1
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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; 146:21034-21043. [PMID: 39023163 PMCID: PMC11295191 DOI: 10.1021/jacs.4c06241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 06/12/2024] [Accepted: 06/13/2024] [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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2
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Wiley S, Griffith C, Eckert P, Mueller AP, Nogle R, Simpson SD, Köpke M, Can M, Sarangi R, Kubarych K, Ragsdale SW. An alcove at the acetyl-CoA synthase nickel active site is required for productive substrate CO binding and anaerobic carbon fixation. J Biol Chem 2024; 300:107503. [PMID: 38944127 PMCID: PMC11321310 DOI: 10.1016/j.jbc.2024.107503] [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: 11/17/2023] [Revised: 06/05/2024] [Accepted: 06/17/2024] [Indexed: 07/01/2024] Open
Abstract
One of the seven natural CO2 fixation pathways, the anaerobic Wood-Ljungdahl pathway (WLP) is unique in generating CO as a metabolic intermediate, operating through organometallic intermediates, and in conserving (versus utilizing) net ATP. The key enzyme in the WLP is acetyl-CoA synthase (ACS), which uses an active site [2Ni-4Fe-4S] cluster (A-cluster), a CO tunnel, and an organometallic (Ni-CO, Ni-methyl, and Ni-acetyl) reaction sequence to generate acetyl-CoA. Here, we reveal that an alcove, which interfaces the tunnel and the A-cluster, is essential for CO2 fixation and autotrophic growth by the WLP. In vitro spectroscopy, kinetics, binding, and in vivo growth experiments reveal that a Phe229A substitution at one wall of the alcove decreases CO affinity thirty-fold and abolishes autotrophic growth; however, a F229W substitution enhances CO binding 80-fold. Our results indicate that the structure of the alcove is exquisitely tuned to concentrate CO near the A-cluster; protect ACS from CO loss during catalysis, provide a haven for inhibitory CO, and stabilize the tetrahedral coordination at the Nip site where CO binds. The directing, concentrating, and protective effects of the alcove explain the inability of F209A to grow autotrophically. The alcove also could help explain current controversies over whether ACS binds CO and methyl through a random or ordered mechanism. Our work redefines what we historically refer to as the metallocenter "active site". The alcove is so crucial for enzymatic function that we propose it is part of the active site. The community should now look for such alcoves in all "gas handling" metalloenzymes.
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Affiliation(s)
- Seth Wiley
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Claire Griffith
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Peter Eckert
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | | | | | | | | | - Mehmet Can
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Ritimukta Sarangi
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Kevin Kubarych
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Stephen W Ragsdale
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, USA.
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3
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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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4
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Luo J, He C. Chemical protein synthesis enabled engineering of saccharide oxidative cleavage activity in artificial metalloenzymes. Int J Biol Macromol 2024; 256:128083. [PMID: 38000595 DOI: 10.1016/j.ijbiomac.2023.128083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/18/2023] [Accepted: 11/12/2023] [Indexed: 11/26/2023]
Abstract
Chemical protein (semi-)synthesis is a powerful technique allowing the incorporation of unnatural functionalities at any desired protein site. Herein we describe a facile one-pot semi-synthetic strategy for the construction of a type 2 copper center in the active site of azurin, which is achieved by substitution of Met121 with unnatural amino acid residues bearing a strong ligand N,N-bis(pyridylmethyl)amine (DPA) to mimic the function of typical histidine brace-bearing copper monooxygenases, such as lytic polysaccharide monooxygenases (LPMOs) involved in polysaccharide breakdown. The semi-synthetic proteins were routinely obtained in over 10-mg scales to allow for spectroscopic measurements (UV-Vis, CD, and EPR), which provides structural evidences for the CuII-DPA-modified azurins. 4-nitrophenyl-β-D-glucopyranoside (PNPG) was used as a model substrate for the H2O2-driven oxidative cleavage reaction facilitated by semi-synthetic azurins, and the CuII-6 complex showed a highest activity (TTN 253). Interestingly, our semi-synthetic azurins were able to tolerate high H2O2 concentrations (up to 4000-fold of the enzyme), making them promising for practical applications. Collectively, we establish that chemical protein synthesis can be exploited as a reliable technology in affording large quantities of artificial metalloproteins to facilitate the transformation of challenging chemical reactions.
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Affiliation(s)
- Jindi Luo
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510640, PR China
| | - Chunmao He
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510640, PR China.
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5
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Selvan D, Chakraborty S. A De Novo Designed Trimeric Metalloprotein as a Ni p Model of the Acetyl-CoA Synthase. Int J Mol Sci 2023; 24:10317. [PMID: 37373464 DOI: 10.3390/ijms241210317] [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] [Received: 03/31/2023] [Revised: 05/30/2023] [Accepted: 06/03/2023] [Indexed: 06/29/2023] Open
Abstract
We present a Nip site model of acetyl coenzyme-A synthase (ACS) within a de novo-designed trimer peptide that self-assembles to produce a homoleptic Ni(Cys)3 binding motif. Spectroscopic and kinetic studies of ligand binding demonstrate that Ni binding stabilizes the peptide assembly and produces a terminal NiI-CO complex. When the CO-bound state is reacted with a methyl donor, a new species is quickly produced with new spectral features. While the metal-bound CO is albeit unactivated, the presence of the methyl donor produces an activated metal-CO complex. Selective outer sphere steric modifications demonstrate that the physical properties of the ligand-bound states are altered differently depending on the location of the steric modification above or below the Ni site.
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Affiliation(s)
- Dhanashree Selvan
- Department of Chemistry and Biochemistry, University of Mississippi, Coulter Hall, Oxford, MS 38677, USA
| | - Saumen Chakraborty
- Department of Chemistry and Biochemistry, University of Mississippi, Coulter Hall, Oxford, MS 38677, USA
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6
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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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7
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Characterization of paramagnetic states in an organometallic nickel hydrogen evolution electrocatalyst. Nat Commun 2023; 14:905. [PMID: 36807358 PMCID: PMC9938211 DOI: 10.1038/s41467-023-36609-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 02/06/2023] [Indexed: 02/19/2023] Open
Abstract
Significant progress has been made in the bioinorganic modeling of the paramagnetic states believed to be involved in the hydrogen redox chemistry catalyzed by [NiFe] hydrogenase. However, the characterization and isolation of intermediates involved in mononuclear Ni electrocatalysts which are reported to operate through a NiI/III cycle have largely remained elusive. Herein, we report a NiII complex (NCHS2)Ni(OTf)2, where NCHS2 is 3,7-dithia-1(2,6)-pyridina-5(1,3)-benzenacyclooctaphane, that is an efficient electrocatalyst for the hydrogen evolution reaction (HER) with turnover frequencies of ~3,000 s-1 and a overpotential of 670 mV in the presence of trifluoroacetic acid. This electrocatalyst follows a hitherto unobserved HER mechanism involving C-H activation, which manifests as an inverse kinetic isotope effect for the overall hydrogen evolution reaction, and NiI/NiIII intermediates, which have been characterized by EPR spectroscopy. We further validate the possibility of the involvement of NiIII intermediates by the independent synthesis and characterization of organometallic NiIII complexes.
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8
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Biester A, Marcano-Delgado AN, Drennan CL. Structural Insights into Microbial One-Carbon Metabolic Enzymes Ni-Fe-S-Dependent Carbon Monoxide Dehydrogenases and Acetyl-CoA Synthases. Biochemistry 2022; 61:2797-2805. [PMID: 36137563 PMCID: PMC9782325 DOI: 10.1021/acs.biochem.2c00425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Ni-Fe-S-dependent carbon monoxide dehydrogenases (CODHs) are enzymes that interconvert CO and CO2 by using their catalytic Ni-Fe-S C-cluster and their Fe-S B- and D-clusters for electron transfer. CODHs are important in the microbiota of animals such as humans, ruminants, and termites because they can facilitate the use of CO and CO2 as carbon sources and serve to maintain redox homeostasis. The bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) is responsible for acetate production via the Wood-Ljungdahl pathway, where acetyl-CoA is assembled from two CO2-derived one-carbon units. A Ni-Fe-S A-cluster is key to this chemistry. Whereas acetogens use the A- and C-clusters of CODH/ACS to produce acetate from CO2, methanogens use A- and C-clusters of an acetyl-CoA decarbonylase/synthase complex (ACDS) to break down acetate en route to CO2 and methane production. Here we review some of the recent advances in understanding the structure and mechanism of CODHs, CODH/ACSs, and ACDSs, their unusual metallocofactors, and their unique metabolic roles in the human gut and elsewhere.
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Affiliation(s)
- Alison Biester
- Department
of Chemistry, Massachusetts Institute of
Technology, Cambridge, Massachusetts 02139, United States
| | - Andrea N. Marcano-Delgado
- Department
of Chemistry, Massachusetts Institute of
Technology, Cambridge, Massachusetts 02139, United States
| | - Catherine L. Drennan
- Department
of Chemistry, Massachusetts Institute of
Technology, Cambridge, Massachusetts 02139, United States,Department
of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States,Howard
Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States,Bio-inspired
Solar Energy Program, Canadian Institute
for Advanced Research, Toronto, ON M5G 1M1, Canada,
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9
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Thioester synthesis by a designed nickel enzyme models prebiotic energy conversion. Proc Natl Acad Sci U S A 2022; 119:e2123022119. [PMID: 35858422 PMCID: PMC9335327 DOI: 10.1073/pnas.2123022119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The formation of carbon-carbon bonds from prebiotic precursors such as carbon dioxide represents the foundation of all primordial life processes. In extant organisms, this reaction is carried out by the carbon monoxide dehydrogenase (CODH)/acetyl coenzyme A synthase (ACS) enzyme, which performs the cornerstone reaction in the ancient Wood-Ljungdahl metabolic pathway to synthesize the key biological metabolite, acetyl-CoA. Despite its significance, a fundamental understanding of this transformation is lacking, hampering efforts to harness analogous chemistry. To address these knowledge gaps, we have designed an artificial metalloenzyme within the azurin protein scaffold as a structural, functional, and mechanistic model of ACS. We demonstrate the intermediacy of the NiI species and requirement for ordered substrate binding in the bioorganometallic carbon-carbon bond-forming reaction from the one-carbon ACS substrates. The electronic and geometric structures of the nickel-acetyl intermediate have been characterized using time-resolved optical, electron paramagnetic resonance, and X-ray absorption spectroscopy in conjunction with quantum chemical calculations. Moreover, we demonstrate that the nickel-acetyl species is chemically competent for selective acyl transfer upon thiol addition to biosynthesize an activated thioester. Drawing an analogy to the native enzyme, a mechanism for thioester generation by this ACS model has been proposed. The fundamental insight into the enzymatic process provided by this rudimentary ACS model has implications for the evolution of primitive ACS-like proteins. Ultimately, these findings offer strategies for development of highly active catalysts for sustainable generation of liquid fuels from one-carbon substrates, with potential for broad applications across diverse fields ranging from energy storage to environmental remediation.
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10
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Cai J, Zhao L, Li Y, He C, Wang C, Duan C. Binding of Dual-Function Hybridized Metal -Organic Capsules to Enzymes for Cascade Catalysis. JACS AU 2022; 2:1736-1746. [PMID: 35911460 PMCID: PMC9327082 DOI: 10.1021/jacsau.2c00322] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The combination of chemo- and biocatalysis for multistep syntheses provides attractive advantages in terms of evolvability, promiscuity, and sustainability striving for desirable catalytic performance. Through the encapsulation of flavin analogues by both NADH and heme mimics codecorated heteroleptic metal-organic capsules, herein, we report a progressive host-guest strategy to imitate cytochrome P450s catalysis for cascade oxidative coupling catalysis. Besides the construction of stable dual-function metal-organic capsules and the modification of cofactor-decorated capsules at the domain of enzymes, this supramolecular strategy involves multistage directional electron flow, affording reactive ferric peroxide species for inducing oxygenation. Under light irradiation, the metal-organic capsule selectively converts stilbene to oxidative coupling products (including 2-oxo-1,2-diphenylethyl formate, 2-alkoxy-1,2-diphenylethanone) in tandem with enzymatic reactions respectively, at the domain of natural enzymes. The ingenious combination of capsules and enzymes with the in situ-regenerated capsule-loaded NADH cofactor promises non-native coupling reactions by forming regional cooperation and division. This abiotic-biotic conjugated host-guest strategy is conducive to the de novo creation of multifunctional components approaching active enzymatic sites for reinforced matter and energy transporting, demonstrating a key role of multicomponent supramolecular catalysts for one-pot integrated catalytic conversions.
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Affiliation(s)
- Junkai Cai
- State
Key Laboratory of Fine Chemicals, Zhang Dayu School of Chemistry, Dalian University of Technology, Dalian 116024, People’s Republic of China
- State
Key Laboratory of Coordination Chemistry, Nanjing University, Nanjing 210023, People’s Republic
of China
| | - Liang Zhao
- State
Key Laboratory of Fine Chemicals, Zhang Dayu School of Chemistry, Dalian University of Technology, Dalian 116024, People’s Republic of China
| | - Yanan Li
- State
Key Laboratory of Fine Chemicals, Zhang Dayu School of Chemistry, Dalian University of Technology, Dalian 116024, People’s Republic of China
| | - Cheng He
- State
Key Laboratory of Fine Chemicals, Zhang Dayu School of Chemistry, Dalian University of Technology, Dalian 116024, People’s Republic of China
| | - Chong Wang
- State
Key Laboratory of Fine Chemicals, Zhang Dayu School of Chemistry, Dalian University of Technology, Dalian 116024, People’s Republic of China
| | - Chunying Duan
- State
Key Laboratory of Fine Chemicals, Zhang Dayu School of Chemistry, Dalian University of Technology, Dalian 116024, People’s Republic of China
- State
Key Laboratory of Coordination Chemistry, Nanjing University, Nanjing 210023, People’s Republic
of China
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11
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Kerns S, Biswas A, Minnetian NM, Borovik AS. Artificial Metalloproteins: At the Interface between Biology and Chemistry. JACS AU 2022; 2:1252-1265. [PMID: 35783165 PMCID: PMC9241007 DOI: 10.1021/jacsau.2c00102] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 04/13/2022] [Accepted: 04/15/2022] [Indexed: 05/22/2023]
Abstract
Artificial metalloproteins (ArMs) have recently gained significant interest due to their potential to address issues in a broad scope of applications, including biocatalysis, biotechnology, protein assembly, and model chemistry. ArMs are assembled by the incorporation of a non-native metallocofactor into a protein scaffold. This can be achieved by a number of methods that apply tools of chemical biology, computational de novo design, and synthetic chemistry. In this Perspective, we highlight select systems in the hope of demonstrating the breadth of ArM design strategies and applications and emphasize how these systems address problems that are otherwise difficult to do so with strictly biochemical or synthetic approaches.
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12
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Griego L, Woods TJ, Mirica LM. A five-coordinate Ni(I) complex supported by 1,4,7-triisopropyl-1,4,7-triazacyclononane. Chem Commun (Camb) 2022; 58:7360-7363. [PMID: 35708524 DOI: 10.1039/d2cc02516g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An isolated Ni(II)-nitrosyl complex supported by the bulky tridentate 1,4,7-triisopropyl-1,4,7-triazacyclononane (iPr3TACN) ligand was obtained from the reaction of a Ni(II) dimethyl complex with NOPF6, suggesting the in situ formation of a Ni(I) species that reacts with the resulting NO product. Use of a π-acceptor ancillary isocyanide ligand led to the isolation and characterization of an uncommon 5-coordinate Ni(I) complex supported by the iPr3TACN ligand and tert-butylisocyanide.
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Affiliation(s)
- Leonel Griego
- Department of Chemistry University of Illinois at Urbana Champaign 600 S. Mathews Avenue, Urbana, Illinois, 61801, USA.
| | - Toby J Woods
- Department of Chemistry University of Illinois at Urbana Champaign 600 S. Mathews Avenue, Urbana, Illinois, 61801, USA.
| | - Liviu M Mirica
- Department of Chemistry University of Illinois at Urbana Champaign 600 S. Mathews Avenue, Urbana, Illinois, 61801, USA.
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13
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14
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Lewis LC, Shafaat HS. Reversible Electron Transfer and Substrate Binding Support [NiFe 3S 4] Ferredoxin as a Protein-Based Model for [NiFe] Carbon Monoxide Dehydrogenase. Inorg Chem 2021; 60:13869-13875. [PMID: 34488341 DOI: 10.1021/acs.inorgchem.1c01323] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The nickel-iron carbon monoxide dehydrogenase (CODH) enzyme catalyzes the reversible and selective interconversion of carbon dioxide (CO2) to carbon monoxide (CO) with high rates and negligible overpotential. Despite decades of research, many questions remain about this complex metalloenzyme system. A simplified model enzyme could provide substantial insight into biological carbon cycling. Here, we demonstrate reversible electron transfer and binding of both CO and cyanide, a substrate and an inhibitor of CODH, respectively, in a Pyrococcus furiosus (Pf) ferredoxin (Fd) protein that has been reconstituted with a nickel-iron sulfide cluster ([NiFe3S4] Fd). The [NiFe3S4] cluster mimics the core of the native CODH active site and thus serves as a protein-based structural model of the CODH subsite. Notably, despite binding cyanide, no CO binding is observed for the physiological [Fe4S4] clusters in Pf Fd, providing chemical rationale underlying the evolution of a site-differentiated cluster for substrate conversion in native CODH. The demonstration of a substrate-binding metalloprotein model of CODH sets the stage for high-resolution spectroscopic and mechanistic studies correlating the subsite structure and function, ultimately guiding the design of anthropogenic catalysts that harness the advantages of CODH for effective CO2 reduction.
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Affiliation(s)
- Luke C Lewis
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Hannah S Shafaat
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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15
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Naughton KJ, Treviño RE, Moore PJ, Wertz AE, Dickson JA, Shafaat HS. In Vivo Assembly of a Genetically Encoded Artificial Metalloenzyme for Hydrogen Production. ACS Synth Biol 2021; 10:2116-2120. [PMID: 34370434 DOI: 10.1021/acssynbio.1c00177] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The genetic encoding of artificial enzymes represents a substantial advantage relative to traditional molecular catalyst optimization, as laboratory-based directed evolution coupled with high-throughput screening methods can provide rapid development and functional characterization of enzyme libraries. However, these techniques have been of limited utility in the field of artificial metalloenzymes due to the need for in vitro cofactor metalation. Here, we report the development of methodology for in vivo production of nickel-substituted rubredoxin, an artificial metalloenzyme that is a structural, functional, and mechanistic mimic of the [NiFe] hydrogenases. Direct voltammetry on cell lysate establishes precedent for the development of an electrochemical screen. This technique will be broadly applicable to the in vivo generation of artificial metalloenzymes that require a non-native metal cofactor, offering a route for rapid enzyme optimization and setting the stage for integration of artificial metalloenzymes into biochemical pathways within diverse hosts.
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Affiliation(s)
- Kassandra J. Naughton
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Regina E. Treviño
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Peter J. Moore
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Ashlee E. Wertz
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - J. Alex Dickson
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Hannah S. Shafaat
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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16
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Tian S, Fan R, Albert T, Khade RL, Dai H, Harnden KA, Hosseinzadeh P, Liu J, Nilges MJ, Zhang Y, Moënne-Loccoz P, Guo Y, Lu Y. Stepwise nitrosylation of the nonheme iron site in an engineered azurin and a molecular basis for nitric oxide signaling mediated by nonheme iron proteins. Chem Sci 2021; 12:6569-6579. [PMID: 34040732 PMCID: PMC8132939 DOI: 10.1039/d1sc00364j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Mononitrosyl and dinitrosyl iron species, such as {FeNO}7, {FeNO}8 and {Fe(NO)2}9, have been proposed to play pivotal roles in the nitrosylation processes of nonheme iron centers in biological systems. Despite their importance, it has been difficult to capture and characterize them in the same scaffold of either native enzymes or their synthetic analogs due to the distinct structural requirements of the three species, using redox reagents compatible with biomolecules under physiological conditions. Here, we report the realization of stepwise nitrosylation of a mononuclear nonheme iron site in an engineered azurin under such conditions. Through tuning the number of nitric oxide equivalents and reaction time, controlled formation of {FeNO}7 and {Fe(NO)2}9 species was achieved, and the elusive {FeNO}8 species was inferred by EPR spectroscopy and observed by Mössbauer spectroscopy, with complemental evidence for the conversion of {FeNO}7 to {Fe(NO)2}9 species by UV-Vis, resonance Raman and FT-IR spectroscopies. The entire pathway of the nitrosylation process, Fe(ii) → {FeNO}7 → {FeNO}8 → {Fe(NO)2}9, has been elucidated within the same protein scaffold based on spectroscopic characterization and DFT calculations. These results not only enhance the understanding of the dinitrosyl iron complex formation process, but also shed light on the physiological roles of nitric oxide signaling mediated by nonheme iron proteins. Stepwise nitrosylation from Fe(ii) to {FeNO}7, {FeNO}8 and then to {Fe(NO)2}9 is reported for the first time in the same protein scaffold, providing deeper understanding of the detailed mechanism of dinitrosyl iron complex formation.![]()
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Affiliation(s)
- Shiliang Tian
- Department of Chemistry, Department of Biochemistry, School of Chemical Sciences Electron Paramagnetic Resonance Lab, University of Illinois at Urbana-Champaign 600 South Mathews Avenue Urbana IL USA +1-217-333-2619
| | - Ruixi Fan
- Department of Chemistry, Carnegie Mellon University 4400 Fifth Avenue Pittsburgh PA USA +1-412-268-1061 +1-412-268-1704
| | - Therese Albert
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University 3181 S.W. Sam Jackson Park Road Portland OR USA +1-503-346-3429
| | - Rahul L Khade
- Department of Chemistry and Chemical Biology, Stevens Institute of Technology 1 Castle Point Terrace Hoboken NJ USA +1-201-216-8240 +1-201-216-5513
| | - Huiguang Dai
- Department of Chemistry, Department of Biochemistry, School of Chemical Sciences Electron Paramagnetic Resonance Lab, University of Illinois at Urbana-Champaign 600 South Mathews Avenue Urbana IL USA +1-217-333-2619
| | - Kevin A Harnden
- Department of Chemistry, Department of Biochemistry, School of Chemical Sciences Electron Paramagnetic Resonance Lab, University of Illinois at Urbana-Champaign 600 South Mathews Avenue Urbana IL USA +1-217-333-2619
| | - Parisa Hosseinzadeh
- Department of Chemistry, Department of Biochemistry, School of Chemical Sciences Electron Paramagnetic Resonance Lab, University of Illinois at Urbana-Champaign 600 South Mathews Avenue Urbana IL USA +1-217-333-2619
| | - Jing Liu
- Department of Chemistry, Department of Biochemistry, School of Chemical Sciences Electron Paramagnetic Resonance Lab, University of Illinois at Urbana-Champaign 600 South Mathews Avenue Urbana IL USA +1-217-333-2619
| | - Mark J Nilges
- Department of Chemistry, Department of Biochemistry, School of Chemical Sciences Electron Paramagnetic Resonance Lab, University of Illinois at Urbana-Champaign 600 South Mathews Avenue Urbana IL USA +1-217-333-2619
| | - Yong Zhang
- Department of Chemistry and Chemical Biology, Stevens Institute of Technology 1 Castle Point Terrace Hoboken NJ USA +1-201-216-8240 +1-201-216-5513
| | - Pierre Moënne-Loccoz
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University 3181 S.W. Sam Jackson Park Road Portland OR USA +1-503-346-3429
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University 4400 Fifth Avenue Pittsburgh PA USA +1-412-268-1061 +1-412-268-1704
| | - Yi Lu
- Department of Chemistry, Department of Biochemistry, School of Chemical Sciences Electron Paramagnetic Resonance Lab, University of Illinois at Urbana-Champaign 600 South Mathews Avenue Urbana IL USA +1-217-333-2619
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17
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DiPrimio DJ, Holland PL. Repurposing metalloproteins as mimics of natural metalloenzymes for small-molecule activation. J Inorg Biochem 2021; 219:111430. [PMID: 33873051 DOI: 10.1016/j.jinorgbio.2021.111430] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 03/11/2021] [Accepted: 03/15/2021] [Indexed: 12/12/2022]
Abstract
Artificial metalloenzymes (ArMs) consist of an unnatural metal or cofactor embedded in a protein scaffold, and are an excellent platform for applying the concepts of protein engineering to catalysis. In this Focused Review, we describe the application of ArMs as simple, tunable artificial models of the active sites of complex natural metalloenzymes for small-molecule activation. In this sense, ArMs expand the strategies of synthetic model chemistry to protein-based supporting ligands with potential for participation from the second coordination sphere. We focus specifically on ArMs that are structural, spectroscopic, and functional models of enzymes for activation of small molecules like CO, CO2, O2, N2, and NO, as well as production/consumption of H2. These ArMs give insight into the identities and roles of metalloenzyme structural features within and near the cofactor. We give examples of ArM work relevant to hydrogenases, acetyl-coenzyme A synthase, superoxide dismutase, heme oxygenases, nitric oxide reductase, methyl-coenzyme M reductase, copper-O2 enzymes, and nitrogenases.
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Affiliation(s)
- Daniel J DiPrimio
- Department of Chemistry, Yale University, New Haven, CT, 06520, United States
| | - Patrick L Holland
- Department of Chemistry, Yale University, New Haven, CT, 06520, United States.
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18
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Patel AY, Jonnalagadda KS, Paradis N, Vaden TD, Wu C, Caputo GA. Effects of Ionic Liquids on Metalloproteins. Molecules 2021; 26:514. [PMID: 33478102 PMCID: PMC7835893 DOI: 10.3390/molecules26020514] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/04/2021] [Accepted: 01/08/2021] [Indexed: 01/28/2023] Open
Abstract
In the past decade, innovative protein therapies and bio-similar industries have grown rapidly. Additionally, ionic liquids (ILs) have been an area of great interest and rapid development in industrial processes over a similar timeline. Therefore, there is a pressing need to understand the structure and function of proteins in novel environments with ILs. Understanding the short-term and long-term stability of protein molecules in IL formulations will be key to using ILs for protein technologies. Similarly, ILs have been investigated as part of therapeutic delivery systems and implicated in numerous studies in which ILs impact the activity and/or stability of protein molecules. Notably, many of the proteins used in industrial applications are involved in redox chemistry, and thus often contain metal ions or metal-associated cofactors. In this review article, we focus on the current understanding of protein structure-function relationship in the presence of ILs, specifically focusing on the effect of ILs on metal containing proteins.
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Affiliation(s)
- Aashka Y. Patel
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ 08028, USA; (A.Y.P.); (N.P.); (T.D.V.); (C.W.)
| | | | - Nicholas Paradis
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ 08028, USA; (A.Y.P.); (N.P.); (T.D.V.); (C.W.)
| | - Timothy D. Vaden
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ 08028, USA; (A.Y.P.); (N.P.); (T.D.V.); (C.W.)
| | - Chun Wu
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ 08028, USA; (A.Y.P.); (N.P.); (T.D.V.); (C.W.)
- Department of Molecular and Cellular Biosciences, Rowan University, Glassboro, NJ 08028, USA
| | - Gregory A. Caputo
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ 08028, USA; (A.Y.P.); (N.P.); (T.D.V.); (C.W.)
- Department of Molecular and Cellular Biosciences, Rowan University, Glassboro, NJ 08028, USA
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19
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Kisgeropoulos EC, Manesis AC, Shafaat HS. Ligand Field Inversion as a Mechanism to Gate Bioorganometallic Reactivity: Investigating a Biochemical Model of Acetyl CoA Synthase Using Spectroscopy and Computation. J Am Chem Soc 2021; 143:849-867. [PMID: 33415980 DOI: 10.1021/jacs.0c10135] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The biological global carbon cycle is largely regulated through microbial nickel enzymes, including carbon monoxide dehydrogenase (CODH), acetyl coenzyme A synthase (ACS), and methyl coenzyme M reductase (MCR). These systems are suggested to utilize organometallic intermediates during catalysis, though characterization of these species has remained challenging. We have established a mutant of nickel-substituted azurin as a scaffold upon which to develop protein-based models of enzymatic intermediates, including the organometallic states of ACS. In this work, we report the comprehensive investigation of the S = 1/2 Ni-CO and Ni-CH3 states using pulsed EPR spectroscopy and computational techniques. While the Ni-CO state shows conventional metal-ligand interactions and a classical ligand field, the Ni-CH3 hyperfine interactions between the methyl protons and the nickel indicate a closer distance than would be expected for an anionic methyl ligand. Structural analysis instead suggests a near-planar methyl ligand that can be best described as cationic. Consistent with this conclusion, the frontier molecular orbitals of the Ni-CH3 species indicate a ligand-centered LUMO, with a d9 population on the metal center, rather than the d7 population expected for a typical metal-alkyl species generated by oxidative addition. Collectively, these data support the presence of an inverted ligand field configuration for the Ni-CH3 Az species, in which the lowest unoccupied orbital is centered on the ligands rather than the more electropositive metal. These analyses provide the first evidence for an inverted ligand field within a biological system. The functional relevance of the electronic structures of both the Ni-CO and Ni-CH3 species are discussed in the context of native ACS, and an inverted ligand field is proposed as a mechanism by which to gate reactivity both within ACS and in other thiolate-containing metalloenzymes.
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Affiliation(s)
- Effie C Kisgeropoulos
- Department of Chemistry and Biochemistry and Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, United States
| | - Anastasia C Manesis
- Department of Chemistry and Biochemistry and Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, United States
| | - Hannah S Shafaat
- Department of Chemistry and Biochemistry and Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, United States
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20
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Cohen SE, Can M, Wittenborn EC, Hendrickson RA, Ragsdale SW, Drennan CL. Crystallographic Characterization of the Carbonylated A-Cluster in Carbon Monoxide Dehydrogenase/Acetyl-CoA Synthase. ACS Catal 2020; 10:9741-9746. [PMID: 33495716 PMCID: PMC7819276 DOI: 10.1021/acscatal.0c03033] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/10/2020] [Indexed: 12/30/2022]
Abstract
![]()
The
Wood–Ljungdahl pathway allows for autotrophic bacterial
growth on carbon dioxide, with the last step in acetyl-CoA synthesis
catalyzed by the bifunctional enzyme carbon monoxide dehydrogenase/acetyl-CoA
synthase (CODH/ACS). ACS uses a complex Ni–Fe–S metallocluster
termed the A-cluster to assemble acetyl-CoA from carbon monoxide,
a methyl moiety and coenzyme A. Here, we report the crystal structure
of CODH/ACS from Moorella thermoacetica with substrate
carbon monoxide bound at the A-cluster, a state previously uncharacterized
by crystallography. Direct structural characterization of this state
highlights the role of second sphere residues and conformational dynamics
in acetyl-CoA assembly, the biological equivalent of the Monsanto
process.
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Affiliation(s)
- Steven E. Cohen
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Mehmet Can
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 04109, United States
| | - Elizabeth C. Wittenborn
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Rachel A. Hendrickson
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Stephen W. Ragsdale
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 04109, United States
| | - Catherine L. Drennan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Howard Hughes Medical Institute, Cambridge, Massachusetts 02139, United States
- Bio-inspired Solar Energy Program, Canadian Institute for Advanced Research, Toronto, ON M5G 1M1, Canada
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21
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James CD, Wiley S, Ragsdale SW, Hoffman BM. 13C Electron Nuclear Double Resonance Spectroscopy Shows Acetyl-CoA Synthase Binds Two Substrate CO in Multiple Binding Modes and Reveals the Importance of a CO-Binding "Alcove". J Am Chem Soc 2020; 142:15362-15370. [PMID: 32786751 DOI: 10.1021/jacs.0c05950] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
EPR and Electron Nuclear Double Resonance spectroscopies here characterize CO binding to the active-site A cluster of wild-type (WT) Acetyl-CoA Synthase (ACS) and two variants, F229W and F229A. The A-cluster binds CO to a proximal Ni (Nip) that bridges a [4Fe-4S] cluster and a distal Nid. An alcove seen in the ACS crystal structure near the A-cluster, defined by hydrophobic residues including F229, forms a cage surrounding a Xe mimic of CO. Previously, we only knew WT ACS bound a single CO to form the Ared-CO intermediate, containing Nip(I)-CO with CO located on the axis of the dz2 odd-electron orbital (g⊥ > g|| ∼ 2). Here, the two-dimensional field-frequency pattern of 2K-35 GHz 13C-ENDOR spectra collected across the Ared-CO EPR envelope reveals a second CO bound in the dz2 orbital's equatorial plane. This WT A-cluster conformer dominates the nearly conservative F229W variant, but 13C-ENDOR reveals a minority "A" conformation with (g|| > g⊥ ∼ 2) characteristic of a "cloverleaf" (e.g., dx2-y2) odd-electron orbital, with Nip binding two, apparently "in-plane" CO. Disruption of the alcove through introduction of the smaller alanine residue in the F229A variant diminishes conversion to Ni(I) ∼ 10-fold and introduces extensive cluster flexibility. 13C-ENDOR shows the F229A cluster is mostly (60%) in the "A" conformation but with ∼20% each of the WT conformer and an "O" state in which dz2 Nip(I) (g⊥ > g|| ∼ 2) surprisingly lacks CO. This paper thus demonstrates the importance of an intact alcove in forming and stabilizing the Ni(I)-CO intermediate in the Wood-Ljungdahl pathway of anaerobic CO and CO2 fixation.
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Affiliation(s)
- Christopher D James
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Seth Wiley
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109-0606 United States
| | - Stephen W Ragsdale
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109-0606 United States
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
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22
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Zhao L, Cai J, Li Y, Wei J, Duan C. A host-guest approach to combining enzymatic and artificial catalysis for catalyzing biomimetic monooxygenation. Nat Commun 2020; 11:2903. [PMID: 32518257 PMCID: PMC7283336 DOI: 10.1038/s41467-020-16714-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 05/12/2020] [Indexed: 12/19/2022] Open
Abstract
Direct transfer of protons and electrons between two tandem reactions is still a great challenge, because overall reaction kinetics is seriously affected by diffusion rate of the proton and electron carriers. We herein report a host–guest supramolecular strategy based on the incorporation of NADH mimics onto the surface of a metal-organic capsule to encapsulate flavin analogues for catalytic biomimetic monooxygenations in conjunction with enzymes. Coupling an artificial catalysis and a natural enzymatic catalysis in the pocket of an enzyme, this host–guest catalyst–enzyme system allows direct proton and electron transport between two catalytic processes via NADH mimics for the monooxygenation of both cyclobutanones and thioethers. This host–guest approach, which involves the direct coupling of abiotic and biotic catalysts via a NADH-containing host, is quite promising compared to normal catalyst–enzyme systems, as it offers the key advantages of supramolecular catalysis in integrated chemical and biological synthetic sequences. Combining artificial and natural enzymes is a strategy to mimic biocatalytic processes with high efficiency and selectivity. This study reports a dual catalytic system composed of flavin adenine dinucleotide model and NADH mimics to catalyze the monooxygenation of cyclobutanones and thioethers.
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Affiliation(s)
- Liang Zhao
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, 116024, Dalian, People's Republic of China
| | - Junkai Cai
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, 116024, Dalian, People's Republic of China
| | - Yanan Li
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, 116024, Dalian, People's Republic of China
| | - Jianwei Wei
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, 116024, Dalian, People's Republic of China
| | - Chunying Duan
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, 116024, Dalian, People's Republic of China. .,Zhang Dayu School of Chemistry, Dalian University of Technology, 116024, Dalian, People's Republic of China.
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23
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Lucio M, Willkommen D, Schroeter M, Sigaroudi A, Schmitt-Kopplin P, Michalke B. Integrative Metabolomic and Metallomic Analysis in a Case-Control Cohort With Parkinson's Disease. Front Aging Neurosci 2019; 11:331. [PMID: 31866853 PMCID: PMC6908950 DOI: 10.3389/fnagi.2019.00331] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 11/18/2019] [Indexed: 01/29/2023] Open
Abstract
Parkinson's disease (PD) is a neurodegenerative disease with a complex etiology. Several factors are known to contribute to the disease onset and its progression. However, the complete underlying mechanisms are still escaping our understanding. To evaluate possible correlations between metabolites and metallomic data, in this research, we combined a control study measured using two different platforms. For the different data sources, we applied a Block Sparse Partial Least Square Discriminant Analysis (Block-sPLS-DA) model that allows for proving their relation, which in turn uncovers alternative influencing factors that remain hidden otherwise. We found two groups of variables that trace a strong relationship between metallomic and metabolomic parameters for disease development. The results confirmed that the redox active metals iron (Fe) and copper (Cu) together with fatty acids are the major influencing factors for the PD. Additionally, the metabolic waste product p-cresol sulfate and the trace element nickel (Ni) showed up as potentially important factors in PD. In summary, the data integration of different types of measurements emphasized the results of both stand-alone measurements providing a new comprehensive set of information and interactions, on PD disease, between different variables sources.
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Affiliation(s)
- Marianna Lucio
- Analytische BioGeoChemie, Helmholtz Zentrum München, Neuherberg, Germany
| | - Desiree Willkommen
- Analytische BioGeoChemie, Helmholtz Zentrum München, Neuherberg, Germany
| | - Michael Schroeter
- Klinik und Poliklinik für Neurologie, Uniklinik Köln, Cologne, Germany
| | - Ali Sigaroudi
- Klinik für Klinische Pharmakologie und Toxikologie, Universitätsspital Zürich, Zurich, Switzerland
- Institut I für Pharmakologie, Zentrum für Pharmakologie, Uniklinik Köln, Cologne, Germany
| | - Philippe Schmitt-Kopplin
- Analytische BioGeoChemie, Helmholtz Zentrum München, Neuherberg, Germany
- Chair of Analytical Food Chemistry, Life Science Center Weihenstephan, Technical University of Munich, Munich, Germany
| | - Bernhard Michalke
- Analytische BioGeoChemie, Helmholtz Zentrum München, Neuherberg, Germany
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24
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Saif B, Zhang W, Zhang X, Gu Q, Yang P. Sn-Triggered Two-Dimensional Fast Protein Assembly with Emergent Functions. ACS NANO 2019; 13:7736-7749. [PMID: 31244042 DOI: 10.1021/acsnano.9b01392] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The discovery of a general strategy for organizing functional proteins into stable nanostructures with the desired dimension, shape, and function is an important focus in developing protein-based self-assembled materials, but the scalable synthesis of such materials and transfer to other substrates remain great challenges. We herein tackle this issue by creating a two-dimensional metal-protein hybrid nanofilm that is flexible and cost-effective with reliable self-recovery, stability, and multifunctionality. As it differs from traditional metal ions, we discover the capability of Sn2+ to initiate fast amyloid-like protein assembly (occurring in seconds) by effectively reducing the disulfide bonds of native globular proteins. The Sn2+-initiated lysozyme aggregation at the air/water interface leads to droplet flattening, a result never before reported in a protein system, which finally affords a multifunctional 2D Sn-doped hybrid lysozyme nanofilm with an ultralarge area (e.g., 0.2 m2) within a few minutes. The hybrid film is distinctive in its ease of coating on versatile material surfaces with endurable chemical and mechanical stability, optical transparency, and diverse end uses in antimicrobial and photo-/electrocatalytic scaffolds. Our approach provides not only insights into the effect of tin ions on macroscopic self-assembly of proteins but also a controllable and scalable synthesis of a potential biomimic framework for biomedical and biocatalytic applications.
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Affiliation(s)
- Bassam Saif
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710062 , P.R. China
| | - Wenxin Zhang
- School and Hospital of Stomatology , Tianjin Medical University , 12 Observatory Road , Tianjin 30070 , P.R. China
| | - Xu Zhang
- School and Hospital of Stomatology , Tianjin Medical University , 12 Observatory Road , Tianjin 30070 , P.R. China
| | - Quan Gu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710062 , P.R. China
| | - Peng Yang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710062 , P.R. China
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25
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Mirts EN, Bhagi-Damodaran A, Lu Y. Understanding and Modulating Metalloenzymes with Unnatural Amino Acids, Non-Native Metal Ions, and Non-Native Metallocofactors. Acc Chem Res 2019; 52:935-944. [PMID: 30912643 DOI: 10.1021/acs.accounts.9b00011] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Metalloproteins set the gold standard for performing important functions, including catalyzing demanding reactions under mild conditions. Designing artificial metalloenzymes (ArMs) to catalyze abiological reactions has been a major endeavor for many years, but most ArM activities are far below those of native enzymes, making them unsuitable for most pratical applications. A critical step to advance the field is to fundamentally understand what it takes to not only confer but also fine-tune ArM activities so they match those of native enzymes. Indeed, only once we can freely modulate ArM activity to rival (or surpass!) natural enzymes can the potential of ArMs be fully realized. A key to unlocking ArM potential is the observation that one metal primary coordination sphere can display a range of functions and levels of activity, leading to the realization that secondary coordination sphere (SCS) interactions are critically important. However, SCS interactions are numerous, long-range, and weak, making them very difficult to reproduce in ArMs. Furthermore, natural enzymes are tied to a small set of biologically available functional moieties from canonical amino acids and physiologically available metal ions and metallocofactors, severely limiting the chemical space available to probe and tune ArMs. In this Account, we summarize the use of unnatural amino acids (UAAs) and non-native metal ions and metallocofactors by our group and our collaborators to probe and modulate ArM functions. We incorporated isostructural UAAs in a type 1 copper (T1Cu) protein azurin to provide conclusive evidence that axial ligand hydrophobicity is a major determinant of T1Cu redunction potential ( E°'). Closely related work from other groups are also discussed. We also probed the role of protein backbone interactions that cannot be altered by standard mutagenesis by replacing the peptide bond with an ester linkage. We used insight gained from these studies to tune the E°' of azurin across the entire physiological range, the broadest range ever achieved in a single metalloprotein. Introducing UAA analogues of Tyr into ArM models of heme-copper oxidase (HCO) revealed a linear relationship between p Ka, E°', and activity. We also substituted non-native hemes and non-native metal ions for their native equivalents in these models to resolve several issues that were intractable in native HCOs and the closely related nitric oxide reductases, such as their roles in modulating substrate affinity, electron transfer rate, and activity. We incorporated abiological cofactors such as ferrocene and Mn(salen) into azurin and myoglobin, respectively, to stabilize these inorganic and organometallic compounds in water, confer abiological functions, tune their E°' and activity through SCS interactions, and show that the approach to metallocofactor anchoring and orientation can tune enantioselectivity and alter function. Replacing Cu in azurin with non-native Fe or Ni can impart novel activities, such as superoxide reduction and C-C bond formation. While progress was made, we have identified only a small fraction of the interactions that can be generally applied to ArMs to fine-tune their functions. Because SCS interactions are subtle and heavily interconnected, it has been difficult to characterize their effects quantitatively. It is vital to develop spectroscopic and computational techniques to detect and quantify their effects in both resting states and catalytic intermediates.
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Affiliation(s)
- Evan N. Mirts
- Department of Chemistry and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Ambika Bhagi-Damodaran
- Department of Chemistry and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Yi Lu
- Department of Chemistry and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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26
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Manesis AC, Musselman BW, Keegan BC, Shearer J, Lehnert N, Shafaat HS. A Biochemical Nickel(I) State Supports Nucleophilic Alkyl Addition: A Roadmap for Methyl Reactivity in Acetyl Coenzyme A Synthase. Inorg Chem 2019; 58:8969-8982. [PMID: 30788970 PMCID: PMC6635881 DOI: 10.1021/acs.inorgchem.8b03546] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
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Nickel-containing
enzymes such as methyl coenzyme M reductase (MCR) and carbon monoxide
dehydrogenase/acetyl coenzyme A synthase (CODH/ACS) play a critical
role in global energy conversion reactions, with significant contributions
to carbon-centered processes. These enzymes are implied to cycle through
a series of nickel-based organometallic intermediates during catalysis,
though identification of these intermediates remains challenging.
In this work, we have developed and characterized a nickel-containing
metalloprotein that models the methyl-bound organometallic intermediates
proposed in the native enzymes. Using a nickel(I)-substituted azurin
mutant, we demonstrate that alkyl binding occurs via nucleophilic
addition of methyl iodide as a methyl donor. The paramagnetic NiIII-CH3 species initially generated can be rapidly
reduced to a high-spin NiII-CH3 species in the
presence of exogenous reducing agent, following a reaction sequence
analogous to that proposed for ACS. These two distinct bioorganometallic
species have been characterized by optical, EPR, XAS, and MCD spectroscopy,
and the overall mechanism describing methyl reactivity with nickel
azurin has been quantitatively modeled using global kinetic simulations.
A comparison between the nickel azurin protein system and existing
ACS model compounds is presented. NiIII-CH3 Az
is only the second example of two-electron addition of methyl iodide
to a NiI center to give an isolable species and the first
to be formed in a biologically relevant system. These results highlight
the divergent reactivity of nickel across the two intermediates, with
implications for likely reaction mechanisms and catalytically relevant
states in the native ACS enzyme. A bioorganometallic model
for acetyl coenzyme A synthase has been developed. This model protein
is able to bind a cationic methyl group via direct addition to the
nickel(I) center. The resultant nickel(III)-methyl species has been
characterized via optical and electron paramagnetic resonance spectroscopy,
and the reduced nickel(II)-methyl state has been characterized using
magnetic circular dichroism and X-ray spectroscopy. Implications for
further reactivity with CO are gleaned from electronic structure analysis
of the nickel-methyl species.
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Affiliation(s)
- Anastasia C Manesis
- Department of Chemistry and Biochemistry , The Ohio State University , 100 W. 18th Avenue , Columbus , Ohio 43210 , United States
| | - Bradley W Musselman
- Department of Chemistry , University of Michigan , 930 N. University Avenue , Ann Arbor , Michigan 48109 , United States
| | - Brenna C Keegan
- Department of Chemistry , Trinity University , One Trinity Place , San Antonio , Texas 78212 , United States
| | - Jason Shearer
- Department of Chemistry , Trinity University , One Trinity Place , San Antonio , Texas 78212 , United States
| | - Nicolai Lehnert
- Department of Chemistry , University of Michigan , 930 N. University Avenue , Ann Arbor , Michigan 48109 , United States
| | - Hannah S Shafaat
- Department of Chemistry and Biochemistry , The Ohio State University , 100 W. 18th Avenue , Columbus , Ohio 43210 , United States
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27
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Bhagi-Damodaran A, Lu Y. The Periodic Table's Impact on Bioinorganic Chemistry and Biology's Selective Use of Metal Ions. STRUCTURE AND BONDING 2019; 182:153-173. [PMID: 36567794 PMCID: PMC9788643 DOI: 10.1007/430_2019_45] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Despite the availability of a vast variety of metal ions in the periodic table, biology uses only a selective few metal ions. Most of the redox active metals used belong to the first row of transition metals in the periodic table and include Fe, Co, Ni, Mn and Cu. On the other hand, Ca, Zn and Mg are the most commonly used redox inactive metals in biology. In this chapter, we discuss the periodic table's impact on bio-inorganic chemistry, by exploring reasons behind this selective choice of metals biology. A special focus is placed on the chemical and functional reasons why one metal ion is preferred over another one. We discuss the implications of metal choice in various biological processes including catalysis, electron transfer, redox sensing and signaling. We find that bioavailability of metal ions along with their redox potentials, coordination flexibility, valency and ligand affinity determine the specificity of metals for biological processes. Understanding the implications underlying the selective choice of metals of the periodic table in these biological processes can help design more efficient catalysts, more precise biosensors and more effective drugs.
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Affiliation(s)
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
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28
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Burton R, Can M, Esckilsen D, Wiley S, Ragsdale SW. Production and properties of enzymes that activate and produce carbon monoxide. Methods Enzymol 2018; 613:297-324. [PMID: 30509471 PMCID: PMC6309614 DOI: 10.1016/bs.mie.2018.10.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The chapter focuses on the methods involved in producing and characterizing two key nickel-iron-sulfur enzymes in the Wood-Ljungdahl pathway (WLP) of anaerobic conversion of carbon dioxide fixation into acetyl-CoA: carbon monoxide dehydrogenase (CODH) and acetyl-CoA synthase (ACS). The WLP is used for biosynthesis of cell material and energy conservation by anaerobic bacteria and archaea, and it is central to several industrial biotechnology processes aimed at using syngas and waste gases for the production of fuels and chemicals. The pathway can run in reverse to allow organisms, e. g., methanogens and sulfate reducers, to grow on acetate. The CODH and ACS intertwine to form a tenacious CODH/ACS complex that converts CO2, a methyl group, and coenzyme A into acetyl-CoA. CODH also behaves as a modular unit that can function as an independent homodimer. Besides coupling to ACS, CODH can interact with hydrogenases to couple CO oxidation to H2 formation. These enzymes have been purified and characterized from several microbes.
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Affiliation(s)
- Rodney Burton
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Mehmet Can
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Daniel Esckilsen
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Seth Wiley
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Stephen W Ragsdale
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, United States.
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