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Malayam Parambath S, Prakash D, Swetman W, Surakanti A, Chakraborty S. Converting a cysteine-rich natively noncatalytic protein to an artificial hydrogenase. Chem Commun (Camb) 2023; 59:13325-13328. [PMID: 37867329 PMCID: PMC10894637 DOI: 10.1039/d3cc02774k] [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] [Indexed: 10/24/2023]
Abstract
An artificial hydrogenase is constructed when the natively noncatalytic α-domain of the Cys-rich protein metallothionein (MT) is assembled with NiII. αMT binds four eq. of NiII in a non-cooperative manner where the addition of the 1st NiII eq. affords the most catalytically active species with little effect on photocatalytic H2 production during subsequent metal addition. The critical role of protonated Cys residue(s) in H-H bond formation is demonstrated.
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Affiliation(s)
- Sreya Malayam Parambath
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677, USA.
| | - Divyansh Prakash
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677, USA.
| | - Windfield Swetman
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677, USA.
| | - Aditya Surakanti
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677, USA.
| | - Saumen Chakraborty
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677, USA.
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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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3
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T Waffo AF, Lorent C, Katz S, Schoknecht J, Lenz O, Zebger I, Caserta G. Structural Determinants of the Catalytic Ni a-L Intermediate of [NiFe]-Hydrogenase. J Am Chem Soc 2023. [PMID: 37328284 DOI: 10.1021/jacs.3c01625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
[NiFe]-hydrogenases catalyze the reversible cleavage of H2 into two protons and two electrons at the inorganic heterobimetallic NiFe center of the enzyme. Their catalytic cycle involves at least four intermediates, some of which are still under debate. While the core reaction, including H2/H- binding, takes place at the inorganic cofactor, a major challenge lies in identifying those amino acid residues that contribute to the reactivity and how they stabilize (short-lived) intermediate states. Using cryogenic infrared and electron paramagnetic resonance spectroscopy on the regulatory [NiFe]-hydrogenase from Cupriavidus necator, a model enzyme for the analysis of catalytic intermediates, we deciphered the structural basis of the hitherto elusive Nia-L intermediates. We unveiled the protonation states of a proton-accepting glutamate and a Ni-bound cysteine residue in the Nia-L1, Nia-L2, and the hydride-binding Nia-C intermediates as well as previously unknown conformational changes of amino acid residues in proximity of the bimetallic active site. As such, this study unravels the complexity of the Nia-L intermediate and reveals the importance of the protein scaffold in fine-tuning proton and electron dynamics in [NiFe]-hydrogenase.
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Affiliation(s)
- Armel F T Waffo
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Christian Lorent
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Sagie Katz
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Janna Schoknecht
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Oliver Lenz
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Ingo Zebger
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Giorgio Caserta
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
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4
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Leone L, Sgueglia G, La Gatta S, Chino M, Nastri F, Lombardi A. Enzymatic and Bioinspired Systems for Hydrogen Production. Int J Mol Sci 2023; 24:ijms24108605. [PMID: 37239950 DOI: 10.3390/ijms24108605] [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: 03/25/2023] [Revised: 04/30/2023] [Accepted: 05/08/2023] [Indexed: 05/28/2023] Open
Abstract
The extraordinary potential of hydrogen as a clean and sustainable fuel has sparked the interest of the scientific community to find environmentally friendly methods for its production. Biological catalysts are the most attractive solution, as they usually operate under mild conditions and do not produce carbon-containing byproducts. Hydrogenases promote reversible proton reduction to hydrogen in a variety of anoxic bacteria and algae, displaying unparallel catalytic performances. Attempts to use these sophisticated enzymes in scalable hydrogen production have been hampered by limitations associated with their production and stability. Inspired by nature, significant efforts have been made in the development of artificial systems able to promote the hydrogen evolution reaction, via either electrochemical or light-driven catalysis. Starting from small-molecule coordination compounds, peptide- and protein-based architectures have been constructed around the catalytic center with the aim of reproducing hydrogenase function into robust, efficient, and cost-effective catalysts. In this review, we first provide an overview of the structural and functional properties of hydrogenases, along with their integration in devices for hydrogen and energy production. Then, we describe the most recent advances in the development of homogeneous hydrogen evolution catalysts envisioned to mimic hydrogenases.
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Affiliation(s)
- Linda Leone
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy
| | - Gianmattia Sgueglia
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy
| | - Salvatore La Gatta
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy
| | - Marco Chino
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy
| | - Flavia Nastri
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy
| | - Angela Lombardi
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy
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Prasad P, Hunt LA, Pall AE, Ranasinghe M, Williams AE, Stemmler TL, Demeler B, Hammer NI, Chakraborty S. Photocatalytic Hydrogen Evolution by a De Novo Designed Metalloprotein that Undergoes Ni-Mediated Oligomerization Shift. Chemistry 2023; 29:e202202902. [PMID: 36440875 PMCID: PMC10308963 DOI: 10.1002/chem.202202902] [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: 09/16/2022] [Revised: 11/25/2022] [Accepted: 11/28/2022] [Indexed: 11/29/2022]
Abstract
De novo metalloprotein design involves the construction of proteins guided by specific repeat patterns of polar and apolar residues, which, upon self-assembly, provide a suitable environment to bind metals and produce artificial metalloenzymes. While a wide range of functionalities have been realized in de novo designed metalloproteins, the functional repertoire of such constructs towards alternative energy-relevant catalysis is currently limited. Here we show the application of de novo approach to design a functional H2 evolving protein. The design involved the assembly of an amphiphilic peptide featuring cysteines at tandem a/d sites of each helix. Intriguingly, upon NiII addition, the oligomers shift from a major trimeric assembly to a mix of dimers and trimers. The metalloprotein produced H2 photocatalytically with a bell-shape pH dependence, having a maximum activity at pH 5.5. Transient absorption spectroscopy is used to determine the timescales of electron transfer as a function of pH. Selective outer sphere mutations are made to probe how the local environment tunes activity. A preferential enhancement of activity is observed via steric modulation above the NiII site, towards the N-termini, compared to below the NiII site towards the C-termini.
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Affiliation(s)
- Pallavi Prasad
- Department of Chemistry and Biochemistry, The University of Mississippi, University, MS, 38677 (USA)
| | - Leigh Anna Hunt
- Department of Chemistry and Biochemistry, The University of Mississippi, University, MS, 38677 (USA)
| | - Ashley E. Pall
- Department of Pharmaceutical Sciences, Wayne State University, 259 Mack Avenue, Detroit, MI, 48201-2417 (USA)
| | - Maduni Ranasinghe
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401,University Dr W, Lethbridge, AB T1K 6T5 (CA)
| | - Ashley E. Williams
- Department of Chemistry and Biochemistry, The University of Mississippi, University, MS, 38677 (USA)
| | - Timothy L. Stemmler
- Department of Pharmaceutical Sciences, Wayne State University, 259 Mack Avenue, Detroit, MI, 48201-2417 (USA)
| | - Borries Demeler
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401,University Dr W, Lethbridge, AB T1K 6T5 (CA)
| | - Nathan I. Hammer
- Department of Chemistry and Biochemistry, The University of Mississippi, University, MS, 38677 (USA)
| | - Saumen Chakraborty
- Department of Chemistry and Biochemistry, The University of Mississippi, University, MS, 38677 (USA)
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Prakash D, Mitra S, Murphy M, Chakraborty S. Oxidation and Peroxygenation of C–H Bonds by Artificial Cu Peptides (ArCuPs): Improved Catalysis via Selective Outer Sphere Modifications. ACS Catal 2022. [DOI: 10.1021/acscatal.2c01882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Divyansh Prakash
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, United States
| | - Suchitra Mitra
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, United States
| | - Morgan Murphy
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, United States
| | - Saumen Chakraborty
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, United States
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