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Gao Y, Wu J, Xia Q, Liu J, Zhu JJ, Zhang JR, Chen X, Zhu W, Chen Z. Operando Spectroscopic Elucidation of the Bubble Sunshade Effect in Inorganic-Biological Hybrids for Photosynthetic Hydrogen Production. ACS NANO 2024; 18:14546-14557. [PMID: 38776420 DOI: 10.1021/acsnano.4c02264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Hydrogen production by photosynthetic hybrid systems (PBSs) offers a promising avenue for renewable energy. However, the light-harvesting efficiency of PBSs remains constrained due to unclear intracellular kinetic factors. Here, we present an operando elucidation of the sluggish light-harvesting behavior for existing PBSs and strategies to circumvent them. By quantifying the spectral shift in the structural color scattering of individual PBSs during the photosynthetic process, we observe the accumulation of product hydrogen bubbles on their outer membrane. These bubbles act as a sunshade and inhibit light absorption. This phenomenon elucidates the intrinsic constraints on the light-harvesting efficiency of PBSs. The introduction of a tension eliminator into the PBSs effectively improves the bubble sunshade effect and results in a 4.5-fold increase in the light-harvesting efficiency. This work provides valuable insights into the dynamics of transmembrane transport gas products and holds the potential to inspire innovative designs for improving the light-harvesting efficiency of PBSs.
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Affiliation(s)
- Yan Gao
- State Key Laboratory of Pollution Control and Resource Reuse, State Key Laboratory of Analytical Chemistry for Life Science, the Frontiers Science Center for Critical Earth Material Cycling, School of the Environment, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Jingyu Wu
- State Key Laboratory of Pollution Control and Resource Reuse, State Key Laboratory of Analytical Chemistry for Life Science, the Frontiers Science Center for Critical Earth Material Cycling, School of the Environment, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Qing Xia
- State Key Laboratory of Pollution Control and Resource Reuse, State Key Laboratory of Analytical Chemistry for Life Science, the Frontiers Science Center for Critical Earth Material Cycling, School of the Environment, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Juan Liu
- State Key Laboratory of Pollution Control and Resource Reuse, State Key Laboratory of Analytical Chemistry for Life Science, the Frontiers Science Center for Critical Earth Material Cycling, School of the Environment, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Jun-Jie Zhu
- State Key Laboratory of Pollution Control and Resource Reuse, State Key Laboratory of Analytical Chemistry for Life Science, the Frontiers Science Center for Critical Earth Material Cycling, School of the Environment, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Jian-Rong Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, State Key Laboratory of Analytical Chemistry for Life Science, the Frontiers Science Center for Critical Earth Material Cycling, School of the Environment, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Xueqin Chen
- State Key Laboratory of Pollution Control and Resource Reuse, State Key Laboratory of Analytical Chemistry for Life Science, the Frontiers Science Center for Critical Earth Material Cycling, School of the Environment, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Wenlei Zhu
- State Key Laboratory of Pollution Control and Resource Reuse, State Key Laboratory of Analytical Chemistry for Life Science, the Frontiers Science Center for Critical Earth Material Cycling, School of the Environment, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Zixuan Chen
- State Key Laboratory of Pollution Control and Resource Reuse, State Key Laboratory of Analytical Chemistry for Life Science, the Frontiers Science Center for Critical Earth Material Cycling, School of the Environment, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
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2
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Wang YZ, Liu HC, Wang JX, Nawab S, Abbas SZ, Zhu D, Mi JL, Zou L, Yong YC. Enzymatic reduction of graphene oxide by a secreted hydrogenase. Biochem Eng J 2024; 204:109220. [DOI: 10.1016/j.bej.2024.109220] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/23/2024]
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3
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Honda Y, Yuki R, Hamakawa R, Fujii H. Photo-Electro-Biochemical H 2 Production Using the Carbon Material-Based Cathode Combined with Genetically Engineered Escherichia coli Whole-Cell Biocatalysis. CHEMSUSCHEM 2024; 17:e202300958. [PMID: 37707171 DOI: 10.1002/cssc.202300958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 09/14/2023] [Accepted: 09/14/2023] [Indexed: 09/15/2023]
Abstract
Abio/bio hybrids, which incorporate biocatalysts that promote efficient and selective material conversions under mild conditions into existing catalytic reactions, have attracted considerable attention for developing new catalytic systems. This study constructed a H2 -forming biocathode based on a carbon material combined with whole-cell biocatalysis of genetically-engineered-hydrogenase-overproducing Escherichia coli for the photoelectrochemical water splitting for clean H2 production. Low-cost and abundant carbon materials are generally not suitable for H2 -forming cathode due to their high overpotential for proton reduction; however, the combination of the reduction of an organic electron mediator on the carbon electrode and the H2 formation with the reduced mediator by the redox enzyme hydrogenase provides a H2 -forming cathodic reaction comparable to that of the noble metal electrode. The present study demonstrates that the recombinant E. coli whole cell can be employed as a part of the H2 -forming biocathode system, and the biocathode system wired with TiO2 photoanode can be a photoelectrochemical water-splitting system without external voltage assistance under natural pH. The findings of this study expand the feasibility of applications of whole-cell biocatalysis and contribute to obtaining solar-to-chemical conversions by abio/bio hybrid systems, especially for low-cost, noble-metal-free, and clean H2 production.
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Affiliation(s)
- Yuki Honda
- Department of Chemistry, Biology, and Environmental Science, Faculty of Science, Nara Women's University Kitauoyanishi-machi, Nara, 630-8506, Japan
| | - Risa Yuki
- Department of Chemistry, Biology, and Environmental Science, Faculty of Science, Nara Women's University Kitauoyanishi-machi, Nara, 630-8506, Japan
| | - Reina Hamakawa
- Department of Chemistry, Biology, and Environmental Science, Faculty of Science, Nara Women's University Kitauoyanishi-machi, Nara, 630-8506, Japan
| | - Hiroshi Fujii
- Department of Chemistry, Biology, and Environmental Science, Faculty of Science, Nara Women's University Kitauoyanishi-machi, Nara, 630-8506, Japan
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4
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Duan J, Veliju A, Lampret O, Liu L, Yadav S, Apfel UP, Armstrong FA, Hemschemeier A, Hofmann E. Insights into the Molecular Mechanism of Formaldehyde Inhibition of [FeFe]-Hydrogenases. J Am Chem Soc 2023; 145:26068-26074. [PMID: 37983562 DOI: 10.1021/jacs.3c07800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
[FeFe]-hydrogenases are efficient H2 converting biocatalysts that are inhibited by formaldehyde (HCHO). The molecular mechanism of this inhibition has so far not been experimentally solved. Here, we obtained high-resolution crystal structures of the HCHO-treated [FeFe]-hydrogenase CpI from Clostridium pasteurianum, showing HCHO reacts with the secondary amine base of the catalytic cofactor and the cysteine C299 of the proton transfer pathway which both are very important for catalytic turnover. Kinetic assays via protein film electrochemistry show the CpI variant C299D is significantly less inhibited by HCHO, corroborating the structural results. By combining our data from protein crystallography, site-directed mutagenesis and protein film electrochemistry, a reaction mechanism involving the cofactor's amine base, the thiol group of C299 and HCHO can be deduced. In addition to the specific case of [FeFe]-hydrogenases, our study provides additional insights into the reactions between HCHO and protein molecules.
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Affiliation(s)
- Jifu Duan
- Photobiotechnology, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Astrit Veliju
- Photobiotechnology, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Oliver Lampret
- Photobiotechnology, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Lingling Liu
- Photobiotechnology, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Shanika Yadav
- Inorganic Chemistry I, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Ulf-Peter Apfel
- Inorganic Chemistry I, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44801 Bochum, Germany
- Department of Energy, Electrosynthesis Group, Fraunhofer UMSICHT, 46047 Oberhausen, Germany
| | - Fraser A Armstrong
- Department of Chemistry, University of Oxford, Oxford OX1 3QR, United Kingdom
| | - Anja Hemschemeier
- Photobiotechnology, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Eckhard Hofmann
- Protein Crystallography, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
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5
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Rutz A, Das CK, Fasano A, Jaenecke J, Yadav S, Apfel UP, Engelbrecht V, Fourmond V, Léger C, Schäfer LV, Happe T. Increasing the O 2 Resistance of the [FeFe]-Hydrogenase CbA5H through Enhanced Protein Flexibility. ACS Catal 2022; 13:856-865. [PMID: 36733639 PMCID: PMC9886219 DOI: 10.1021/acscatal.2c04031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 12/08/2022] [Indexed: 12/29/2022]
Abstract
The high turnover rates of [FeFe]-hydrogenases under mild conditions and at low overpotentials provide a natural blueprint for the design of hydrogen catalysts. However, the unique active site (H-cluster) degrades upon contact with oxygen. The [FeFe]-hydrogenase fromClostridium beijerinckii (CbA5H) is characterized by the flexibility of its protein structure, which allows a conserved cysteine to coordinate to the active site under oxidative conditions. Thereby, intrinsic cofactor degradation induced by dioxygen is minimized. However, the protection from O2 is only partial, and the activity of the enzyme decreases upon each exposure to O2. By using site-directed mutagenesis in combination with electrochemistry, ATR-FTIR spectroscopy, and molecular dynamics simulations, we show that the kinetics of the conversion between the oxygen-protected inactive state (cysteine-bound) and the oxygen-sensitive active state can be accelerated by replacing a surface residue that is very distant from the active site. This sole exchange of methionine for a glutamate residue leads to an increased resistance of the hydrogenase to dioxygen. With our study, we aim to understand how local modifications of the protein structure can have a crucial impact on protein dynamics and how they can control the reactivity of inorganic active sites through outer sphere effects.
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Affiliation(s)
- Andreas Rutz
- Photobiotechnology,
Department of Plant Biochemistry, Ruhr-Universität
Bochum, 44801 Bochum, Germany
| | - Chandan K. Das
- Theoretical
Chemistry, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Andrea Fasano
- Laboratoire
de Bioénergétique et Ingénierie des Protéines, CNRS, Aix-Marseille Université, Institut de
Microbiologie de la Méditerranée, 13009 Marseille, France
| | - Jan Jaenecke
- Photobiotechnology,
Department of Plant Biochemistry, Ruhr-Universität
Bochum, 44801 Bochum, Germany
| | - Shanika Yadav
- Inorganic
Chemistry Ι, Department of Chemistry and Biochemistry, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Ulf-Peter Apfel
- Inorganic
Chemistry Ι, Department of Chemistry and Biochemistry, Ruhr-Universität Bochum, 44801 Bochum, Germany,Fraunhofer
UMSICHT, 46047 Oberhausen, Germany
| | - Vera Engelbrecht
- Photobiotechnology,
Department of Plant Biochemistry, Ruhr-Universität
Bochum, 44801 Bochum, Germany
| | - Vincent Fourmond
- Laboratoire
de Bioénergétique et Ingénierie des Protéines, CNRS, Aix-Marseille Université, Institut de
Microbiologie de la Méditerranée, 13009 Marseille, France
| | - Christophe Léger
- Laboratoire
de Bioénergétique et Ingénierie des Protéines, CNRS, Aix-Marseille Université, Institut de
Microbiologie de la Méditerranée, 13009 Marseille, France
| | - Lars V. Schäfer
- Theoretical
Chemistry, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Thomas Happe
- Photobiotechnology,
Department of Plant Biochemistry, Ruhr-Universität
Bochum, 44801 Bochum, Germany,
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6
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Biswas P, Adhikari A, Pal U, Mondal S, Mukherjee D, Ghosh R, Obaid RJ, Moussa Z, Choudhury SS, Ahmed SA, Das R, Pal SK. A combined spectroscopic and molecular modeling Study on structure-function-dynamics under chemical modification: Alpha-chymotrypsin with formalin preservative. Front Chem 2022; 10:978668. [PMID: 36118312 PMCID: PMC9473634 DOI: 10.3389/fchem.2022.978668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 08/01/2022] [Indexed: 11/13/2022] Open
Abstract
Enzyme function can be altered via modification of its amino acid residues, side chains and large-scale domain modifications. Herein, we have addressed the role of residue modification in catalytic activity and molecular recognition of an enzyme alpha-chymotrypsin (CHT) in presence of a covalent cross-linker formalin. Enzyme assay reveals reduced catalytic activity upon increased formalin concentration. Polarization gated anisotropy studies of a fluorophore 8-Anilino-1-naphthalenesulfonic acid (ANS) in CHT show a dip rise pattern in presence of formalin which is consistent with the generation of multiple ANS binding sites in the enzyme owing to modifications of its local amino acid residues. Molecular docking study on amino acid residue modifications in CHT also indicate towards the formation of multiple ANS binding site. The docking model also predicted no change in binding behavior for the substrate Ala-Ala-Phe-7-amido-4-methylcoumarin (AMC) at the active site upon formalin induced amino acid cross-linking.
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Affiliation(s)
- Pritam Biswas
- Department of Microbiology, St. Xavier’s College, Kolkata, India
| | - Aniruddha Adhikari
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Kolkata, India
| | - Uttam Pal
- Technical Research Centre, S. N. Bose National Centre for Basic Sciences, Kolkata, India
| | - Susmita Mondal
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Kolkata, India
| | - Dipanjan Mukherjee
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Kolkata, India
| | - Ria Ghosh
- Technical Research Centre, S. N. Bose National Centre for Basic Sciences, Kolkata, India
| | - Rami J. Obaid
- Department of Chemistry, Faculty of Applied Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Ziad Moussa
- Department of Chemistry, College of Science, United Arab Emirates University, Al Ain, Abu Dhabi, United Arab Emirates
| | - Sudeshna Shyam Choudhury
- Department of Microbiology, St. Xavier’s College, Kolkata, India
- *Correspondence: Sudeshna Shyam Choudhury, ; Saleh A. Ahmed, ; Ranjan Das, ; Samir Kumar Pal,
| | - Saleh A. Ahmed
- Department of Chemistry, Faculty of Applied Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
- Chemistry Department, Faculty of Science, Assiut University, Assiut, Egypt
- *Correspondence: Sudeshna Shyam Choudhury, ; Saleh A. Ahmed, ; Ranjan Das, ; Samir Kumar Pal,
| | - Ranjan Das
- Department of Chemistry, West Bengal State University, Barasat, Kolkata, India
- *Correspondence: Sudeshna Shyam Choudhury, ; Saleh A. Ahmed, ; Ranjan Das, ; Samir Kumar Pal,
| | - Samir Kumar Pal
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Kolkata, India
- Technical Research Centre, S. N. Bose National Centre for Basic Sciences, Kolkata, India
- *Correspondence: Sudeshna Shyam Choudhury, ; Saleh A. Ahmed, ; Ranjan Das, ; Samir Kumar Pal,
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7
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Chatelain L, Breton JB, Arrigoni F, Schollhammer P, Zampella G. Geometrical influence on the non-biomimetic heterolytic splitting of H 2 by bio-inspired [FeFe]-hydrogenase complexes: a rare example of inverted frustrated Lewis pair based reactivity. Chem Sci 2022; 13:4863-4873. [PMID: 35655865 PMCID: PMC9067592 DOI: 10.1039/d1sc06975f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 03/13/2022] [Indexed: 11/28/2022] Open
Abstract
Despite the high levels of interest in the synthesis of bio-inspired [FeFe]-hydrogenase complexes, H2 oxidation, which is one specific aspect of hydrogenase enzymatic activity, is not observed for most reported complexes. To attempt H-H bond cleavage, two disubstituted diiron dithiolate complexes in the form of [Fe2(μ-pdt)L2(CO)4] (L: PMe3, dmpe) have been used to play the non-biomimetic role of a Lewis base, with frustrated Lewis pairs (FLPs) formed in the presence of B(C6F5)3 Lewis acid. These unprecedented FLPs, based on the bimetallic Lewis base partner, allow the heterolytic splitting of the H2 molecule, forming a protonated diiron cation and hydrido-borate anion. The substitution, symmetrical or asymmetrical, of two phosphine ligands at the diiron dithiolate core induces a strong difference in the H2 bond cleavage abilities, with the FLP based on the first complex being more efficient than the second. DFT investigations examined the different mechanistic pathways involving each accessible isomer and rationalized the experimental findings. One of the main DFT results highlights that the iron site acting as a Lewis base for the asymmetrical complex is the {Fe(CO)3} subunit, which is less electron-rich than the {FeL(CO)2} site of the symmetrical complex, diminishing the reactivity towards H2. Calculations relating to the different mechanistic pathways revealed the presence of a terminal hydride intermediate at the apical site of a rotated {Fe(CO)3} site, which is experimentally observed, and a semi-bridging hydride intermediate from H2 activation at the Fe-Fe site; these are responsible for a favourable back-reaction, reducing the conversion yield observed in the case of the asymmetrical complex. The use of two equivalents of Lewis acid allows for more complete and faster H2 bond cleavage due to the encapsulation of the hydrido-borate species by a second borane, favouring the reactivity of each FLP, in agreement with DFT calculations.
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Affiliation(s)
- Lucile Chatelain
- UMR CNRS 6521 Chimie, Electrochimie Moléculaires et Chimie Analytique, Université de Bretagne Occidentale, UFR Sciences et Techniques 6 Avenue Victor le Gorgeu, CS 93837 Brest-Cedex 3 29238 France
| | - Jean-Baptiste Breton
- UMR CNRS 6521 Chimie, Electrochimie Moléculaires et Chimie Analytique, Université de Bretagne Occidentale, UFR Sciences et Techniques 6 Avenue Victor le Gorgeu, CS 93837 Brest-Cedex 3 29238 France
| | - Federica Arrigoni
- Department of Biotechnology and Bioscience, University of Milano-Bicocca Piazza della Scienza 2 20126 Milan Italy
| | - Philippe Schollhammer
- UMR CNRS 6521 Chimie, Electrochimie Moléculaires et Chimie Analytique, Université de Bretagne Occidentale, UFR Sciences et Techniques 6 Avenue Victor le Gorgeu, CS 93837 Brest-Cedex 3 29238 France
| | - Giuseppe Zampella
- Department of Biotechnology and Bioscience, University of Milano-Bicocca Piazza della Scienza 2 20126 Milan Italy
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8
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Senger M, Kernmayr T, Lorenzi M, Redman HJ, Berggren G. Hydride state accumulation in native [FeFe]-hydrogenase with the physiological reductant H2 supports its catalytic relevance. Chem Commun (Camb) 2022; 58:7184-7187. [PMID: 35670542 PMCID: PMC9219605 DOI: 10.1039/d2cc00671e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Small molecules in solution may interfere with mechanistic investigations, as they can affect the stability of catalytic states and produce off-cycle states that can be mistaken for catalytically relevant species. Here we show that the hydride state (Hhyd), a proposed central intermediate in the catalytic cycle of [FeFe]-hydrogenase, can be formed in wild-type [FeFe]-hydrogenases treated with H2 in absence of other, non-biological, reductants. Moreover, we reveal a new state with unclear role in catalysis induced by common low pH buffers. Studies of enzymatic catalysis often rely on non-biological reagents, which may affect catalytic intermediates and produce off-cycle states. Here the influence of buffer and reductant on key intermediates of [FeFe]-hydrogenase are explored.![]()
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Affiliation(s)
- Moritz Senger
- Department of Chemistry, Physical Chemistry, Uppsala University, 75120 Uppsala, Sweden.
| | - Tobias Kernmayr
- Department of Chemistry, Molecular Biomimetics, Uppsala University, 75120 Uppsala, Sweden.
| | - Marco Lorenzi
- Department of Chemistry, Molecular Biomimetics, Uppsala University, 75120 Uppsala, Sweden.
| | - Holly J Redman
- Department of Chemistry, Molecular Biomimetics, Uppsala University, 75120 Uppsala, Sweden.
| | - Gustav Berggren
- Department of Chemistry, Molecular Biomimetics, Uppsala University, 75120 Uppsala, Sweden.
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9
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Zhang F, Woods TJ, Zhu L, Rauchfuss TB. Inhibition of [FeFe]-hydrogenase by formaldehyde: proposed mechanism and reactivity of FeFe alkyl complexes. Chem Sci 2021; 12:15673-15681. [PMID: 35003598 PMCID: PMC8653999 DOI: 10.1039/d1sc05803g] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 11/15/2021] [Indexed: 11/21/2022] Open
Abstract
The mechanism for inhibition of [FeFe]-hydrogenases by formaldehyde is examined with model complexes. Key findings: (i) CH2 donated by formaldehyde covalently link Fe and the amine cofactor, blocking the active site and (ii) the resulting Fe-alkyl is a versatile electrophilic alkylating agent. Solutions of Fe2[(μ-SCH2)2NH](CO)4(PMe3)2 (1) react with a mixture of HBF4 and CH2O to give three isomers of [Fe2[(μ-SCH2)2NCH2](CO)4(PMe3)2]+ ([2]+). X-ray crystallography verified the NCH2Fe linkage to an octahedral Fe(ii) site. Although [2]+ is stereochemically rigid on the NMR timescale, spin-saturation transfer experiments implicate reversible dissociation of the Fe-CH2 bond, allowing interchange of all three diastereoisomers. Using 13CH2O, the methylenation begins with formation of [Fe2[(μ-SCH2)2N13CH2OH](CO)4(PMe3)2]+. Protonation converts this hydroxymethyl derivative to [2]+, concomitant with 13C-labelling of all three methylene groups. The Fe-CH2N bond in [2]+ is electrophilic: PPh3, hydroxide, and hydride give, respectively, the phosphonium [Fe2[(μ-SCH2)2NCH2PPh3](CO)4(PMe3)2]+, 1, and the methylamine Fe2[(μ-SCH2)2NCH3](CO)4(PMe3)2. The reaction of [Fe2[(μ-SCH2)2NH](CN)2(CO)4]2- with CH2O/HBF4 gave [Fe2[(μ-SCH2)2NCH2CN](CN)(CO)5]- ([4]-), the result of reductive elimination from [Fe2[(μ-SCH2)2NCH2](CN)2(CO)4]-. The phosphine derivative [Fe2[(μ-SCH2)2NCH2CN](CN)(CO)4(PPh3)]- ([5]-) was characterized crystallographically.
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Affiliation(s)
- Fanjun Zhang
- School of Chemical Sciences, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Toby J Woods
- School of Chemical Sciences, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Lingyang Zhu
- School of Chemical Sciences, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Thomas B Rauchfuss
- School of Chemical Sciences, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
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10
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Abstract
[FeFe]-hydrogenases are efficient H2-catalysts, yet upon contact with dioxygen their catalytic cofactor (H-cluster) is irreversibly inactivated. Here, we combine X-ray crystallography, rational protein design, direct electrochemistry, and Fourier-transform infrared spectroscopy to describe a protein morphing mechanism that controls the reversible transition between the catalytic Hox-state and the inactive but oxygen-resistant Hinact-state in [FeFe]-hydrogenase CbA5H of Clostridium beijerinckii. The X-ray structure of air-exposed CbA5H reveals that a conserved cysteine residue in the local environment of the active site (H-cluster) directly coordinates the substrate-binding site, providing a safety cap that prevents O2-binding and consequently, cofactor degradation. This protection mechanism depends on three non-conserved amino acids situated approximately 13 Å away from the H-cluster, demonstrating that the 1st coordination sphere chemistry of the H-cluster can be remote-controlled by distant residues.
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11
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Benoit SL, Maier RJ, Sawers RG, Greening C. Molecular Hydrogen Metabolism: a Widespread Trait of Pathogenic Bacteria and Protists. Microbiol Mol Biol Rev 2020; 84:e00092-19. [PMID: 31996394 PMCID: PMC7167206 DOI: 10.1128/mmbr.00092-19] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Pathogenic microorganisms use various mechanisms to conserve energy in host tissues and environmental reservoirs. One widespread but often overlooked means of energy conservation is through the consumption or production of molecular hydrogen (H2). Here, we comprehensively review the distribution, biochemistry, and physiology of H2 metabolism in pathogens. Over 200 pathogens and pathobionts carry genes for hydrogenases, the enzymes responsible for H2 oxidation and/or production. Furthermore, at least 46 of these species have been experimentally shown to consume or produce H2 Several major human pathogens use the large amounts of H2 produced by colonic microbiota as an energy source for aerobic or anaerobic respiration. This process has been shown to be critical for growth and virulence of the gastrointestinal bacteria Salmonella enterica serovar Typhimurium, Campylobacter jejuni, Campylobacter concisus, and Helicobacter pylori (including carcinogenic strains). H2 oxidation is generally a facultative trait controlled by central regulators in response to energy and oxidant availability. Other bacterial and protist pathogens produce H2 as a diffusible end product of fermentation processes. These include facultative anaerobes such as Escherichia coli, S Typhimurium, and Giardia intestinalis, which persist by fermentation when limited for respiratory electron acceptors, as well as obligate anaerobes, such as Clostridium perfringens, Clostridioides difficile, and Trichomonas vaginalis, that produce large amounts of H2 during growth. Overall, there is a rich literature on hydrogenases in growth, survival, and virulence in some pathogens. However, we lack a detailed understanding of H2 metabolism in most pathogens, especially obligately anaerobic bacteria, as well as a holistic understanding of gastrointestinal H2 transactions overall. Based on these findings, we also evaluate H2 metabolism as a possible target for drug development or other therapies.
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Affiliation(s)
- Stéphane L Benoit
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Robert J Maier
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - R Gary Sawers
- Institute of Microbiology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Chris Greening
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
- Department of Microbiology, Monash Biomedicine Discovery Institute, Clayton, VIC, Australia
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12
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Barrio M, Fourmond V. Redox (In)activations of Metalloenzymes: A Protein Film Voltammetry Approach. ChemElectroChem 2019. [DOI: 10.1002/celc.201901028] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Melisa Barrio
- CNRSAix-Marseille Université, BIP UMR 7281 31 chemin J. Aiguier F-13402 Marseille cedex 20 France
| | - Vincent Fourmond
- CNRSAix-Marseille Université, BIP UMR 7281 31 chemin J. Aiguier F-13402 Marseille cedex 20 France
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Mebs S, Duan J, Wittkamp F, Stripp ST, Happe T, Apfel UP, Winkler M, Haumann M. Differential Protonation at the Catalytic Six-Iron Cofactor of [FeFe]-Hydrogenases Revealed by 57Fe Nuclear Resonance X-ray Scattering and Quantum Mechanics/Molecular Mechanics Analyses. Inorg Chem 2019; 58:4000-4013. [PMID: 30802044 DOI: 10.1021/acs.inorgchem.9b00100] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
[FeFe]-hydrogenases are efficient biological hydrogen conversion catalysts and blueprints for technological fuel production. The relations between substrate interactions and electron/proton transfer events at their unique six-iron cofactor (H-cluster) need to be elucidated. The H-cluster comprises a four-iron cluster, [4Fe4S], linked to a diiron complex, [FeFe]. We combined 57Fe-specific X-ray nuclear resonance scattering experiments (NFS, nuclear forward scattering; NRVS, nuclear resonance vibrational spectroscopy) with quantum-mechanics/molecular-mechanics computations to study the [FeFe]-hydrogenase HYDA1 from a green alga. Selective 57Fe labeling at only [4Fe4S] or [FeFe], or at both subcomplexes was achieved by protein expression with a 57Fe salt and in vitro maturation with a synthetic diiron site precursor containing 57Fe. H-cluster states were populated under infrared spectroscopy control. NRVS spectral analyses facilitated assignment of the vibrational modes of the cofactor species. This approach revealed the H-cluster structure of the oxidized state (Hox) with a bridging carbon monoxide at [FeFe] and ligand rearrangement in the CO-inhibited state (Hox-CO). Protonation at a cysteine ligand of [4Fe4S] in the oxidized state occurring at low pH (HoxH) was indicated, in contrast to bridging hydride binding at [FeFe] in a one-electron reduced state (Hred). These findings are direct evidence for differential protonation either at the four-iron or diiron subcomplex of the H-cluster. NFS time-traces provided Mössbauer parameters such as the quadrupole splitting energy, which differ among cofactor states, thereby supporting selective protonation at either subcomplex. In combination with data for reduced states showing similar [4Fe4S] protonation as HoxH without (Hred') or with (Hhyd) a terminal hydride at [FeFe], our results imply that coordination geometry dynamics at the diiron site and proton-coupled electron transfer to either the four-iron or the diiron subcomplex discriminate catalytic and regulatory functions of [FeFe]-hydrogenases. We support a reaction cycle avoiding diiron site geometry changes during rapid H2 turnover.
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Affiliation(s)
| | | | | | | | | | - Ulf-Peter Apfel
- Fraunhofer UMSICHT , Osterfelder Straße 3 , 46047 Oberhausen , Germany
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Bachmeier A, Esselborn J, Hexter SV, Krämer T, Klein K, Happe T, McGrady JE, Myers WK, Armstrong FA. How Formaldehyde Inhibits Hydrogen Evolution by [FeFe]-Hydrogenases: Determination by ¹³C ENDOR of Direct Fe-C Coordination and Order of Electron and Proton Transfers. J Am Chem Soc 2015; 137:5381-9. [PMID: 25871921 DOI: 10.1021/ja513074m] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Formaldehyde (HCHO), a strong electrophile and a rapid and reversible inhibitor of hydrogen production by [FeFe]-hydrogenases, is used to identify the point in the catalytic cycle at which a highly reactive metal-hydrido species is formed. Investigations of the reaction of Chlamydomonas reinhardtii [FeFe]-hydrogenase with formaldehyde using pulsed-EPR techniques including electron-nuclear double resonance spectroscopy establish that formaldehyde binds close to the active site. Density functional theory calculations support an inhibited super-reduced state having a short Fe-(13)C bond in the 2Fe subsite. The adduct forms when HCHO is available to compete with H(+) transfer to a vacant, nucleophilic Fe site: had H(+) transfer already occurred, the reaction of HCHO with the Fe-hydrido species would lead to methanol, release of which is not detected. Instead, Fe-bound formaldehyde is a metal-hydrido mimic, a locked, inhibited form analogous to that in which two electrons and only one proton have transferred to the H-cluster. The results provide strong support for a mechanism in which the fastest pathway for H2 evolution involves two consecutive proton transfer steps to the H-cluster following transfer of a second electron to the active site.
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Affiliation(s)
- Andreas Bachmeier
- †Inorganic Chemistry Laboratory and ‡Centre for Advanced Electron Spin Resonance, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom.,§Lehrstuhl für Biochemie der Pflanzen, AG Photobiotechnologie and ∥Lehrstuhl für Anorganische Chemie I, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Julian Esselborn
- †Inorganic Chemistry Laboratory and ‡Centre for Advanced Electron Spin Resonance, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom.,§Lehrstuhl für Biochemie der Pflanzen, AG Photobiotechnologie and ∥Lehrstuhl für Anorganische Chemie I, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Suzannah V Hexter
- †Inorganic Chemistry Laboratory and ‡Centre for Advanced Electron Spin Resonance, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom.,§Lehrstuhl für Biochemie der Pflanzen, AG Photobiotechnologie and ∥Lehrstuhl für Anorganische Chemie I, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Tobias Krämer
- †Inorganic Chemistry Laboratory and ‡Centre for Advanced Electron Spin Resonance, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom.,§Lehrstuhl für Biochemie der Pflanzen, AG Photobiotechnologie and ∥Lehrstuhl für Anorganische Chemie I, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Kathrin Klein
- †Inorganic Chemistry Laboratory and ‡Centre for Advanced Electron Spin Resonance, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom.,§Lehrstuhl für Biochemie der Pflanzen, AG Photobiotechnologie and ∥Lehrstuhl für Anorganische Chemie I, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Thomas Happe
- †Inorganic Chemistry Laboratory and ‡Centre for Advanced Electron Spin Resonance, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom.,§Lehrstuhl für Biochemie der Pflanzen, AG Photobiotechnologie and ∥Lehrstuhl für Anorganische Chemie I, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - John E McGrady
- †Inorganic Chemistry Laboratory and ‡Centre for Advanced Electron Spin Resonance, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom.,§Lehrstuhl für Biochemie der Pflanzen, AG Photobiotechnologie and ∥Lehrstuhl für Anorganische Chemie I, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - William K Myers
- †Inorganic Chemistry Laboratory and ‡Centre for Advanced Electron Spin Resonance, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom.,§Lehrstuhl für Biochemie der Pflanzen, AG Photobiotechnologie and ∥Lehrstuhl für Anorganische Chemie I, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Fraser A Armstrong
- †Inorganic Chemistry Laboratory and ‡Centre for Advanced Electron Spin Resonance, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom.,§Lehrstuhl für Biochemie der Pflanzen, AG Photobiotechnologie and ∥Lehrstuhl für Anorganische Chemie I, Ruhr-Universität Bochum, 44801 Bochum, Germany
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15
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Chernev P, Lambertz C, Brünje A, Leidel N, Sigfridsson KGV, Kositzki R, Hsieh CH, Yao S, Schiwon R, Driess M, Limberg C, Happe T, Haumann M. Hydride Binding to the Active Site of [FeFe]-Hydrogenase. Inorg Chem 2014; 53:12164-77. [DOI: 10.1021/ic502047q] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Petko Chernev
- Institute for Experimental
Physics, Free University Berlin, 14195 Berlin, Germany
| | - Camilla Lambertz
- Institute for Biochemistry of Plants, Department
of Photobiotechnology, Ruhr-University Bochum, 44801 Bochum, Germany
| | - Annika Brünje
- Institute for Biochemistry of Plants, Department
of Photobiotechnology, Ruhr-University Bochum, 44801 Bochum, Germany
| | - Nils Leidel
- Institute for Experimental
Physics, Free University Berlin, 14195 Berlin, Germany
| | | | - Ramona Kositzki
- Institute for Experimental
Physics, Free University Berlin, 14195 Berlin, Germany
| | - Chung-Hung Hsieh
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Shenglai Yao
- Department of Chemistry, Technical University Berlin, 10623 Berlin, Germany
| | - Rafael Schiwon
- Department of Chemistry, Humboldt University Berlin, 12489 Berlin, Germany
| | - Matthias Driess
- Department of Chemistry, Technical University Berlin, 10623 Berlin, Germany
| | - Christian Limberg
- Department of Chemistry, Humboldt University Berlin, 12489 Berlin, Germany
| | - Thomas Happe
- Institute for Biochemistry of Plants, Department
of Photobiotechnology, Ruhr-University Bochum, 44801 Bochum, Germany
| | - Michael Haumann
- Institute for Experimental
Physics, Free University Berlin, 14195 Berlin, Germany
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16
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Affiliation(s)
- Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Hideaki Ogata
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Olaf Rüdiger
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Edward Reijerse
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
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17
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Lambertz C, Chernev P, Klingan K, Leidel N, Sigfridsson KGV, Happe T, Haumann M. Electronic and molecular structures of the active-site H-cluster in [FeFe]-hydrogenase determined by site-selective X-ray spectroscopy and quantum chemical calculations. Chem Sci 2014. [DOI: 10.1039/c3sc52703d] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Site-selective X-ray spectroscopy discriminated the cubane and diiron units in the H-cluster of [FeFe]-hydrogenase revealing its electronic and structural configurations.
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Affiliation(s)
- Camilla Lambertz
- Institute for Biochemistry of Plants
- Department of Photobiotechnology
- Ruhr-University Bochum
- 44780 Bochum, Germany
| | - Petko Chernev
- Institute for Experimental Physics
- Freie Universität Berlin
- FB Physik
- 14195 Berlin, Germany
| | - Katharina Klingan
- Institute for Experimental Physics
- Freie Universität Berlin
- FB Physik
- 14195 Berlin, Germany
| | - Nils Leidel
- Institute for Experimental Physics
- Freie Universität Berlin
- FB Physik
- 14195 Berlin, Germany
| | | | - Thomas Happe
- Institute for Biochemistry of Plants
- Department of Photobiotechnology
- Ruhr-University Bochum
- 44780 Bochum, Germany
| | - Michael Haumann
- Institute for Experimental Physics
- Freie Universität Berlin
- FB Physik
- 14195 Berlin, Germany
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18
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Kaur-Ghumaan S, Stein M. [NiFe] hydrogenases: how close do structural and functional mimics approach the active site? Dalton Trans 2014; 43:9392-405. [DOI: 10.1039/c4dt00539b] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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19
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Does the environment around the H-cluster allow coordination of the pendant amine to the catalytic iron center in [FeFe] hydrogenases? Answers from theory. J Biol Inorg Chem 2013; 18:693-700. [DOI: 10.1007/s00775-013-1014-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Accepted: 05/29/2013] [Indexed: 01/08/2023]
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Winkler M, Esselborn J, Happe T. Molecular basis of [FeFe]-hydrogenase function: an insight into the complex interplay between protein and catalytic cofactor. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:974-85. [PMID: 23507618 DOI: 10.1016/j.bbabio.2013.03.004] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Revised: 02/21/2013] [Accepted: 03/08/2013] [Indexed: 12/20/2022]
Abstract
The precise electrochemical features of metal cofactors that convey the functions of redox enzymes are essentially determined by the specific interaction pattern between cofactor and enclosing protein environment. However, while biophysical techniques allow a detailed understanding of the features characterizing the cofactor itself, knowledge about the contribution of the protein part is much harder to obtain. [FeFe]-hydrogenases are an interesting class of enzymes that catalyze both, H2 oxidation and the reduction of protons to molecular hydrogen with significant efficiency. The active site of these proteins consists of an unusual prosthetic group (H-cluster) with six iron and six sulfur atoms. While H-cluster architecture and catalytic states during the different steps of H2 turnover have been thoroughly investigated during the last 20 years, possible functional contributions from the polypeptide framework were only assumed according to the level of conservancy and X-ray structure analyses. Due to the recent development of simpler and more efficient expression systems the role of single amino acids can now be experimentally investigated. This article summarizes, compares and categorizes the results of recent investigations based on site directed and random mutagenesis according to their informative value about structure function relationships in [FeFe]-hydrogenases. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems.
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Affiliation(s)
- Martin Winkler
- Ruhr-Universität Bochum, Fakultät für Biologie und Biotechnologie, Lehrstuhl für Biochemie der Pflanzen, AG Photobiotechnologie, Bochum, Germany
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21
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Foster CE, Krämer T, Wait AF, Parkin A, Jennings DP, Happe T, McGrady JE, Armstrong FA. Inhibition of [FeFe]-hydrogenases by formaldehyde and wider mechanistic implications for biohydrogen activation. J Am Chem Soc 2012; 134:7553-7. [PMID: 22512303 DOI: 10.1021/ja302096r] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Formaldehyde-a rapid and reversible inhibitor of hydrogen evolution by [FeFe]-hydrogenases-binds with a strong potential dependence that is almost complementary to that of CO. Whereas exogenous CO binds tightly to the oxidized state known as H(ox) but very weakly to a state two electrons more reduced, formaldehyde interacts most strongly with the latter. Formaldehyde thus intercepts increasingly reduced states of the catalytic cycle, and density functional theory calculations support the proposal that it reacts with the H-cluster directly, most likely targeting an otherwise elusive and highly reactive Fe-hydrido (Fe-H) intermediate.
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Affiliation(s)
- Carina E Foster
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, OX1 3QR, United Kingdom
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22
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Insights into [FeFe]-hydrogenase structure, mechanism, and maturation. Structure 2011; 19:1038-52. [PMID: 21827941 DOI: 10.1016/j.str.2011.06.008] [Citation(s) in RCA: 158] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Revised: 06/01/2011] [Accepted: 06/09/2011] [Indexed: 01/06/2023]
Abstract
Hydrogenases are metalloenzymes that are key to energy metabolism in a variety of microbial communities. Divided into three classes based on their metal content, the [Fe]-, [FeFe]-, and [NiFe]-hydrogenases are evolutionarily unrelated but share similar nonprotein ligand assemblies at their active site metal centers that are not observed elsewhere in biology. These nonprotein ligands are critical in tuning enzyme reactivity, and their synthesis and incorporation into the active site clusters require a number of specific maturation enzymes. The wealth of structural information on different classes and different states of hydrogenase enzymes, biosynthetic intermediates, and maturation enzymes has contributed significantly to understanding the biochemistry of hydrogen metabolism. This review highlights the unique structural features of hydrogenases and emphasizes the recent biochemical and structural work that has created a clearer picture of the [FeFe]-hydrogenase maturation pathway.
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Knörzer P, Silakov A, Foster CE, Armstrong FA, Lubitz W, Happe T. Importance of the protein framework for catalytic activity of [FeFe]-hydrogenases. J Biol Chem 2011; 287:1489-99. [PMID: 22110126 DOI: 10.1074/jbc.m111.305797] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The active center (H-cluster) of [FeFe]-hydrogenases is embedded into a hydrophobic pocket within the protein. We analyzed several amino acids, located in the vicinity of this niche, by site-directed mutagenesis of the [FeFe]-hydrogenases from Clostridium pasteurianum (CpI) and Chlamydomonas reinhardtii (CrHydA1). These amino acids are highly conserved and predicted to be involved in H-cluster coordination. Characterization of two hydrogenase variants confirmed this hypothesis. The exchange of residues CrHydA1Met(415) and CrHydA1Lys(228) resulted in inactive proteins, which, according to EPR and FTIR analyses, contain no intact H-cluster. However, [FeFe]-hydrogenases in which CpIMet(353) (CrHydA1Met(223)) and CpICys(299) (CrHydA1Cys(169)) were exchanged to leucine and serine, respectively, showed a structurally intact H-cluster with catalytic activity either absent (CpIC299S) or strongly diminished (CpIM353L). In the case of CrHydA1C169S, the H-cluster was trapped in an inactive state exhibiting g values and vibrational frequencies that resembled the H(trans) state of DdH from Desulfovibrio desulfuricans. This cysteine residue, interacting with the bridge head nitrogen of the di(methyl)amine ligand, seems therefore to represent an essential contribution of the immediate protein environment to the reaction mechanism. Exchanging methionine CpIM(353) (CrHydA1M(223)) to leucine led to a strong decrease in turnover without affecting the K(m) value of the electron donor. We suggest that this methionine constitutes a "fine-tuning" element of hydrogenase activity.
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Affiliation(s)
- Philipp Knörzer
- AG Photobiotechnologie, Lehrstuhl für Biochemie der Pflanzen, Ruhr-Universität Bochum, 44780 Bochum, Germany
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