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Newman-Stonebraker SH, Gerard TJ, Holland PL. Opportunities for Insight into the Mechanism of Efficient CO 2/CO Interconversion at a Nickel-Iron Cluster in CO Dehydrogenase. Chem 2024; 10:1655-1667. [PMID: 38966253 PMCID: PMC11221784 DOI: 10.1016/j.chempr.2024.04.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2024]
Abstract
The reduction of CO2 with low overpotential and high selectivity is a crucial challenge in catalysis. Fortunately, natural systems have evolved enzymes that achieve this catalytic reaction very efficiently at a complex nickel-iron-sulfur cluster within carbon monoxide dehydrogenase (CODH). Extensive biochemical, crystallographic, and spectroscopic work has been done to understand the structures and mechanism involved in the catalytic cycle, which are summarized here from the perspective of mechanistic organometallic chemistry. We highlight the ambiguities in the data and suggest experiments that could lead to clearer understanding of the mechanism and structures of intermediates at the active-site cluster. These include parallel crystallography and spectroscopy, as well as the preparation of synthetic analogues that help to interpret structural and spectroscopic signatures.
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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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Deng Y, Dwaraknath S, Ouyang WO, Matsumoto CJ, Ouchida S, Lu Y. Engineering an Oxygen-Binding Protein for Photocatalytic CO 2 Reductions in Water. Angew Chem Int Ed Engl 2023; 62:e202215719. [PMID: 36916067 PMCID: PMC10946749 DOI: 10.1002/anie.202215719] [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: 10/25/2022] [Revised: 03/10/2023] [Accepted: 03/10/2023] [Indexed: 03/16/2023]
Abstract
While native CO2 -reducing enzymes display remarkable catalytic efficiency and product selectivity, few artificial biocatalysts have been engineered to allow understanding how the native enzymes work. To address this issue, we report cobalt porphyrin substituted myoglobin (CoMb) as a homogeneous catalyst for photo-driven CO2 to CO conversion in water. The activity and product selectivity were optimized by varying pH and concentrations of the enzyme and the photosensitizer. Up to 2000 TON(CO) was attained at low enzyme concentrations with low product selectivity (15 %), while a product selectivity of 74 % was reached by increasing the enzyme loading but with a compromised TON(CO). The efficiency of CO generation and overall TON(CO) were further improved by introducing positively charged residues (Lys or Arg) near the active stie of CoMb, which demonstrates the value of tuning the enzyme secondary coordination sphere to enhance the CO2 -reducing performance of a protein-based photocatalytic system.
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Affiliation(s)
- Yunling Deng
- Department of ChemistryUniversity of Texas at AustinAustinTX 78712USA
| | - Sudharsan Dwaraknath
- Department of ChemistryUniversity of Illinois at Urbana-ChampaignUrbanaIL 61801USA
| | - Wenhao O. Ouyang
- Department of ChemistryUniversity of Illinois at Urbana-ChampaignUrbanaIL 61801USA
| | - Cory J. Matsumoto
- Department of ChemistryUniversity of Illinois at Urbana-ChampaignUrbanaIL 61801USA
| | - Stephanie Ouchida
- Department of ChemistryUniversity of Illinois at Urbana-ChampaignUrbanaIL 61801USA
| | - Yi Lu
- Department of ChemistryUniversity of Texas at AustinAustinTX 78712USA
- Department of ChemistryUniversity of Illinois at Urbana-ChampaignUrbanaIL 61801USA
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Van Stappen C, Deng Y, Liu Y, Heidari H, Wang JX, Zhou Y, Ledray AP, Lu Y. Designing Artificial Metalloenzymes by Tuning of the Environment beyond the Primary Coordination Sphere. Chem Rev 2022; 122:11974-12045. [PMID: 35816578 DOI: 10.1021/acs.chemrev.2c00106] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metalloenzymes catalyze a variety of reactions using a limited number of natural amino acids and metallocofactors. Therefore, the environment beyond the primary coordination sphere must play an important role in both conferring and tuning their phenomenal catalytic properties, enabling active sites with otherwise similar primary coordination environments to perform a diverse array of biological functions. However, since the interactions beyond the primary coordination sphere are numerous and weak, it has been difficult to pinpoint structural features responsible for the tuning of activities of native enzymes. Designing artificial metalloenzymes (ArMs) offers an excellent basis to elucidate the roles of these interactions and to further develop practical biological catalysts. In this review, we highlight how the secondary coordination spheres of ArMs influence metal binding and catalysis, with particular focus on the use of native protein scaffolds as templates for the design of ArMs by either rational design aided by computational modeling, directed evolution, or a combination of both approaches. In describing successes in designing heme, nonheme Fe, and Cu metalloenzymes, heteronuclear metalloenzymes containing heme, and those ArMs containing other metal centers (including those with non-native metal ions and metallocofactors), we have summarized insights gained on how careful controls of the interactions in the secondary coordination sphere, including hydrophobic and hydrogen bonding interactions, allow the generation and tuning of these respective systems to approach, rival, and, in a few cases, exceed those of native enzymes. We have also provided an outlook on the remaining challenges in the field and future directions that will allow for a deeper understanding of the secondary coordination sphere a deeper understanding of the secondary coordintion sphere to be gained, and in turn to guide the design of a broader and more efficient variety of ArMs.
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Affiliation(s)
- Casey Van Stappen
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yunling Deng
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yiwei Liu
- Department of Chemistry, University of Illinois, Urbana-Champaign, 505 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Hirbod Heidari
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Jing-Xiang Wang
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yu Zhou
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Aaron P Ledray
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yi Lu
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States.,Department of Chemistry, University of Illinois, Urbana-Champaign, 505 South Mathews Avenue, Urbana, Illinois 61801, United States
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Treviño RE, Shafaat HS. Protein-based models offer mechanistic insight into complex nickel metalloenzymes. Curr Opin Chem Biol 2022; 67:102110. [PMID: 35101820 DOI: 10.1016/j.cbpa.2021.102110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/22/2021] [Accepted: 12/06/2021] [Indexed: 11/03/2022]
Abstract
There are ten nickel enzymes found across biological systems, each with a distinct active site and reactivity that spans reductive, oxidative, and redox-neutral processes. We focus on the reductive enzymes, which catalyze reactions that are highly germane to the modern-day climate crisis: [NiFe] hydrogenase, carbon monoxide dehydrogenase, acetyl coenzyme A synthase, and methyl coenzyme M reductase. The current mechanistic understanding of each enzyme system is reviewed along with existing knowledge gaps, which are addressed through the development of protein-derived models, as described here. This opinion is intended to highlight the advantages of using robust protein scaffolds for modeling multiscale contributions to reactivity and inspire the development of novel artificial metalloenzymes for other small molecule transformations.
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Affiliation(s)
- Regina E Treviño
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Hannah S Shafaat
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA.
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