paths for CO from this docking site using molecular dynamics calculations. The simulations support the notion of a gas channel with multiple internal pockets from the active site to the protein exterior. Travel between pockets is gated by the motion of protein residues. Implications for the mechanism of nitrogenase reactions with CO and N2 are discussed.
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Affiliation(s)
- Leland B Gee
- †Department of Chemistry, University of California, Davis, California 95616, United States
| | - Igor Leontyev
- §InterX Inc., Berkeley, California 94710, United States
| | - Alexei Stuchebrukhov
- †Department of Chemistry, University of California, Davis, California 95616, United States
| | - Aubrey D Scott
- †Department of Chemistry, University of California, Davis, California 95616, United States
| | | | - Stephen P Cramer
- †Department of Chemistry, University of California, Davis, California 95616, United States.,‡Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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18
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Morrison CN, Hoy JA, Zhang L, Einsle O, Rees DC. Substrate pathways in the nitrogenase MoFe protein by experimental identification of small molecule binding sites. Biochemistry 2015; 54:2052-60. [PMID: 25710326 PMCID: PMC4590346 DOI: 10.1021/bi501313k] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
![]()
In
the nitrogenase molybdenum-iron (MoFe) protein, we have identified
five potential substrate access pathways from the protein surface
to the FeMo-cofactor (the active site) or the P-cluster using experimental
structures of Xe pressurized into MoFe protein crystals from Azotobacter vinelandii and Clostridium pasteurianum. Additionally, all published structures of the MoFe protein, including
those from Klebsiella pneumoniae, were analyzed for
the presence of nonwater, small molecules bound to the protein interior.
Each pathway is based on identification of plausible routes from buried
small molecule binding sites to both the protein surface and a metallocluster.
Of these five pathways, two have been previously suggested as substrate
access pathways. While the small molecule binding sites are not conserved
among the three species of MoFe protein, residues lining the pathways
are generally conserved, indicating that the proposed pathways may
be accessible in all three species. These observations imply that
there is unlikely a unique pathway utilized for substrate access from
the protein surface to the active site; however, there may be preferred
pathways such as those described here.
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Affiliation(s)
- Christine N Morrison
- †Division of Chemistry and Chemical Engineering, California Institute of Technology 114-96, Pasadena, California 91125, United States
| | - Julie A Hoy
- †Division of Chemistry and Chemical Engineering, California Institute of Technology 114-96, Pasadena, California 91125, United States
| | - Limei Zhang
- †Division of Chemistry and Chemical Engineering, California Institute of Technology 114-96, Pasadena, California 91125, United States
| | - Oliver Einsle
- ‡Institut für Biochemie and BIOSS Centre for Biological Signaling Studies, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany
| | - Douglas C Rees
- †Division of Chemistry and Chemical Engineering, California Institute of Technology 114-96, Pasadena, California 91125, United States.,§Howard Hughes Medical Institute, California Institute of Technology, Pasadena, California 91125, United States
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19
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Dance I. The pathway for serial proton supply to the active site of nitrogenase: enhanced density functional modeling of the Grotthuss mechanism. Dalton Trans 2015; 44:18167-86. [DOI: 10.1039/c5dt03223g] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Proton translocation along a chain of eight waters to the active site of nitrogenase is described in detail, using density functional simulations with a 269 atom system that includes surrounding amino acids.
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Affiliation(s)
- Ian Dance
- School of Chemistry
- UNSW Australia
- Sydney 2052
- Australia
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20
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Fisher K, Hare ND, Newton WE. Another Role for CO with Nitrogenase? CO Stimulates Hydrogen Evolution Catalyzed by Variant Azotobacter vinelandii Mo-Nitrogenases. Biochemistry 2014; 53:6151-60. [DOI: 10.1021/bi500546k] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Karl Fisher
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| | - Nathan D. Hare
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| | - William E. Newton
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
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21
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Smith D, Danyal K, Raugei S, Seefeldt LC. Substrate channel in nitrogenase revealed by a molecular dynamics approach. Biochemistry 2014; 53:2278-85. [PMID: 24654842 DOI: 10.1021/bi401313j] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mo-dependent nitrogenase catalyzes the biological reduction of N2 to two NH3 molecules at FeMo-cofactor buried deep inside the MoFe protein. Access of substrates, such as N2, to the active site is likely restricted by the surrounding protein, requiring substrate channels that lead from the surface to the active site. Earlier studies on crystallographic structures of the MoFe protein have suggested three putative substrate channels. Here, we have utilized submicrosecond atomistic molecular dynamics simulations to allow the nitrogenase MoFe protein to explore its conformational space in an aqueous solution at physiological ionic strength, revealing a putative substrate channel. The viability of this observed channel was tested by examining the free energy of passage of N2 from the surface through the channel to FeMo-cofactor, resulting in the discovery of a very low energy barrier. These studies point to a viable substrate channel in nitrogenase that appears during thermal motions of the protein in an aqueous environment and that approaches a face of FeMo-cofactor earlier implicated in substrate binding.
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Affiliation(s)
- Dayle Smith
- Pacific Northwestern National Laboratory , Richland, Washington 99352, United States
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22
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Hoffman BM, Lukoyanov D, Yang ZY, Dean DR, Seefeldt LC. Mechanism of nitrogen fixation by nitrogenase: the next stage. Chem Rev 2014; 114:4041-62. [PMID: 24467365 PMCID: PMC4012840 DOI: 10.1021/cr400641x] [Citation(s) in RCA: 979] [Impact Index Per Article: 97.9] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Brian M Hoffman
- Department of Chemistry and Biochemistry, Utah State University , 0300 Old Main Hill, Logan, Utah 84322, United States
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23
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Dance I. A molecular pathway for the egress of ammonia produced by nitrogenase. Sci Rep 2013; 3:3237. [PMID: 24241241 PMCID: PMC3831235 DOI: 10.1038/srep03237] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 11/01/2013] [Indexed: 01/19/2023] Open
Abstract
Nitrogenase converts N2 to NH3, at one face of an Fe-Mo-S cluster (FeMo-co) buried in the protein. Through exploration of cavities in the structures of nitrogenase proteins, a pathway for the egress of ammonia from its generation site to the external medium is proposed. This pathway is conserved in the three species Azotobacter vinelandii, Klebsiella pneumoniae and Clostridium pasteurianum. A molecular mechanism for the translocation of NH3 by skipping through a sequence of hydrogen bonds involving eleven water molecules and surrounding aminoacids has been developed. The putative mechanism requires movement aside of some water molecules by up to ~ 1Å. Consistent with this, the surrounding protein is comprised of different chains and has little secondary structure: protein fluctuations are part of the mechanism. This NH3 pathway is well separated from the water chain and embedded proton wire that have been proposed for serial supply of protons to FeMo-co. Verification procedures are suggested.
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Affiliation(s)
- Ian Dance
- School of Chemistry, University of New South Wales, Sydney 2052, Australia
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24
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Dance I. The Stereochemistry and Dynamics of the Introduction of Hydrogen Atoms onto FeMo-co, the Active Site of Nitrogenase. Inorg Chem 2013; 52:13068-77. [DOI: 10.1021/ic401818k] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ian Dance
- School of Chemistry, University of New South Wales, Sydney 2052, Australia
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25
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Howard JB, Kechris KJ, Rees DC, Glazer AN. Multiple amino acid sequence alignment nitrogenase component 1: insights into phylogenetics and structure-function relationships. PLoS One 2013; 8:e72751. [PMID: 24019874 PMCID: PMC3760896 DOI: 10.1371/journal.pone.0072751] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 07/18/2013] [Indexed: 02/05/2023] Open
Abstract
Amino acid residues critical for a protein's structure-function are retained by natural selection and these residues are identified by the level of variance in co-aligned homologous protein sequences. The relevant residues in the nitrogen fixation Component 1 α- and β-subunits were identified by the alignment of 95 protein sequences. Proteins were included from species encompassing multiple microbial phyla and diverse ecological niches as well as the nitrogen fixation genotypes, anf, nif, and vnf, which encode proteins associated with cofactors differing at one metal site. After adjusting for differences in sequence length, insertions, and deletions, the remaining >85% of the sequence co-aligned the subunits from the three genotypes. Six Groups, designated Anf, Vnf , and Nif I-IV, were assigned based upon genetic origin, sequence adjustments, and conserved residues. Both subunits subdivided into the same groups. Invariant and single variant residues were identified and were defined as “core” for nitrogenase function. Three species in Group Nif-III, Candidatus Desulforudis audaxviator, Desulfotomaculum kuznetsovii, and Thermodesulfatator indicus, were found to have a seleno-cysteine that replaces one cysteinyl ligand of the 8Fe:7S, P-cluster. Subsets of invariant residues, limited to individual groups, were identified; these unique residues help identify the gene of origin (anf, nif, or vnf) yet should not be considered diagnostic of the metal content of associated cofactors. Fourteen of the 19 residues that compose the cofactor pocket are invariant or single variant; the other five residues are highly variable but do not correlate with the putative metal content of the cofactor. The variable residues are clustered on one side of the cofactor, away from other functional centers in the three dimensional structure. Many of the invariant and single variant residues were not previously recognized as potentially critical and their identification provides the bases for new analyses of the three-dimensional structure and for mutagenesis studies.
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Affiliation(s)
- James B. Howard
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United States of America
- * E-mail: (JBH); (KJK); (DCR); (ANG)
| | - Katerina J. Kechris
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, Colorado, United States of America
- * E-mail: (JBH); (KJK); (DCR); (ANG)
| | - Douglas C. Rees
- Division of Chemistry and Chemical Engineering, Howard Hughes Medical Institute, California Institute of Technology, Pasadena, California, United States of America
- * E-mail: (JBH); (KJK); (DCR); (ANG)
| | - Alexander N. Glazer
- Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
- * E-mail: (JBH); (KJK); (DCR); (ANG)
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26
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27
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Asatryan R, Bozzelli JW, Ruckenstein E. Dihydrogen Catalysis: A Degradation Mechanism for N2-Fixation Intermediates. J Phys Chem A 2012; 116:11618-42. [DOI: 10.1021/jp303692v] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Rubik Asatryan
- Department of Chemical and Biological
Engineering, State University of New York, Buffalo, New York 14260, United States
- Department of Chemistry and
Environmental Science, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
| | - Joseph W. Bozzelli
- Department of Chemistry and
Environmental Science, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
| | - Eli Ruckenstein
- Department of Chemical and Biological
Engineering, State University of New York, Buffalo, New York 14260, United States
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28
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Murakami J, Yamaguchi W. Reduction of N2 by supported tungsten clusters gives a model of the process by nitrogenase. Sci Rep 2012; 2:407. [PMID: 22586517 PMCID: PMC3350986 DOI: 10.1038/srep00407] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Accepted: 04/25/2012] [Indexed: 02/06/2023] Open
Abstract
Metalloenzymes catalyze difficult chemical reactions under mild conditions. Mimicking their functions is a challenging task and it has been investigated using homogeneous systems containing metal complexes. The nitrogenase that converts N(2) to NH(3) under mild conditions is one of such enzymes. Efforts to realize the biological function have continued for more than four decades, which has resulted in several reports of reduction of N(2), ligated to metal complexes in solutions, to NH(3) by protonation under mild conditions. Here, we show that seemingly distinct supported small tungsten clusters in a dry environment reduce N(2) under mild conditions like the nitrogenase. N(2) is reduced to NH(3) via N(2)H(4) by addition of neutral H atoms, which agrees with the mechanism recently proposed for the N(2) reduction on the active site of nitrogenase. The process on the supported clusters gives a model of the biological N(2) reduction.
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Affiliation(s)
- Junichi Murakami
- Nanosystem Research Institute, National Institute of Advanced Industrial Science and Technology, Central 5, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan.
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29
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Dance I. The controlled relay of multiple protons required at the active site of nitrogenase. Dalton Trans 2012; 41:7647-59. [DOI: 10.1039/c2dt30518f] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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30
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Harris TV, Szilagyi RK. Comparative assessment of the composition and charge state of nitrogenase FeMo-cofactor. Inorg Chem 2011; 50:4811-24. [PMID: 21545160 DOI: 10.1021/ic102446n] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A significant limitation in our understanding of the molecular mechanism of biological nitrogen fixation is the uncertain composition of the FeMo-cofactor (FeMo-co) of nitrogenase. In this study we present a systematic, density functional theory-based evaluation of spin-coupling schemes, iron oxidation states, ligand protonation states, and interstitial ligand composition using a wide range of experimental criteria. The employed functionals and basis sets were validated with molecular orbital information from X-ray absorption spectroscopic data of relevant iron-sulfur clusters. Independently from the employed level of theory, the electronic structure with the greatest number of antiferromagnetic interactions corresponds to the lowest energy state for a given charge and oxidation state distribution of the iron ions. The relative spin state energies of resting and oxidized FeMo-co already allowed exclusion of certain iron oxidation state distributions and interstitial ligand compositions. Geometry-optimized FeMo-co structures of several models further eliminated additional states and compositions, while reduction potentials indicated a strong preference for the most likely charge state of FeMo-co. Mössbauer and ENDOR parameter calculations were found to be remarkably dependent on the employed training set, density functional, and basis set. Overall, we found that a more oxidized [Mo(IV)-2Fe(II)-5Fe(III)-9S(2-)-C(4-)] composition with a hydroxyl-protonated homocitrate ligand satisfies all of the available experimental criteria and is thus favored over the currently preferred composition of [Mo(IV)-4Fe(II)-3Fe(III)-9S(2-)-N(3-)] from the literature.
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Affiliation(s)
- Travis V Harris
- NAI Astrobiology Biogeocatalysis Research Center, Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, USA
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31
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Yan L, Dapper CH, George SJ, Wang H, Mitra D, Dong W, Newton WE, Cramer SP. Photolysis of Hi-CO Nitrogenase - Observation of a Plethora of Distinct CO Species using Infrared Spectroscopy. Eur J Inorg Chem 2011; 2011:2064-2074. [PMID: 27630531 DOI: 10.1002/ejic.201100029] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Fourier transform infrared spectroscopy (FT-IR) was used to study the photochemistry of CO-inhibited Azotobacter vinelandii nitrogenase using visible light at cryogenic temperatures. The FT-IR difference spectrum of photolyzed hi-CO at 4 K comprises negative bands at 1973 cm-1 and 1679 cm-1 together with positive bands at 1711 cm-1, 2135 and 2123 cm-1. The negative bands are assigned to a hi-CO state that comprises 2 metal-bound CO ligands, one terminally bound, and one bridged and/or protonated species. The positive band at 1711 cm-1 is assigned to a lo-CO product with a single bridged and/or protonated metal-CO group. We term these species 'Hi-1' and 'Lo-1' respectively. The high-energy bands are assigned to a liberated CO trapped in the protein pocket. Warming results in CO recombination, and the temperature dependence of the recombination rate yields an activation energy of 4 kJ mol-1. Two α-H195 variant enzymes yielded additional signals. Asparagine substitution, α-H195N, gives a spectrum containing 2 negative 'Hi-2' bands at 1936 and 1858 cm-1 with a positive 'Lo-2' band at 1780 cm-1, while glutamine substitution, α-H195Q, produces a complex spectrum that includes a third CO species, with negative 'Hi-3' bands at 1938 and 1911 cm-1 and a positive feature 'Lo-3' band at 1921 cm-1. These species can be assigned to a combination of terminal, bridged, and possibly protonated CO groups bound to the FeMo-cofactor active site. The proposed structures are discussed in terms of both CO inhibition and the mechanism nitrogenase catalysis. Given the intractability of observing nitrogenase intermediates by crystallographic methods, IR-monitored photolysis appears to be a promising and information-rich probe of nitrogenase structure and chemistry.
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Affiliation(s)
- Lifen Yan
- Department of Applied Science, University of California, One Shields Avenue, Davis, CA 95616 USA
| | - Christie H Dapper
- Department of Biochemistry, Virginia Polytechnic Institute and State University, 123 Engel Hall, Blacksburg, VA 24061, USA
| | - Simon J George
- Department of Applied Science, University of California, One Shields Avenue, Davis, CA 95616 USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS 6R2100, Berkeley, CA 94720, USA
| | - Hongxin Wang
- Department of Applied Science, University of California, One Shields Avenue, Davis, CA 95616 USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS 6R2100, Berkeley, CA 94720, USA
| | - Devrani Mitra
- Department of Applied Science, University of California, One Shields Avenue, Davis, CA 95616 USA
| | - Weibing Dong
- Department of Applied Science, University of California, One Shields Avenue, Davis, CA 95616 USA
| | - William E Newton
- Department of Biochemistry, Virginia Polytechnic Institute and State University, 123 Engel Hall, Blacksburg, VA 24061, USA
| | - Stephen P Cramer
- Department of Applied Science, University of California, One Shields Avenue, Davis, CA 95616 USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS 6R2100, Berkeley, CA 94720, USA
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32
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Site-directed mutagenesis of the Anabaena sp. strain PCC 7120 nitrogenase active site to increase photobiological hydrogen production. Appl Environ Microbiol 2010; 76:6741-50. [PMID: 20709836 DOI: 10.1128/aem.01056-10] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cyanobacteria use sunlight and water to produce hydrogen gas (H₂), which is potentially useful as a clean and renewable biofuel. Photobiological H₂ arises primarily as an inevitable by-product of N₂ fixation by nitrogenase, an oxygen-labile enzyme typically containing an iron-molybdenum cofactor (FeMo-co) active site. In Anabaena sp. strain 7120, the enzyme is localized to the microaerobic environment of heterocysts, a highly differentiated subset of the filamentous cells. In an effort to increase H₂ production by this strain, six nitrogenase amino acid residues predicted to reside within 5 Å of the FeMo-co were mutated in an attempt to direct electron flow selectively toward proton reduction in the presence of N₂. Most of the 49 variants examined were deficient in N₂-fixing growth and exhibited decreases in their in vivo rates of acetylene reduction. Of greater interest, several variants examined under an N₂ atmosphere significantly increased their in vivo rates of H₂ production, approximating rates equivalent to those under an Ar atmosphere, and accumulated high levels of H₂ compared to the reference strains. These results demonstrate the feasibility of engineering cyanobacterial strains for enhanced photobiological production of H₂ in an aerobic, nitrogen-containing environment.
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33
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34
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A substrate channel in the nitrogenase MoFe protein. J Biol Inorg Chem 2009; 14:1015-22. [PMID: 19458968 DOI: 10.1007/s00775-009-0544-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2009] [Accepted: 04/23/2009] [Indexed: 10/20/2022]
Abstract
Nitrogenase catalyzes the six electron/six proton reduction of N2 to two ammonia molecules at a complex organometallocluster called "FeMo cofactor." This cofactor is buried within the alpha-subunit of the MoFe protein, with no obvious access for substrates. Examination of high-resolution X-ray crystal structures of MoFe proteins from several organisms has revealed the existence of a water-filled channel that extends from the solvent-exposed surface to a specific face of FeMo cofactor. This channel could provide a pathway for substrate and product access to the active site. In the present work, we examine this possibility by substituting four different amino acids that line the channel with other residues and analyze the impact of these substitutions on substrate reduction kinetic parameters. Each of the MoFe protein variants was purified and kinetic parameters were established for the reduction of the substrates N2, acetylene, azide, and propyne. For each MoFe protein, V (max) values for the different substrates were found to be nearly unchanged when compared with the values for the wild-type MoFe protein, indicating that electron delivery to the active site is not compromised by the various substitutions. In contrast, the K(m) values for these substrates were found to increase significantly (up to 22-fold) in some of the MoFe protein variants compared with the wild-type MoFe protein values. Given that each of the amino acids that were substituted is remote from the active site, these results are consistent with the water-filled channel functioning as a substrate channel in the MoFe protein.
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35
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Dance I. The chemical mechanism of nitrogenase: calculated details of the intramolecular mechanism for hydrogenation of η2-N2 on FeMo-co to NH3. Dalton Trans 2008:5977-91. [DOI: 10.1039/b806100a] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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36
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Abstract
How does the enzyme nitrogenase reduce the inert molecule N2 to NH3 under ambient conditions that are so different from the energy-expensive conditions of the best industrial practices? This review focuses on recent theoretical investigations of the catalytic site, the iron-molybdenum cofactor FeMo-co, and the way in which it is hydrogenated by protons and electrons and then binds N2. Density functional calculations provide reaction profiles and activation energies for possible mechanistic steps. This establishes a conceptual framework and the principles for the coordination chemistry of FeMo-co that are essential to the chemical mechanism of catalysis. The model advanced herein explains relevant experimental data.
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Affiliation(s)
- Ian Dance
- School of Chemistry, University of New South Wales, Sydney 2052, Australia.
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37
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Analysis of active sites for N2 and H+ reduction on FeMo-cofactor of nitrogenase. CHINESE SCIENCE BULLETIN-CHINESE 2007. [DOI: 10.1007/s11434-007-0294-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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38
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Wu Y, Ilan B, Voth GA. Charge delocalization in proton channels, II: the synthetic LS2 channel and proton selectivity. Biophys J 2006; 92:61-9. [PMID: 17056732 PMCID: PMC1697870 DOI: 10.1529/biophysj.106.091942] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In this study, the minimalist synthetic LS2 channel is used as a prototype to examine the selectivity of protons over other cations. The free-energy profiles along the transport pathway of LS2 are calculated for three cation species: a realistic delocalized proton (including Grotthuss shuttling)--H(+), a classical (nonshuttling) hydronium--H(3)O(+), and a potassium cation--K(+). The overall barrier for K(+) is approximately twice as large as that for H(+), explaining the >100 times larger maximal ion conductance for the latter, in qualitative agreement with the experimental result. The profile for the classical hydronium is quantitatively intermediate between those of H(+) and K(+) and qualitatively more similar to that of H(+), for which the locations of the peaks are well correlated with the troughs of the pore radius profile. There is a strong correlation between the free-energy profiles and the very different characteristic hydration structures of the three cation species. This work suggests that the passage of various cations through ion channels cannot always be explained by simple electrostatic desolvation considerations.
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Affiliation(s)
- Yujie Wu
- Center for Biophysical Modeling and Simulation, Department of Chemistry, University of Utah, Salt Lake City, Utah, 84112-0850, USA
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39
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Durrant M, Francis A, Lowe D, Newton W, Fisher K. Evidence for a dynamic role for homocitrate during nitrogen fixation: the effect of substitution at the alpha-Lys426 position in MoFe-protein of Azotobacter vinelandii. Biochem J 2006; 397:261-70. [PMID: 16566750 PMCID: PMC1513279 DOI: 10.1042/bj20060102] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Although it is generally accepted that the active site of nitrogenase is located on the FeMo-cofactor, the exact site(s) of N2 binding and reduction remain the subject of continuing debate, with both molybdenum and iron atoms being suggested as key players. The current consensus favours binding of acetylene and some other non-biologically relevant substrates to the central iron atoms of the FeMo-cofactor [Dos Santos, Igarashi, Lee, Hoffman, Seefeldt and Dean (2005) Acc. Chem. Res. 38, 208-214]. The reduction of N2 is, however, a more demanding process than reduction of these alternative substrates because it has a much higher activation energy and does not bind until three electrons have been accumulated on the enzyme. The possible conversion of bidentate into monodentate homocitrate on this three electron-reduced species has been proposed to free up a binding site for N2 on the molybdenum atom. One of the features of this hypothesis is that alpha-Lys426 facilitates chelate ring opening and subsequent orientation of the monodentate homocitrate by forming a specific hydrogen bond to the homocitrate -CH2CH2CO2- carboxylate group. In support of this concept, we show that mutation of alpha-Lys426 can selectively perturb N2 reduction without affecting acetylene reduction. We interpret our experimental observations in the light of a detailed molecular mechanics modelling study of the wild-type and altered MoFe-nitrogenases.
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Affiliation(s)
- Marcus C. Durrant
- *Biomolecular and Biomedical Research Centre, School of Applied Sciences, Ellison Building, Northumbria University, Newcastle upon Tyne NE1 8ST, U.K
| | - Amanda Francis
- †Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, U.K
| | - David J. Lowe
- †Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, U.K
- Correspondence may be addressed to either of these authors (email or )
| | - William E. Newton
- ‡Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, U.S.A
| | - Karl Fisher
- †Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, U.K
- Correspondence may be addressed to either of these authors (email or )
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Kästner J, Hemmen S, Blöchl PE. Activation and protonation of dinitrogen at the FeMo cofactor of nitrogenase. J Chem Phys 2005; 123:074306. [PMID: 16229569 DOI: 10.1063/1.2008227] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The protonation of N2 bound to the active center of nitrogenase has been investigated using state-of-the-art density-functional theory calculations. Dinitrogen in the bridging mode is activated by forming two bonds to Fe sites, which results in a reduction of the energy for the first hydrogen transfer by 123 kJ/mol. The axial binding mode with open sulfur bridge is less reactive by 30 kJ/mol and the energetic ordering of the axial and bridged binding modes is reversed in favor of the bridging dinitrogen during the first protonation. Protonation of the central ligand is thermodynamically favorable but kinetically hindered. If the central ligand is protonated, the proton is transferred to dinitrogen following the second protonation. Protonation of dinitrogen at the Mo site does not lead to low-energy intermediates.
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Affiliation(s)
- Johannes Kästner
- Institute for Theoretical Physics, Clausthal University of Technology, D-38678 Clausthal-Zellerfeld, Germany
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Abstract
The chemical mechanism by which nitrogenase enzymes catalyze the hydrogenation of N(2) (and other multiply bonded substrates) at the N(c)Fe(7)MoS(9)(homocitrate) active site (FeMo-co) is unknown, despite the accumulation of much data on enzyme reactivity and the influences of key amino acids surrounding FeMo-co. The mutual influences of H(2), substrates, and the inhibitor CO on reactivity are key experimental tests for postulated mechanisms. Fundamental to all aspects of mechanism is the accumulation of H atoms (from e(-) + H(+)) on FeMo-co, and the generation and influences of coordinated H(2). Here, I argue that the first introduction of H is via a water chain terminating at water 679 (PDB structure , Azotobacter vinelandii) to one of the mu(3)-S atoms (S3B) of FeMo-co. Next, using validated density functional calculations of a full chemical representation of FeMo-co and its connected residues (alpha-275(Cys), alpha-442(His)), I have characterized more than 80 possibilities for the coordination of up to three H atoms, and H(2), and H + H(2), on the S2A, Fe2, S2B, Fe6, S3B domain of FeMo-co, which is favored by recent targeted mutagenesis results. Included are calculated reaction profiles for movements of H atoms (between S and Fe, and between Fe and Fe), for the generation of Fe-H(2), for association and dissociation of Fe-H(2) at various reduction levels, and for H/H(2) exchange. This is new hydrogen chemistry on an unprecedented coordination frame, with some similarities to established hydrogen coordination chemistry, and with unexpected and unprecedented structures such as Fe(S)(3)(H(2))(2)(H) octahedral coordination. General principles for the hydrogen chemistry of FeMo-co include (1) the stereochemical mobility of H bound to mu(3)-S, (2) the differentiated endo- and exo- positions at Fe for coordination of H and/or H(2), and (3) coordinative allosteric influences in which structural and dynamic aspects of coordination at one Fe atom are affected by coordination at another Fe atom, and by H on S atoms. Evidence of end-differentiation in FeMo-co is described, providing a rationale for the occurrence of Mo. The reactivity results are discussed in the context of the Thorneley-Lowe scheme for nitrogenase reactions, and especially the scheme for the HD reaction (2H(+) + 2e(-) + D(2) --> 2HD), using a model containing an H-entry site and at least two coordinative sites on FeMo-co. I propose that S3B is the H-entry site, suggest details for the H(+) shuttle to S3B and subsequent movement of H atoms around FeMo-co preparatory to the binding and hydrogenation of N(2) and other substrates, and suggest how H could be transferred to an alkyne substrate. I propose that S2B (normally hydrogen bonded to alpha-195(His)) has a modulatory function and is not an H-entry site. Finally, the recent first experimental trapping of a hydrogenated intermediate with EPR and ENDOR characterization is discussed, leading to a consensual model for the intermediate.
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Affiliation(s)
- Ian Dance
- School of Chemistry, University of New South Wales, Sydney 2052, Australia
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Kästner J, Blöchl PE. Model for Acetylene Reduction by Nitrogenase Derived from Density Functional Theory. Inorg Chem 2005; 44:4568-75. [PMID: 15962963 DOI: 10.1021/ic0500311] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The catalytic cycle of acetylene reduction at the FeMo cofactor of nitrogenase has been investigated on the basis of density functional theory. C2H2 binds to the same site as N2, but it binds to a less reduced state of the cofactor. In a manner similar to that of N2 binding, one of the sulfur bridges opens during acetylene binding. The model explains the strong noncompetitive inhibition of N2 reduction by C2H2 and the weak competitive inhibition of C2H2 reduction by N2. Our proposed mechanism is consistent with experimentally observed stereoselectivity and the ability of C2H2 to suppress H2 production by nitrogenase.
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Affiliation(s)
- Johannes Kästner
- Institute for Theoretical Physics, Clausthal University of Technology, D-38678 Clausthal-Zellerfeld, Germany
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Dance I. The Mechanism of Nitrogenase. Computed Details of the Site and Geometry of Binding of Alkyne and Alkene Substrates and Intermediates. J Am Chem Soc 2004; 126:11852-63. [PMID: 15382920 DOI: 10.1021/ja0481070] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The chemical mechanism by which the enzyme nitrogenase effects the remarkable reduction of N(2) to NH(3) under ambient conditions continues to be enigmatic, because no intermediate has been observed directly. Recent experimental investigation of the enzymatic consequences of the valine --> alanine modification of residue alpha-70 of the component MoFe protein on the reduction of alkynes, together with EPR and ENDOR spectroscopic characterization of a trappable intermediate in the reduction of propargyl alcohol or propargyl amine (HCC[triple bond]C-CH(2)OH/NH(2)), has localized the site of binding and reduction of these substrates on the FeMo-cofactor and led to proposed eta(2)-Fe coordination geometry. Here these experimental data are modeled using density functional calculations of the allyl alcohol/amine intermediates and the propargyl alcohol/amine reactants coordinated to the FeMo-cofactor, together with force-field calculations of the interactions of these models with the surrounding MoFe protein. The results support and elaborate the earlier proposals, with the most probable binding site and geometry being eta(2)-coordination at Fe6 of the FeMo-cofactor (crystal structure in the Protein Database), in a position that is intermediate between the exo and endo coordination extremes at Fe6. The models described account for (1) the steric influence of the alpha-70 residue, (2) the crucial hydrogen bonding with Nepsilon of alpha-195(His), (3) the spectroscopic symmetry of the allyl-alcohol intermediate, and (4) the preferential stabilization of the allyl alcohol/amine relative to propargyl alcohol/amine. Alternative binding sites and geometries for ethyne and ethene, relevant to the wild-type protein, are described. This model defines the location and scene for detailed investigation of the mechanism of nitrogenase.
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Affiliation(s)
- Ian Dance
- School of Chemical Sciences, University of New South Wales, Sydney 2052, Australia.
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45
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Construction and characterization of double mutants in nitrogenase ofKlebsiella pneumoniae. CHINESE SCIENCE BULLETIN-CHINESE 2004. [DOI: 10.1007/bf03184303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Noodleman L, Lovell T, Han WG, Li J, Himo F. Quantum chemical studies of intermediates and reaction pathways in selected enzymes and catalytic synthetic systems. Chem Rev 2004; 104:459-508. [PMID: 14871132 DOI: 10.1021/cr020625a] [Citation(s) in RCA: 330] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Louis Noodleman
- Department of Molecular Biology TPC-15, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.
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Han J, Newton WE. Differentiation of acetylene-reduction sites by stereoselective proton addition during Azotobacter vinelandii nitrogenase-catalyzed C2D2 reduction. Biochemistry 2004; 43:2947-56. [PMID: 15005631 DOI: 10.1021/bi035247y] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The interactions of acetylene with its binding site(s) on the FeMo cofactor of the MoFe protein of Azotobacter vinelandii nitrogenase were probed using C(2)D(2). Specifically, the effects of changing the C(2)D(2) concentration, electron flux, pH, or the individual presence of N(2), ethylene, or CO on the formation of both cis- and trans-1,2-ethylene-d(2) from C(2)D(2) were measured. A hypothesis, involving two acetylene-reduction sites, was developed to explain the changes observed in the stereoselective protonation during both substrate-concentration-dependent and electron-flux-dependent C(2)D(2) reduction. One of these sites is a higher-affinity acetylene-binding site that produces only cis-1,2-ethylene-d(2) from C(2)D(2). The other is a lower-affinity acetylene-binding site, which produces both cis- and trans-1,2-ethylene-d(2). Added N(2) specifically inhibited the production of cis-1,2-ethylene-d(2) from C(2)D(2), which indicates that N(2) binds to (and is reduced at) the higher-affinity acetylene-binding site. High concentrations of added ethylene behaved like very high concentrations of acetylene and inhibited both the electron flux flowing through the enzyme and cis-isomer formation. Added CO, at very low concentrations, did not affect the relative distribution of cis- and trans-isomers, indicating a separate CO-binding site. The results of pH-dependence experiments showed that substrate inhibition at high C(2)D(2) concentrations is enhanced under acidic conditions but is absent under basic conditions and suggest that a low proton flux has a similar impact to that of a low electron flux; both inhibit cis-1,2-ethylene-d(2) formation selectively. Apparently, the factors affecting stereoselective protonation during C(2)D(2) reduction could be the same as those that perturb protonation of the FeMo cofactor when acetylene is reduced. The observed nitrogenase-catalyzed production of ethylene-d(1) from C(2)D(2) implicates a reversible protonation step in the mechanistic pathway.
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Affiliation(s)
- Jaehong Han
- Department of Biochemistry, The Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
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Hinnemann B, Nørskov JK. Chemical activity of the nitrogenase FeMo cofactor with a central nitrogen ligand: density functional study. J Am Chem Soc 2004; 126:3920-7. [PMID: 15038746 DOI: 10.1021/ja037792s] [Citation(s) in RCA: 111] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We investigate the chemical consequences of a central ligand in the nitrogenase FeMo cofactor using density functional calculations. Several studies have shown that the central ligand most probably is a nitrogen atom, but the consequences for the chemical reactivity of the cofactor are unknown. We investigate several possible routes for insertion of the central nitrogen ligand and conclude that all routes involve barriers and intermediate states, which are inaccessible at ambient conditions. On this basis we suggest that the central nitrogen ligand is present at all times during the reaction. Furthermore, we investigate how the FeMoco with the central ligand can interact with N(2) and reduce it.
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Affiliation(s)
- Berit Hinnemann
- Center for Atomic-scale Materials Physics, Department of Physics, Building 307, Technical University of Denmark, DK-2800 Lyngby, Denmark
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Durrant MC. An Atomic Level Model for the Interactions of Molybdenum Nitrogenase with Carbon Monoxide, Acetylene, and Ethylene. Biochemistry 2004; 43:6030-42. [PMID: 15147187 DOI: 10.1021/bi036300l] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A combination of density functional theory and molecular mechanics calculations has been used to study the possible interactions of CO, C(2)H(2), and C(2)H(4) with the central Fe and terminal Mo sites of the iron-molybdenum cofactor of nitrogenase. The most favorable binding mode for CO on the central section of the FeMoco appears to be end-on to a single Fe and results in a change from high to low spin for the ligating Fe atom. If a coordination site for CO is available on the Mo, this becomes the preferred CO binding site. Calculated nu(CO) infrared frequencies are compared with the experimental values given in the literature. C(2)H(2) binds weakly in a side-on orientation to a single Fe site; addition of a single H(+)/e(-) couple to the substrate results in spontaneous migration of the resulting -CH=CH(2) group from Fe to a central S atom of the cofactor. Further reduction liberates C(2)H(4) or alternatively can give an S=CHCH(3) intermediate, which then goes on to produce C(2)H(6). A model for C(2)H(2) reduction by nitrogenase is proposed, based on the results of the calculations and the extensive literature on this process.
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Affiliation(s)
- Marcus C Durrant
- Computational Biology Group, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK.
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Huniar U, Ahlrichs R, Coucouvanis D. Density Functional Theory Calculations and Exploration of a Possible Mechanism of N2 Reduction by Nitrogenase. J Am Chem Soc 2004; 126:2588-601. [PMID: 14982469 DOI: 10.1021/ja030541z] [Citation(s) in RCA: 95] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Density functional theory (DFT) calculations have been performed on the nitrogenase cofactor, FeMoco. Issues that have been addressed concern the nature of M-M interactions and the identity and origin of the central light atom, revealed in a recent crystallographic study of the FeMo protein of nitrogenase (Einsle, O.; et al. Science 2002, 297, 871). Introduction of Se in place of the S atoms in the cofactor and energy minimization results in an optimized structure very similar to that in the native enzyme. The nearly identical, short, lengths of the Fe-Fe distances in the Se and S analogues are interpreted in terms of M-M weak bonding interactions. DFT calculations with O or N as the central atoms in the FeMoco marginally support the assignment of the central atom as N rather than O. The assumption was made that the central atom is the N atom, and steps of a catalytic cycle were calculated starting with either of two possible states for the cofactor and maintaining the same charge throughout (by addition of equal numbers of H(+) and e(-)) between steps. The states were [(Cl)Fe(II)(6)Fe(III)Mo(IV)S(9)(H(+))(3)N(3-)(Gl)(Im)](2-), [I-N-3H](2-), and [(Cl)Fe(II)(4)Fe(III)(3)Mo(IV)S(9)(H(+))(3)N(3-)(Gl)(Im)], [I-N-3H](0) (Gl = deprotonated glycol; Im = imidazole). These are the triply protonated ENDOR/ESEEM [I-N](5-) and Mössbauer [I-N](3-) models, respectively. The proposed mechanism explores the possibilities that (a) redox-induced distortions facilitate insertion of N(2) and derivative substrates into the Fe(6) central unit of the cofactor, (b) the central atom in the cofactor is an exchangeable nitrogen, and (c) the individual steps are related by H(+)/e(-) additions (and reduction of substrate) or aquation/dehydration (and distortion of the Fe(6) center). The Delta E's associated with the individual steps of the proposed mechanism are small and either positive or negative. The largest positive Delta E is +121 kJ/mol. The largest negative Delta E of -333 kJ/mol is for the FeMoco with a N(3-) in the center (the isolated form) and an intermediate in the proposed mechanism.
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Affiliation(s)
- Uwe Huniar
- Department of Chemistry, University of Karlsruhe, Karlsruhe, Germany
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