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Wilson DWN, Thompson BC, Collauto A, Hooper RX, Knapp CE, Roessler MM, Musgrave RA. Mixed Valence {Ni 2+Ni 1+} Clusters as Models of Acetyl Coenzyme A Synthase Intermediates. J Am Chem Soc 2024. [PMID: 39023163 DOI: 10.1021/jacs.4c06241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Acetyl coenzyme A synthase (ACS) catalyzes the formation and deconstruction of the key biological metabolite, acetyl coenzyme A (acetyl-CoA). The active site of ACS features a {NiNi} cluster bridged to a [Fe4S4]n+ cubane known as the A-cluster. The mechanism by which the A-cluster functions is debated, with few model complexes able to replicate the oxidation states, coordination features, or reactivity proposed in the catalytic cycle. In this work, we isolate the first bimetallic models of two hypothesized intermediates on the paramagnetic pathway of the ACS function. The heteroligated {Ni2+Ni1+} cluster, [K(12-crown-4)2][1], effectively replicates the coordination number and oxidation state of the proposed "Ared" state of the A-cluster. Addition of carbon monoxide to [1]- allows for isolation of a dinuclear {Ni2+Ni1+(CO)} complex, [K(12-crown-2)n][2] (n = 1-2), which bears similarity to the "ANiFeC" enzyme intermediate. Structural and electronic properties of each cluster are elucidated by X-ray diffraction, nuclear magnetic resonance, cyclic voltammetry, and UV/vis and electron paramagnetic resonance spectroscopies, which are supplemented by density functional theory (DFT) calculations. Calculations indicate that the pseudo-T-shaped geometry of the three-coordinate nickel in [1]- is more stable than the Y-conformation by 22 kcal mol-1, and that binding of CO to Ni1+ is barrierless and exergonic by 6 kcal mol-1. UV/vis absorption spectroscopy on [2]- in conjunction with time-dependent DFT calculations indicates that the square-planar nickel site is involved in electron transfer to the CO π*-orbital. Further, we demonstrate that [2]- promotes thioester synthesis in a reaction analogous to the production of acetyl coenzyme A by ACS.
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Affiliation(s)
- Daniel W N Wilson
- Department of Chemistry, King's College London, 7 Trinity Street, London SE1 1DB, U.K
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, U.K
| | - Benedict C Thompson
- Department of Chemistry, King's College London, 7 Trinity Street, London SE1 1DB, U.K
| | - Alberto Collauto
- Department of Chemistry and Centre for Pulse EPR Spectroscopy, Imperial College London, 82 Wood Lane, London W12 0BZ, U.K
| | - Reagan X Hooper
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Caroline E Knapp
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, U.K
| | - Maxie M Roessler
- Department of Chemistry and Centre for Pulse EPR Spectroscopy, Imperial College London, 82 Wood Lane, London W12 0BZ, U.K
| | - Rebecca A Musgrave
- Department of Chemistry, King's College London, 7 Trinity Street, London SE1 1DB, U.K
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Park S, Seo MS, Kim M, Lee KM, Graham PM, Lee Y. Reactivity of low-valent nickel carbonyl species supported by acridane based PNP ligands towards iodoalkanes. Dalton Trans 2024; 53:10120-10125. [PMID: 38817194 DOI: 10.1039/d4dt01022a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Nickel monocarbonyl species with Ni(I) and Ni(0) have been synthesized and fully characterized by employing an acriPNP-Ph pincer ligand having a -C(Ph)2- bridge moiety to tether two aromatic rings. To see the effect of the bridge moiety, these complexes were structurally compared with the previously studied nickel complexes supported by PNP and acriPNP-Me ligands and methylation of the nickel carbonyl species was particularly investigated. Since a Ni(I)-CO species is known to be one of the key intermediates during the C-C coupling reaction to give an acetyl species, according to the paramagnetic mechanism of acetyl coenzyme A synthase (ACS), their reactivity toward MeI has been examined. Methylation of a nickel(I)-CO species reveals enhanced C-C coupling when both acriPNP-Me and acriPNP-Ph ligands were used. According to spin density analysis calculated by density functional theory, all Ni(I)-CO species reveal similar spin density at nickel and the carbon atom of CO. X-ray crystallographic data suggest that the corresponding selectivity may be related to the steric influence. For both (acriPNP-Ph)Ni-CO (2) and (acriPNP-Me)Ni-CO (2'), the nickel(I) site is sterically well protected, leading to selective interaction with a methyl radical to give a nickel acyl product. Steric influence was marginally observed when an anionic {(acriPNP-R)Ni-CO}- (R = Me or Ph) species reacted with MeI. The corresponding C-C coupled product was also observed from the methylation of nickel(0)-CO species.
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Affiliation(s)
- Sanha Park
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea.
| | - Mi Sook Seo
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea.
| | - Mingi Kim
- Department of Chemistry, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Kang Mun Lee
- Department of Chemistry, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Peter M Graham
- Department of Chemistry, Saint Joseph's University, 5600 City Avenue, Philadelphia, PA 19131, USA
| | - Yunho Lee
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea.
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Lewis LC, Sanabria-Gracia JA, Lee Y, Jenkins AJ, Shafaat HS. Electronic isomerism in a heterometallic nickel-iron-sulfur cluster models substrate binding and cyanide inhibition of carbon monoxide dehydrogenase. Chem Sci 2024; 15:5916-5928. [PMID: 38665523 PMCID: PMC11040638 DOI: 10.1039/d4sc00023d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 03/04/2024] [Indexed: 04/28/2024] Open
Abstract
The nickel-iron carbon monoxide dehydrogenase (CODH) enzyme uses a heterometallic nickel-iron-sulfur ([NiFe4S4]) cluster to catalyze the reversible interconversion of carbon dioxide (CO2) and carbon monoxide (CO). These reactions are essential for maintaining the global carbon cycle and offer a route towards sustainable greenhouse gas conversion but have not been successfully replicated in synthetic models, in part due to a poor understanding of the natural system. Though the general protein architecture of CODH is known, the electronic structure of the active site is not well-understood, and the mechanism of catalysis remains unresolved. To better understand the CODH enzyme, we have developed a protein-based model containing a heterometallic [NiFe3S4] cluster in the Pyrococcus furiosus (Pf) ferredoxin (Fd). This model binds small molecules such as carbon monoxide and cyanide, analogous to CODH. Multiple redox- and ligand-bound states of [NiFe3S4] Fd (NiFd) have been investigated using a suite of spectroscopic techniques, including resonance Raman, Ni and Fe K-edge X-ray absorption spectroscopy, and electron paramagnetic resonance, to resolve charge and spin delocalization across the cluster, site-specific electron density, and ligand activation. The facile movement of charge through the cluster highlights the fluidity of electron density within iron-sulfur clusters and suggests an electronic basis by which CN- inhibits the native system while the CO-bound state continues to elude isolation in CODH. The detailed characterization of isolable states that are accessible in our CODH model system provides valuable insight into unresolved enzymatic intermediates and offers design principles towards developing functional mimics of CODH.
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Affiliation(s)
- Luke C Lewis
- Department of Chemistry and Biochemistry, The Ohio State University Columbus OH 43210 USA
| | - José A Sanabria-Gracia
- Department of Chemistry and Biochemistry, The Ohio State University Columbus OH 43210 USA
| | - Yuri Lee
- Department of Chemistry and Biochemistry, The Ohio State University Columbus OH 43210 USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles Los Angeles CA 90095 USA
| | - Adam J Jenkins
- Department of Chemistry and Biochemistry, The Ohio State University Columbus OH 43210 USA
| | - Hannah S Shafaat
- Department of Chemistry and Biochemistry, The Ohio State University Columbus OH 43210 USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles Los Angeles CA 90095 USA
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Wilson DWN, Fataftah MS, Mathe Z, Mercado BQ, DeBeer S, Holland PL. Three-Coordinate Nickel and Metal-Metal Interactions in a Heterometallic Iron-Sulfur Cluster. J Am Chem Soc 2024; 146:4013-4025. [PMID: 38308743 PMCID: PMC10993082 DOI: 10.1021/jacs.3c12157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2024]
Abstract
Biological multielectron reactions often are performed by metalloenzymes with heterometallic sites, such as anaerobic carbon monoxide dehydrogenase (CODH), which has a nickel-iron-sulfide cubane with a possible three-coordinate nickel site. Here, we isolate the first synthetic iron-sulfur clusters having a nickel atom with only three donors, showing that this structural feature is feasible. These have a core with two tetrahedral irons, one octahedral tungsten, and a three-coordinate nickel connected by sulfide and thiolate bridges. Electron paramagnetic resonance (EPR), Mössbauer, and superconducting quantum interference device (SQUID) data are combined with density functional theory (DFT) computations to show how the electronic structure of the cluster arises from strong magnetic coupling between the Ni, Fe, and W sites. X-ray absorption spectroscopy, together with spectroscopically validated DFT analysis, suggests that the electronic structure can be described with a formal Ni1+ atom participating in a nonpolar Ni-W σ-bond. This metal-metal bond, which minimizes spin density at Ni1+, is conserved in two cluster oxidation states. Fe-W bonding is found in all clusters, in one case stabilizing a local non-Hund state at tungsten. Based on these results, we compare different M-M interactions and speculate that other heterometallic clusters, including metalloenzyme active sites, could likewise store redox equivalents and stabilize low-valent metal centers through metal-metal bonding.
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Affiliation(s)
- Daniel W. N. Wilson
- Department of Chemistry, Yale University, 225 Prospect St., New Haven, Connecticut 06520, USA
| | - Majed S. Fataftah
- Department of Chemistry, Yale University, 225 Prospect St., New Haven, Connecticut 06520, USA
| | - Zachary Mathe
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Brandon Q. Mercado
- Department of Chemistry, Yale University, 225 Prospect St., New Haven, Connecticut 06520, USA
| | - Serena DeBeer
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Patrick L. Holland
- Department of Chemistry, Yale University, 225 Prospect St., New Haven, Connecticut 06520, USA
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Gencic S, Duin EC, Grahame DA. The two-electron reduced A cluster in acetyl-CoA synthase: Preparation, characteristics and mechanistic implications. J Inorg Biochem 2023; 240:112098. [PMID: 36580832 DOI: 10.1016/j.jinorgbio.2022.112098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 12/05/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022]
Abstract
Acetyl-CoA synthase (ACS) is a central enzyme in the carbon and energy metabolism of certain anaerobic species of bacteria and archaea that catalyzes the direct synthesis and cleavage of the acetyl CC bond of acetyl-CoA by an unusual enzymatic mechanism of special interest for its use of organonickel intermediates. An Fe4S4 cluster associated with a proximal, reactive Nip and distal spectator Nid comprise the active site metal complex, known as the A cluster. Experimental and theoretical methods have uncovered much about the ACS mechanism, but have also opened new unanswered questions about the structure and reactivity of the A cluster in various intermediate forms. Here we report a method for large scale isolation of ACS with its A cluster in the acetylated state. Isolated acetyl-ACS and the two-electron reduced ACS, produced by acetyl-ACS reaction with CoA, were characterized by UV-visible and EPR spectroscopy. Reactivity with electron acceptors provided an assessment of the apparent Em for two-electron reduction of the A cluster. The results help to distinguish between alternative electronic states of the reduced cluster, provide evidence for a role of the Fe/S cluster in catalysis, and offer an explanation of why one-electron reductive activation is observed for a reaction cycle involving 2-electron chemistry.
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Affiliation(s)
- Simonida Gencic
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Evert C Duin
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL 36849, USA
| | - David A Grahame
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA.
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