1
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Kim SM, Kang SH, Lee J, Heo Y, Poloniataki EG, Kang J, Yoon HJ, Kong SY, Yun Y, Kim H, Ryu J, Lee HH, Kim YH. Identifying a key spot for electron mediator-interaction to tailor CO dehydrogenase's affinity. Nat Commun 2024; 15:2732. [PMID: 38548760 PMCID: PMC10979024 DOI: 10.1038/s41467-024-46909-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 03/13/2024] [Indexed: 04/01/2024] Open
Abstract
Fe‒S cluster-harboring enzymes, such as carbon monoxide dehydrogenases (CODH), employ sophisticated artificial electron mediators like viologens to serve as potent biocatalysts capable of cleaning-up industrial off-gases at stunning reaction rates. Unraveling the interplay between these enzymes and their associated mediators is essential for improving the efficiency of CODHs. Here we show the electron mediator-interaction site on ChCODHs (Ch, Carboxydothermus hydrogenoformans) using a systematic approach that leverages the viologen-reactive characteristics of superficial aromatic residues. By enhancing mediator-interaction (R57G/N59L) near the D-cluster, the strategically tailored variants exhibit a ten-fold increase in ethyl viologen affinity relative to the wild-type without sacrificing the turn-over rate (kcat). Viologen-complexed structures reveal the pivotal positions of surface phenylalanine residues, serving as external conduits for the D-cluster to/from viologen. One variant (R57G/N59L/A559W) can treat a broad spectrum of waste gases (from steel-process and plastic-gasification) containing O2. Decoding mediator interactions will facilitate the development of industrially high-efficient biocatalysts encompassing gas-utilizing enzymes.
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Affiliation(s)
- Suk Min Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan, 44919, Republic of Korea.
| | - Sung Heuck Kang
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan, 44919, Republic of Korea
| | - Jinhee Lee
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan, 44919, Republic of Korea
| | - Yoonyoung Heo
- Department of Chemistry, College of Natural Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Eleni G Poloniataki
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan, 44919, Republic of Korea
| | - Jingu Kang
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan, 44919, Republic of Korea
| | - Hye-Jin Yoon
- Department of Chemistry, College of Natural Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - So Yeon Kong
- Department of Chemistry, College of Natural Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Yaejin Yun
- Department of Chemistry, College of Natural Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Hyunwoo Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan, 44919, Republic of Korea
| | - Jungki Ryu
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan, 44919, Republic of Korea
| | - Hyung Ho Lee
- Department of Chemistry, College of Natural Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea.
| | - Yong Hwan Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan, 44919, Republic of Korea.
- Graduate School of Carbon Neutrality, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan, 44919, Republic of Korea.
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2
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Jovanovic S, Jakes P, Merz S, Daniel DT, Eichel RA, Granwehr J. In operando NMR investigations of the aqueous electrolyte chemistry during electrolytic CO 2 reduction. Commun Chem 2023; 6:268. [PMID: 38057421 PMCID: PMC10700511 DOI: 10.1038/s42004-023-01065-3] [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: 07/21/2023] [Accepted: 11/20/2023] [Indexed: 12/08/2023] Open
Abstract
The electrolytic reduction of CO2 in aqueous media promises a pathway for the utilization of the green house gas by converting it to base chemicals or building blocks thereof. However, the technology is currently not economically feasible, where one reason lies in insufficient reaction rates and selectivities. Current research of CO2 electrolysis is becoming aware of the importance of the local environment and reactions at the electrodes and their proximity, which can be only assessed under true catalytic conditions, i.e. by in operando techniques. In this work, multinuclear in operando NMR techniques were applied in order to investigate the evolution of the electrolyte chemistry during CO2 electrolysis. The CO2 electroreduction was performed in aqueous NaHCO3 or KHCO3 electrolytes at silver electrodes. Based on 13C and 23Na NMR studies at different magnetic fields, it was found that the dynamic equilibrium of the electrolyte salt in solution, existing as ion pairs and free ions, decelerates with increasingly negative potential. In turn, this equilibrium affects the resupply rate of CO2 to the electrolysis reaction from the electrolyte. Substantiated by relaxation measurements, a mechanism was proposed where stable ion pairs in solution catalyze the bicarbonate dehydration reaction, which may provide a new pathway for improving educt resupply during CO2 electrolysis.
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Affiliation(s)
- Sven Jovanovic
- Institute of Energy and Climate Research - Fundamental Electrochemistry (IEK-9), Forschungszentrum Jülich GmbH, Willhelm-Johnen-Straße, Jülich, Germany.
| | - Peter Jakes
- Institute of Energy and Climate Research - Fundamental Electrochemistry (IEK-9), Forschungszentrum Jülich GmbH, Willhelm-Johnen-Straße, Jülich, Germany
| | - Steffen Merz
- Institute of Energy and Climate Research - Fundamental Electrochemistry (IEK-9), Forschungszentrum Jülich GmbH, Willhelm-Johnen-Straße, Jülich, Germany
| | - Davis Thomas Daniel
- Institute of Energy and Climate Research - Fundamental Electrochemistry (IEK-9), Forschungszentrum Jülich GmbH, Willhelm-Johnen-Straße, Jülich, Germany
| | - Rüdiger-A Eichel
- Institute of Energy and Climate Research - Fundamental Electrochemistry (IEK-9), Forschungszentrum Jülich GmbH, Willhelm-Johnen-Straße, Jülich, Germany
- Institute of Physical Chemistry (IPC), RWTH Aachen University, Aachen, Germany
| | - Josef Granwehr
- Institute of Energy and Climate Research - Fundamental Electrochemistry (IEK-9), Forschungszentrum Jülich GmbH, Willhelm-Johnen-Straße, Jülich, Germany
- Institute of Technical and Macromolecular Chemistry (ITMC), RWTH Aachen University, Aachen, Germany
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3
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Fickenscher Z, Hey-Hawkins E. Added Complexity!-Mechanistic Aspects of Heterobimetallic Complexes for Application in Homogeneous Catalysis. Molecules 2023; 28:4233. [PMID: 37241974 PMCID: PMC10224482 DOI: 10.3390/molecules28104233] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 05/16/2023] [Accepted: 05/17/2023] [Indexed: 05/28/2023] Open
Abstract
Inspired by multimetallic assemblies and their role in enzyme catalysis, chemists have developed a plethora of heterobimetallic complexes for application in homogeneous catalysis. Starting with small heterobimetallic complexes with σ-donating and π-accepting ligands, such as N-heterocyclic carbene and carbonyl ligands, more and more complex systems have been developed over the past two decades. These systems can show a significant increase in catalytic activity compared with their monometallic counterparts. This increase can be attributed to new reaction pathways enabled by the presence of a second metal center in the active catalyst. This review focuses on mechanistic aspects of heterobimetallic complexes in homogeneous catalysis. Depending on the type of interaction of the second metal with the substrates, heterobimetallic complexes can be subdivided into four classes. Each of these classes is illustrated with multiple examples, showcasing the versatility of both, the types of interactions possible, and the reactions accessible.
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Affiliation(s)
| | - Evamarie Hey-Hawkins
- Institute of Inorganic Chemistry, Universität Leipzig, Johannisallee 29, D-04103 Leipzig, Germany;
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4
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Wang KY, Zhang J, Hsu YC, Lin H, Han Z, Pang J, Yang Z, Liang RR, Shi W, Zhou HC. Bioinspired Framework Catalysts: From Enzyme Immobilization to Biomimetic Catalysis. Chem Rev 2023; 123:5347-5420. [PMID: 37043332 PMCID: PMC10853941 DOI: 10.1021/acs.chemrev.2c00879] [Citation(s) in RCA: 48] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Indexed: 04/13/2023]
Abstract
Enzymatic catalysis has fueled considerable interest from chemists due to its high efficiency and selectivity. However, the structural complexity and vulnerability hamper the application potentials of enzymes. Driven by the practical demand for chemical conversion, there is a long-sought quest for bioinspired catalysts reproducing and even surpassing the functions of natural enzymes. As nanoporous materials with high surface areas and crystallinity, metal-organic frameworks (MOFs) represent an exquisite case of how natural enzymes and their active sites are integrated into porous solids, affording bioinspired heterogeneous catalysts with superior stability and customizable structures. In this review, we comprehensively summarize the advances of bioinspired MOFs for catalysis, discuss the design principle of various MOF-based catalysts, such as MOF-enzyme composites and MOFs embedded with active sites, and explore the utility of these catalysts in different reactions. The advantages of MOFs as enzyme mimetics are also highlighted, including confinement, templating effects, and functionality, in comparison with homogeneous supramolecular catalysts. A perspective is provided to discuss potential solutions addressing current challenges in MOF catalysis.
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Affiliation(s)
- Kun-Yu Wang
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
- Department
of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry
(MOE) and Renewable Energy Conversion and Storage Center (RECAST),
College of Chemistry, Nankai University, Tianjin 300071, China
| | - Jiaqi Zhang
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
- Department
of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry
(MOE) and Renewable Energy Conversion and Storage Center (RECAST),
College of Chemistry, Nankai University, Tianjin 300071, China
| | - Yu-Chuan Hsu
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Hengyu Lin
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Zongsu Han
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
- Department
of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry
(MOE) and Renewable Energy Conversion and Storage Center (RECAST),
College of Chemistry, Nankai University, Tianjin 300071, China
| | - Jiandong Pang
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
- School
of Materials Science and Engineering, Tianjin Key Laboratory of Metal
and Molecule-Based Material Chemistry, Nankai
University, Tianjin 300350, China
| | - Zhentao Yang
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
- Department
of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry
(MOE) and Renewable Energy Conversion and Storage Center (RECAST),
College of Chemistry, Nankai University, Tianjin 300071, China
| | - Rong-Ran Liang
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Wei Shi
- Department
of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry
(MOE) and Renewable Energy Conversion and Storage Center (RECAST),
College of Chemistry, Nankai University, Tianjin 300071, China
| | - Hong-Cai Zhou
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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5
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Kash BC, Gomes RJ, Amanchukwu CV. Mitigating Electrode Inactivation during CO 2 Electrocatalysis in Aprotic Solvents with Alkali Cations. J Phys Chem Lett 2023; 14:920-926. [PMID: 36669142 DOI: 10.1021/acs.jpclett.2c03498] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
CO2 electrochemical reduction (CO2R) in aprotic media is a promising alternative to aqueous electrocatalysis, as it minimizes the competing hydrogen evolution reaction while enhancing CO2 solubility. To date, state-of-the-art alkali salts used as electrolytes for selective aqueous CO2R are inaccessible in aprotic systems due to the inactivation of the electrode surface from carbonate deposition. In this work, we demonstrate that an acidic nonaqueous environment enables sustained CO2 electrochemical reduction with common alkali salts in dimethyl sulfoxide. Electrochemical and spectroscopic techniques show that at low pH carbonate buildup can be prevented, allowing CO2R to proceed. Product distribution with a copper electrode revealed up to 80% Faradaic efficiency for CO2R products, including carbon monoxide, formic acid, and methane. By understanding the mechanism for electrode inactivation in an aprotic medium and addressing that challenge with dilute acid addition, we pave the way toward the development of more efficient and selective electrolytes for CO2R.
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Affiliation(s)
- Benjamin C Kash
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois60637, United States
| | - Reginaldo J Gomes
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois60637, United States
| | - Chibueze V Amanchukwu
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois60637, United States
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6
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O2-tolerant CO dehydrogenase via tunnel redesign for the removal of CO from industrial flue gas. Nat Catal 2022. [DOI: 10.1038/s41929-022-00834-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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7
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Piers W, Clapson M, Dubrawski Z, Gelfand B. Facile Deoxygenative Reduction of a Bridging Carbonato Ligand with Silyl and Boryl 4,4’‐Bipyridinylidene Reagents. Z Anorg Allg Chem 2022. [DOI: 10.1002/zaac.202200272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Warren Piers
- University of Calgary Department of Chemistry 2500 University Dr. NW T2N 1N4 Calgary CANADA
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8
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Terranova U. Residues surrounding the active centre of carbon monoxide dehydrogenase are key in converting [Formula: see text] to CO. J Biol Inorg Chem 2021; 26:617-624. [PMID: 34255144 DOI: 10.1007/s00775-021-01878-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 06/17/2021] [Indexed: 10/20/2022]
Abstract
The enzyme carbon monoxide dehydrogenase is capable of efficiently converting [Formula: see text] to CO and, therefore, can enable an affordable [Formula: see text] recycling strategy. The reduction of [Formula: see text] occurs at a peculiar nickel-iron-sulfur cluster, following a mechanism that remains little understood. In this study, we have used ab initio molecular dynamics simulations to explore the free energy landscape of the reaction. We predict the existence of a COOH ligand that strongly interacts with the surrounding protein residues and favours a mechanism where a [Formula: see text] molecule is eliminated before CO. We have taken advantages of the insights offered by our simulations to revisit the catalytic mechanism and the role of the residues surrounding the active centre in particular, thus assisting in the design of inorganic catalysts that mimic the enzyme.
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Affiliation(s)
- Umberto Terranova
- Faculty of Medicine and Health Sciences, Crewe Campus, University of Buckingham, Crewe, CW1 5DU, UK.
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9
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Mulder DW, Peters JW, Raugei S. Catalytic bias in oxidation-reduction catalysis. Chem Commun (Camb) 2021; 57:713-720. [PMID: 33367317 DOI: 10.1039/d0cc07062a] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Cataytic bias refers to the propensity of a reaction catalyst to effect a different rate acceleration in one direction versus the other in a chemical reaction under non-equilibrium conditions. In biocatalysis, the inherent bias of an enzyme is often advantagous to augment the innate thermodynamics of a reaction to promote efficiency and fidelity in the coordination of catabolic and anabolic pathways. In industrial chemical catalysis a directional cataltyic bias is a sought after property in facilitating the engineering of systems that couple catalysis with harvest and storage of for example fine chemicals or energy compounds. Interestingly, there is little information about catalytic bias in biocatalysis likely in large part due to difficulties in developing tractible assays sensitive enough to study detailed kinetics. For oxidation-reduction reactions, colorimetric redox indicators exist in a range of reduction potentials to provide a mechanism to study both directions of reactions in a fairly facile manner. The current short review attempts to define catalytic bias conceptually and to develop model systems for defining the parameters that control catalytic bias in enzyme catalyzed oxidation-reduction catalysis.
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Affiliation(s)
- David W Mulder
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
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10
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Breglia R, Arrigoni F, Sensi M, Greco C, Fantucci P, De Gioia L, Bruschi M. First-Principles Calculations on Ni,Fe-Containing Carbon Monoxide Dehydrogenases Reveal Key Stereoelectronic Features for Binding and Release of CO 2 to/from the C-Cluster. Inorg Chem 2020; 60:387-402. [PMID: 33321036 PMCID: PMC7872322 DOI: 10.1021/acs.inorgchem.0c03034] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
In view of the depletion of fossil
fuel reserves and climatic effects
of greenhouse gas emissions, Ni,Fe-containing carbon monoxide dehydrogenase
(Ni-CODH) enzymes have attracted increasing interest in recent years
for their capability to selectively catalyze the reversible reduction
of CO2 to CO (CO2 + 2H+ + 2e– CO + H2O). The possibility of
converting the greenhouse gas CO2 into useful materials
that can be used as synthetic building blocks or, remarkably, as carbon
fuels makes Ni-CODH a very promising target for reverse-engineering
studies. In this context, in order to provide insights into the chemical
principles underlying the biological catalysis of CO2 activation
and reduction, quantum mechanics calculations have been carried out
in the framework of density functional theory (DFT) on different-sized
models of the Ni-CODH active site. With the aim of uncovering which
stereoelectronic properties of the active site (known as the C-cluster)
are crucial for the efficient binding and release of CO2, different coordination modes of CO2 to different forms
and redox states of the C-cluster have been investigated. The results
obtained from this study highlight the key role of the protein environment
in tuning the reactivity and the geometry of the C-cluster. In particular,
the protonation state of His93 is found to be crucial for promoting
the binding or the dissociation of CO2. The oxidation state
of the C-cluster is also shown to be critical. CO2 binds
to Cred2 according to a dissociative mechanism (i.e., CO2 binds to the C-cluster after the release of possible ligands
from Feu) when His93 is doubly protonated. CO2 can also bind noncatalytically to Cred1 according to
an associative mechanism (i.e., CO2 binding is preceded
by the binding of H2O to Feu). Conversely, CO2 dissociates when His93 is singly protonated and the C-cluster
is oxidized at least to the Cint redox state. Density functional theory was used to investigate Ni,Fe-containing
carbon monoxide dehydrogenase enzymes. Different coordination modes
of the substrate CO2 to several forms and redox states
of the C-cluster—the enzyme active site—were considered.
The obtained results highlight the key role of the protein environment
in tuning the reactivity and the geometry of the C-cluster. This helps
to uncover which stereoelectronic properties of the active site are
crucial for the efficient binding and release of CO2.
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Affiliation(s)
- Raffaella Breglia
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza 1, 20126 Milan, Italy
| | - Federica Arrigoni
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Matteo Sensi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Claudio Greco
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza 1, 20126 Milan, Italy
| | - Piercarlo Fantucci
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Luca De Gioia
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Maurizio Bruschi
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza 1, 20126 Milan, Italy
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11
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Schneider CR, Lewis LC, Shafaat HS. The good, the neutral, and the positive: buffer identity impacts CO 2 reduction activity by nickel(ii) cyclam. Dalton Trans 2019; 48:15810-15821. [PMID: 31560360 PMCID: PMC6843992 DOI: 10.1039/c9dt03114f] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Development of new synthetic catalysts for CO2 reduction has been a central focus of chemical research efforts towards mitigating rising global carbon dioxide levels. In parallel with generating new molecular systems, characterization and benchmarking of these compounds across well-defined catalytic conditions are essential. Nickel(ii) cyclam is known to be an active catalyst for CO2 reduction to CO. The degree of selectivity and activity has been found to differ widely across electrodes used and upon modification of the ligand environment, though without a molecular-level understanding of this variation. Moreover, while proton transfer is key for catalytic activity, the effects of varying the nature of the proton donor remain unclear. In this work, a systematic investigation of the electrochemical and light-driven catalytic behaviour of nickel(ii) cyclam under different aqueous reaction conditions has been performed. The activity and selectivity are seen to vary widely depending on the nature of the buffering agent, even at a constant pH, highlighting the importance of proton transfer for catalysis. Buffer binding to the nickel center is negatively correlated with selectivity, and cationic buffers show high levels of selectivity and activity. These results are discussed in the context of molecular design principles for developing increasingly efficient and selective catalysts. Moreover, identifying these key contributors towards activity has implications for understanding the role of the conserved secondary coordination environments in naturally occurring CO2-reducing enzymes, including carbon monoxide dehydrogenase and formate dehydrogenase.
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Affiliation(s)
- Camille R Schneider
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH, USA
| | - Luke C Lewis
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH, USA.
| | - Hannah S Shafaat
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH, USA and Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH, USA.
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12
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Gottschling K, Stegbauer L, Savasci G, Prisco NA, Berkson ZJ, Ochsenfeld C, Chmelka BF, Lotsch BV. Molecular Insights into Carbon Dioxide Sorption in Hydrazone-Based Covalent Organic Frameworks with Tertiary Amine Moieties. CHEMISTRY OF MATERIALS : A PUBLICATION OF THE AMERICAN CHEMICAL SOCIETY 2019; 31:1946-1955. [PMID: 30930535 PMCID: PMC6438324 DOI: 10.1021/acs.chemmater.8b04643] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 02/12/2019] [Indexed: 05/05/2023]
Abstract
Tailorable sorption properties at the molecular level are key for efficient carbon capture and storage and a hallmark of covalent organic frameworks (COFs). Although amine functional groups are known to facilitate CO2 uptake, atomistic insights into CO2 sorption by COFs modified with amine-bearing functional groups are scarce. Herein, we present a detailed study of the interactions of carbon dioxide and water with two isostructural hydrazone-linked COFs with different polarities based on the 2,5-diethoxyterephthalohydrazide linker. Varying amounts of tertiary amines were introduced in the COF backbones by means of a copolymerization approach using 2,5-bis(2-(dimethylamino)ethoxy)terephthalohydrazide in different amounts ranging from 25 to 100% substitution of the original DETH linker. The interactions of the frameworks with CO2 and H2O were comprehensively studied by means of sorption analysis, solid-state NMR spectroscopy, and quantum-chemical calculations. We show that the addition of the tertiary amine linker increases the overall CO2 sorption capacity normalized by the surface area and of the heat of adsorption, whereas surface areas and pore size diameters decrease. The formation of ammonium bicarbonate species in the COF pores is shown to occur, revealing the contributing role of water for CO2 uptake by amine-modified porous frameworks.
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Affiliation(s)
- Kerstin Gottschling
- Max
Planck Institute for Solid State Research, Heisenbergstraße 1, 70569 Stuttgart, Germany
- Department
of Chemistry, University of Munich (LMU), Butenandtstraße 5-13, 81377 München, Germany
- Nanosystems
Initiative Munich (NIM), Schellingstraße 4, 80799 München, Germany
- Center
for Nanoscience, Schellingstraβe
4, 80799 München, Germany
| | - Linus Stegbauer
- Max
Planck Institute for Solid State Research, Heisenbergstraße 1, 70569 Stuttgart, Germany
- Department
of Chemistry, University of Munich (LMU), Butenandtstraße 5-13, 81377 München, Germany
- Nanosystems
Initiative Munich (NIM), Schellingstraße 4, 80799 München, Germany
| | - Gökcen Savasci
- Max
Planck Institute for Solid State Research, Heisenbergstraße 1, 70569 Stuttgart, Germany
- Department
of Chemistry, University of Munich (LMU), Butenandtstraße 5-13, 81377 München, Germany
- Center
for Nanoscience, Schellingstraβe
4, 80799 München, Germany
| | - Nathan A. Prisco
- Department
of Chemical Engineering, University of California,
Santa Barbara, Santa Barbara, California 93106, United States
| | - Zachariah J. Berkson
- Department
of Chemical Engineering, University of California,
Santa Barbara, Santa Barbara, California 93106, United States
| | - Christian Ochsenfeld
- Department
of Chemistry, University of Munich (LMU), Butenandtstraße 5-13, 81377 München, Germany
- Center
for Nanoscience, Schellingstraβe
4, 80799 München, Germany
| | - Bradley F. Chmelka
- Department
of Chemical Engineering, University of California,
Santa Barbara, Santa Barbara, California 93106, United States
| | - Bettina V. Lotsch
- Max
Planck Institute for Solid State Research, Heisenbergstraße 1, 70569 Stuttgart, Germany
- Department
of Chemistry, University of Munich (LMU), Butenandtstraße 5-13, 81377 München, Germany
- Nanosystems
Initiative Munich (NIM), Schellingstraße 4, 80799 München, Germany
- Center
for Nanoscience, Schellingstraβe
4, 80799 München, Germany
- E-mail:
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13
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Wittenborn EC, Merrouch M, Ueda C, Fradale L, Léger C, Fourmond V, Pandelia ME, Dementin S, Drennan CL. Redox-dependent rearrangements of the NiFeS cluster of carbon monoxide dehydrogenase. eLife 2018; 7:39451. [PMID: 30277213 PMCID: PMC6168284 DOI: 10.7554/elife.39451] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 08/23/2018] [Indexed: 01/03/2023] Open
Abstract
The C-cluster of the enzyme carbon monoxide dehydrogenase (CODH) is a structurally distinctive Ni-Fe-S cluster employed to catalyze the reduction of CO2 to CO as part of the Wood-Ljungdahl carbon fixation pathway. Using X-ray crystallography, we have observed unprecedented conformational dynamics in the C-cluster of the CODH from Desulfovibrio vulgaris, providing the first view of an oxidized state of the cluster. Combined with supporting spectroscopic data, our structures reveal that this novel, oxidized cluster arrangement plays a role in avoiding irreversible oxidative degradation at the C-cluster. Furthermore, mutagenesis of a conserved cysteine residue that binds the C-cluster in the oxidized state but not in the reduced state suggests that the oxidized conformation could be important for proper cluster assembly, in particular Ni incorporation. Together, these results lay a foundation for future investigations of C-cluster activation and assembly, and contribute to an emerging paradigm of metallocluster plasticity.
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Affiliation(s)
- Elizabeth C Wittenborn
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States
| | - Mériem Merrouch
- Aix Marseille Univ, CNRS, Laboratoire de Bioénergétique et Ingénierie des Protéines, Marseille, France
| | - Chie Ueda
- Department of Biochemistry, Brandeis University, Waltham, United States
| | - Laura Fradale
- Aix Marseille Univ, CNRS, Laboratoire de Bioénergétique et Ingénierie des Protéines, Marseille, France
| | - Christophe Léger
- Aix Marseille Univ, CNRS, Laboratoire de Bioénergétique et Ingénierie des Protéines, Marseille, France
| | - Vincent Fourmond
- Aix Marseille Univ, CNRS, Laboratoire de Bioénergétique et Ingénierie des Protéines, Marseille, France
| | | | - Sébastien Dementin
- Aix Marseille Univ, CNRS, Laboratoire de Bioénergétique et Ingénierie des Protéines, Marseille, France
| | - Catherine L Drennan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, United States.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United States.,Bio-inspired Solar Energy Program, Canadian Institute for Advanced Research, Toronto, Canada
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14
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Sonkar PK, Ganesan V, Gupta R, Yadav DK, Yadav M. Nickel phthalocyanine integrated graphene architecture as bifunctional electrocatalyst for CO2 and O2 reductions. J Electroanal Chem (Lausanne) 2018. [DOI: 10.1016/j.jelechem.2018.08.020] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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15
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Buss JA, VanderVelde DG, Agapie T. Lewis Acid Enhancement of Proton Induced CO2 Cleavage: Bond Weakening and Ligand Residence Time Effects. J Am Chem Soc 2018; 140:10121-10125. [DOI: 10.1021/jacs.8b05874] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Joshua A. Buss
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Boulevard MC 127-72, Pasadena, California 91125, United States
| | - David G. VanderVelde
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Boulevard MC 127-72, Pasadena, California 91125, United States
| | - Theodor Agapie
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Boulevard MC 127-72, Pasadena, California 91125, United States
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16
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Giboulot S, Baldino S, Ballico M, Nedden HG, Zuccaccia D, Baratta W. Cyclometalated Dicarbonyl Ruthenium Catalysts for Transfer Hydrogenation and Hydrogenation of Carbonyl Compounds. Organometallics 2018. [DOI: 10.1021/acs.organomet.8b00267] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Steven Giboulot
- Dipartimento DI4A - Università di Udine, Via Cotonificio 108, I-33100 Udine, Italy
- Johnson Matthey, 28 Cambridge Science Park, Milton Road, Cambridge, CB4 0FP, United Kingdom
| | - Salvatore Baldino
- Dipartimento DI4A - Università di Udine, Via Cotonificio 108, I-33100 Udine, Italy
| | - Maurizio Ballico
- Dipartimento DI4A - Università di Udine, Via Cotonificio 108, I-33100 Udine, Italy
| | - Hans Günter Nedden
- Johnson Matthey, 28 Cambridge Science Park, Milton Road, Cambridge, CB4 0FP, United Kingdom
| | - Daniele Zuccaccia
- Dipartimento DI4A - Università di Udine, Via Cotonificio 108, I-33100 Udine, Italy
| | - Walter Baratta
- Dipartimento DI4A - Università di Udine, Via Cotonificio 108, I-33100 Udine, Italy
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17
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Liu M, Hilty C. Metabolic Measurements of Nonpermeating Compounds in Live Cells Using Hyperpolarized NMR. Anal Chem 2018; 90:1217-1222. [PMID: 29227628 PMCID: PMC6200330 DOI: 10.1021/acs.analchem.7b03901] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Hyperpolarization by dissolution dynamic nuclear polarization (D-DNP) has emerged as a technique for enhancing NMR signals by several orders of magnitude, thereby facilitating the characterization of metabolic pathways both in vivo and in vitro. Following the introduction of an externally hyperpolarized compound, real-time NMR enables the measurement of metabolic flux in the corresponding pathway. Spin relaxation however limits the maximum experimental time and prevents the use of this method with compounds exhibiting slow membrane transport rates. Here, we demonstrate that on-line electroporation can serve as a method for membrane permeabilization for use with D-DNP in cell cultures. An electroporation apparatus hyphenated with stopped-flow sample injection permits the introduction of the hyperpolarized metabolite within 3 s after the electrical pulse. In yeast cells that do not readily take up pyruvate, the addition of the electroporation pulse to the D-DNP experiment increases the signals of the downstream metabolic products CO2 and HCO3-, which otherwise are near the detection limit, by 8.2- and 8.6-fold. Modeling of the time dependence of these signals then permits the determination of the respective kinetic rate constants. The observed conversion rate from pyruvate to CO2 normalized for cell density was found to increase by a factor of 12 due to the alleviation of the membrane transport limitation. The use of electroporation therefore extends the applicability of D-DNP to in vitro studies with a wider range of metabolites and at the same time reduces the influence of membrane transport on the observed conversion rates.
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Affiliation(s)
- Mengxiao Liu
- Department of Chemistry, Texas A&M University, 3255 TAMU, College Station, TX 77843, USA
| | - Christian Hilty
- Department of Chemistry, Texas A&M University, 3255 TAMU, College Station, TX 77843, USA
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18
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Puerta-Oteo R, Hölscher M, Jiménez MV, Leitner W, Passarelli V, Pérez-Torrente JJ. Experimental and Theoretical Mechanistic Investigation on the Catalytic CO2 Hydrogenation to Formate by a Carboxylate-Functionalized Bis(N-heterocyclic carbene) Zwitterionic Iridium(I) Compound. Organometallics 2017. [DOI: 10.1021/acs.organomet.7b00509] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Raquel Puerta-Oteo
- Departamento de Química Inorgánica, Instituto de Síntesis Química y Catálisis Homogénea−ISQCH, Facultad de Ciencias, Universidad de Zaragoza−CSIC, C/Pedro Cerbuna, 12, 50009 Zaragoza, Spain
- Institut für Technische und Makromolekulare Chemie, RWTH Aachen University, Worringerweg 2, D-52074 Aachen, Germany
| | - Markus Hölscher
- Institut für Technische und Makromolekulare Chemie, RWTH Aachen University, Worringerweg 2, D-52074 Aachen, Germany
| | - M. Victoria Jiménez
- Departamento de Química Inorgánica, Instituto de Síntesis Química y Catálisis Homogénea−ISQCH, Facultad de Ciencias, Universidad de Zaragoza−CSIC, C/Pedro Cerbuna, 12, 50009 Zaragoza, Spain
| | - Walter Leitner
- Institut für Technische und Makromolekulare Chemie, RWTH Aachen University, Worringerweg 2, D-52074 Aachen, Germany
| | - Vincenzo Passarelli
- Departamento de Química Inorgánica, Instituto de Síntesis Química y Catálisis Homogénea−ISQCH, Facultad de Ciencias, Universidad de Zaragoza−CSIC, C/Pedro Cerbuna, 12, 50009 Zaragoza, Spain
- Centro Universitario de la Defensa, Ctra. Huesca s/n, ES−50090 Zaragoza, Spain
| | - Jesús J. Pérez-Torrente
- Departamento de Química Inorgánica, Instituto de Síntesis Química y Catálisis Homogénea−ISQCH, Facultad de Ciencias, Universidad de Zaragoza−CSIC, C/Pedro Cerbuna, 12, 50009 Zaragoza, Spain
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19
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Diender M, Stams AJM, Sousa DZ. Pathways and Bioenergetics of Anaerobic Carbon Monoxide Fermentation. Front Microbiol 2015; 6:1275. [PMID: 26635746 PMCID: PMC4652020 DOI: 10.3389/fmicb.2015.01275] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 10/31/2015] [Indexed: 11/29/2022] Open
Abstract
Carbon monoxide can act as a substrate for different modes of fermentative anaerobic metabolism. The trait of utilizing CO is spread among a diverse group of microorganisms, including members of bacteria as well as archaea. Over the last decade this metabolism has gained interest due to the potential of converting CO-rich gas, such as synthesis gas, into bio-based products. Three main types of fermentative CO metabolism can be distinguished: hydrogenogenesis, methanogenesis, and acetogenesis, generating hydrogen, methane and acetate, respectively. Here, we review the current knowledge on these three variants of microbial CO metabolism with an emphasis on the potential enzymatic routes and bio-energetics involved.
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Affiliation(s)
- Martijn Diender
- Laboratory of Microbiology, Wageningen University Wageningen, Netherlands
| | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen University Wageningen, Netherlands ; Centre of Biological Engineering, University of Minho Braga, Portugal
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University Wageningen, Netherlands
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20
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Wang VCC, Islam STA, Can M, Ragsdale SW, Armstrong FA. Investigations by Protein Film Electrochemistry of Alternative Reactions of Nickel-Containing Carbon Monoxide Dehydrogenase. J Phys Chem B 2015; 119:13690-7. [PMID: 26176986 DOI: 10.1021/acs.jpcb.5b03098] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein film electrochemistry has been used to investigate reactions of highly active nickel-containing carbon monoxide dehydrogenases (CODHs). When attached to a pyrolytic graphite electrode, these enzymes behave as reversible electrocatalysts, displaying CO2 reduction or CO oxidation at minimal overpotential. The O2 sensitivity of CODH is suppressed by adding cyanide, a reversible inhibitor of CO oxidation, or by raising the electrode potential. Reduction of N2O, isoelectronic with CO2, is catalyzed by CODH, but the reaction is sluggish, despite a large overpotential, and results in inactivation. Production of H2 and formate under highly reducing conditions is consistent with calculations predicting that a nickel-hydrido species might be formed, but the very low rates suggest that such a species is not on the main catalytic pathway.
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Affiliation(s)
- Vincent C-C Wang
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford , South Parks Road, Oxford, OX1 3QR, U.K
| | - Shams T A Islam
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford , South Parks Road, Oxford, OX1 3QR, U.K
| | - Mehmet Can
- 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
| | - Fraser A Armstrong
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford , South Parks Road, Oxford, OX1 3QR, U.K
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21
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Jeoung JH, Goetzl S, Hennig SE, Fesseler J, Wörmann C, Dendra J, Dobbek H. The extended reductive acetyl-CoA pathway: ATPases in metal cluster maturation and reductive activation. Biol Chem 2014; 395:545-58. [PMID: 24477517 DOI: 10.1515/hsz-2013-0290] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 01/27/2014] [Indexed: 11/15/2022]
Abstract
The reductive acetyl-coenzyme A (acetyl-CoA) pathway, also known as the Wood-Ljungdahl pathway, allows reduction and condensation of two molecules of carbon dioxide (CO2) to build the acetyl-group of acetyl-CoA. Productive utilization of CO2 relies on a set of oxygen sensitive metalloenzymes exploiting the metal organic chemistry of nickel and cobalt to synthesize acetyl-CoA from activated one-carbon compounds. In addition to the central catalysts, CO dehydrogenase and acetyl-CoA synthase, ATPases are needed in the pathway. This allows the coupling of ATP binding and hydrolysis to electron transfer against a redox potential gradient and metal incorporation to (re)activate one of the central players of the pathway. This review gives an overview about our current knowledge on how these ATPases achieve their tasks of maturation and reductive activation.
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22
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A Simple, Large-Scale Overexpression Method of Deriving Carbon Monoxide Dehydrogenase II from Thermophilic BacteriumCarboxydothermus hydrogenoformans. Biosci Biotechnol Biochem 2014; 75:1392-4. [DOI: 10.1271/bbb.110159] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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23
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Can M, Armstrong F, Ragsdale SW. Structure, function, and mechanism of the nickel metalloenzymes, CO dehydrogenase, and acetyl-CoA synthase. Chem Rev 2014; 114:4149-74. [PMID: 24521136 PMCID: PMC4002135 DOI: 10.1021/cr400461p] [Citation(s) in RCA: 392] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Indexed: 12/19/2022]
Affiliation(s)
- Mehmet Can
- Department
of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Fraser
A. Armstrong
- Inorganic
Chemistry Laboratory, University of Oxford Oxford, OX1 3QR, United Kingdom
| | - Stephen W. Ragsdale
- Department
of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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24
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Bachmeier A, Wang VCC, Woolerton TW, Bell S, Fontecilla-Camps JC, Can M, Ragsdale SW, Chaudhary YS, Armstrong FA. How light-harvesting semiconductors can alter the bias of reversible electrocatalysts in favor of H2 production and CO2 reduction. J Am Chem Soc 2013; 135:15026-32. [PMID: 24070184 PMCID: PMC3838662 DOI: 10.1021/ja4042675] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The most efficient catalysts for solar fuel production should operate close to reversible potentials, yet possess a bias for the fuel-forming direction. Protein film electrochemical studies of Ni-containing carbon monoxide dehydrogenase and [NiFeSe]-hydrogenase, each a reversible electrocatalyst, show that the electronic state of the electrode strongly biases the direction of electrocatalysis of CO2/CO and H(+)/H2 interconversions. Attached to graphite electrodes, these enzymes show high activities for both oxidation and reduction, but there is a marked shift in bias, in favor of CO2 or H(+) reduction, when the respective enzymes are attached instead to n-type semiconductor electrodes constructed from CdS and TiO2 nanoparticles. This catalytic rectification effect can arise for a reversible electrocatalyst attached to a semiconductor electrode if the electrode transforms between semiconductor- and metallic-like behavior across the same narrow potential range (<0.25 V) that the electrocatalytic current switches between oxidation and reduction.
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Affiliation(s)
- Andreas Bachmeier
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford OX1 3QR, Oxfordshire, United Kingdom
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25
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Wang VCC, Ragsdale SW, Armstrong FA. Investigations of two bidirectional carbon monoxide dehydrogenases from Carboxydothermus hydrogenoformans by protein film electrochemistry. Chembiochem 2013; 14:1845-51. [PMID: 24002936 DOI: 10.1002/cbic.201300270] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Indexed: 11/08/2022]
Abstract
Carbon monoxide dehydrogenases (CODHs) catalyse the reversible conversion between CO and CO2 . Several small molecules or ions are inhibitors and probes for different oxidation states of the unusual [Ni-4 Fe-4 S] cluster that forms the active site. The actions of these small probes on two enzymes-CODH ICh and CODH IICh -produced by Carboxydothermus hydrogenoformans have been studied by protein film voltammetry to compare their behaviour and to establish general characteristics. Whereas CODH ICh is, so far, the better studied of the two isozymes in terms of its electrocatalytic properties, it is CODH IICh that has been characterised by X-ray crystallography. The two isozymes, which share 58.3% sequence identity and 73.9% sequence similarity, show similar patterns of behaviour with regard to selective inhibition of CO2 reduction by CO (product) and cyanate, potent and selective inhibition of CO oxidation by cyanide, and the action of sulfide, which promotes oxidative inactivation of the enzyme. For both isozymes, rates of binding of substrate analogues CN(-) (for CO) and NCO(-) (for CO2 ) are orders of magnitude lower than turnover, a feature that is clearly revealed through hysteresis of cyclic voltammetry. Inhibition by CN(-) and CO is much stronger for CODH IICh than for CODH ICh, a property that has relevance for applying these enzymes as model catalysts in solar-driven CO2 reduction.
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Affiliation(s)
- Vincent C-C Wang
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QR (UK)
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26
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Appel AM, Bercaw JE, Bocarsly AB, Dobbek H, DuBois DL, Dupuis M, Ferry JG, Fujita E, Hille R, Kenis PJA, Kerfeld CA, Morris RH, Peden CHF, Portis AR, Ragsdale SW, Rauchfuss TB, Reek JNH, Seefeldt LC, Thauer RK, Waldrop GL. Frontiers, opportunities, and challenges in biochemical and chemical catalysis of CO2 fixation. Chem Rev 2013; 113:6621-58. [PMID: 23767781 PMCID: PMC3895110 DOI: 10.1021/cr300463y] [Citation(s) in RCA: 1304] [Impact Index Per Article: 118.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Aaron M. Appel
- Institute for Integrated Catalysis, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
| | - John E. Bercaw
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Andrew B. Bocarsly
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Holger Dobbek
- Institut für Biologie, Strukturbiologie/Biochemie, Humboldt Universität zu Berlin, Berlin, Germany
| | - Daniel L. DuBois
- Institute for Integrated Catalysis, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
| | - Michel Dupuis
- Institute for Integrated Catalysis, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
| | - James G. Ferry
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16801, United States
| | - Etsuko Fujita
- Chemistry Department, Brookhaven National Laboratory, Upton, New York 11973-5000, United States
| | - Russ Hille
- Department of Biochemistry, University of California, Riverside, California 92521, United States
| | - Paul J. A. Kenis
- Department of Chemical and Biochemical Engineering, University of Illinois, Urbana, Illinois 61801, United States
| | - Cheryl A. Kerfeld
- DOE Joint Genome Institute, 2800 Mitchell Drive Walnut Creek, California 94598, United States, and Department of Plant and Microbial Biology, University of California, Berkeley, 111 Koshland Hall Berkeley, California 94720, United States
| | - Robert H. Morris
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Charles H. F. Peden
- Institute for Integrated Catalysis, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
| | - Archie R. Portis
- Departments of Crop Sciences and Plant Biology, University of Illinois, Urbana, Illinois 61801, United States
| | - Stephen W. Ragsdale
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Thomas B. Rauchfuss
- Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Joost N. H. Reek
- van’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Lance C. Seefeldt
- Department of Chemistry and Biochemistry, Utah State University, 0300 Old Main Hill, Logan, Utah 84322, United States
| | - Rudolf K. Thauer
- Max Planck Institute for Terrestrial Microbiology, Karl von Frisch Strasse 10, D-35043 Marburg, Germany
| | - Grover L. Waldrop
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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27
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Wang VCC, Can M, Pierce E, Ragsdale SW, Armstrong FA. A unified electrocatalytic description of the action of inhibitors of nickel carbon monoxide dehydrogenase. J Am Chem Soc 2013; 135:2198-206. [PMID: 23368960 PMCID: PMC3894609 DOI: 10.1021/ja308493k] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Several small molecules and ions, notably carbon monoxide, cyanide, cyanate, and hydrogen sulfide, are potent inhibitors of Ni-containing carbon monoxide dehydrogenases (Ni-CODH) that catalyze very rapid, efficient redox interconversions of CO(2) and CO. Protein film electrochemistry, which probes the dependence of steady-state catalytic rate over a wide potential range, reveals how these inhibitors target particular oxidation levels of Ni-CODH relating to intermediates (C(ox), C(red1), and C(red2)) that have been established for the active site. The following properties are thus established: (1) CO suppresses CO(2) reduction (CO is a product inhibitor), but its binding affinity decreases as the potential becomes more negative. (2) Cyanide totally inhibits CO oxidation, but its effect on CO(2) reduction is limited to a narrow potential region (between -0.5 and -0.6 V), below which CO(2) reduction activity is restored. (3) Cyanate is a strong inhibitor of CO(2) reduction but inhibits CO oxidation only within a narrow potential range just above the CO(2)/CO thermodynamic potential--EPR spectra confirm that cyanate binds selectively to C(red2). (4) Hydrogen sulfide (H(2)S/HS(-)) inhibits CO oxidation but not CO(2) reduction--the complex on/off characteristics are consistent with it binding at the same oxidation level as C(ox) and forming a modified version of this inactive state rather than reacting directly with C(red1). The results provide a new perspective on the properties of different catalytic intermediates of Ni-CODH--uniting and clarifying many previous investigations.
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Affiliation(s)
- Vincent C.-C. Wang
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, South Park Road, Oxford OX1 3QR, U.K
| | - Mehmet Can
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109-0606, United States
| | - Elizabeth Pierce
- 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
| | - Fraser A. Armstrong
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, South Park Road, Oxford OX1 3QR, U.K
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28
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Farhana A, Guidry L, Srivastava A, Singh A, Hondalus MK, Steyn AJC. Reductive stress in microbes: implications for understanding Mycobacterium tuberculosis disease and persistence. Adv Microb Physiol 2011; 57:43-117. [PMID: 21078441 DOI: 10.1016/b978-0-12-381045-8.00002-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Mycobacterium tuberculosis (Mtb) is a remarkably successful pathogen that is capable of persisting in host tissues for decades without causing disease. Years after initial infection, the bacilli may resume growth, the outcome of which is active tuberculosis (TB). In order to establish infection, resist host defences and re-emerge, Mtb must coordinate its metabolism with the in vivo environmental conditions and nutrient availability within the primary site of infection, the lung. Maintaining metabolic homeostasis for an intracellular pathogen such as Mtb requires a carefully orchestrated series of oxidation-reduction reactions, which, if unbalanced, generate oxidative or reductive stress. The importance of oxidative stress in microbial pathogenesis has been appreciated and well studied over the past several decades. However, the role of its counterpart, reductive stress, has been largely ignored. Reductive stress is defined as an aberrant increase in reducing equivalents, the magnitude and identity of which is determined by host carbon source utilisation and influenced by the presence of host-generated gases (e.g. NO, CO, O(2) and CO(2)). This increased reductive power must be dissipated for bacterial survival. To recycle reducing equivalents, microbes have evolved unique electron 'sinks' that are distinct for their particular environmental niche. In this review, we describe the specific mechanisms that some microbes have evolved to dispel reductive stress. The intention of this review is to introduce the concept of reductive stress, in tuberculosis research in particular, in the hope of stimulating new avenues of investigation.
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Affiliation(s)
- Aisha Farhana
- Department of Microbiology, University of Alabama at Birmingham, AL, USA
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29
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Kung Y, Drennan CL. A role for nickel-iron cofactors in biological carbon monoxide and carbon dioxide utilization. Curr Opin Chem Biol 2010; 15:276-83. [PMID: 21130022 DOI: 10.1016/j.cbpa.2010.11.005] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Accepted: 11/03/2010] [Indexed: 11/27/2022]
Abstract
Ni-Fe containing enzymes are involved in the biological utilization of carbon monoxide, carbon dioxide, and hydrogen. Interest in these enzymes has increased in recent years due to hydrogen fuel initiatives and concerns over development of new methods for CO2 sequestration. One Ni-Fe enzyme called carbon monoxide dehydrogenase (CODH) is a key player in the global carbon cycle and carries out the interconversion of the environmental pollutant CO and the greenhouse gas CO2. The Ni-Fe center responsible for this important chemistry, the C-cluster, has been the source of much controversy, but several recent structural studies have helped to direct the field toward a unifying mechanism. Here we summarize the current state of understanding of this fascinating metallocluster.
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Affiliation(s)
- Yan Kung
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
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Kung Y, Doukov TI, Seravalli J, Ragsdale SW, Drennan CL. Crystallographic snapshots of cyanide- and water-bound C-clusters from bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase. Biochemistry 2009; 48:7432-40. [PMID: 19583207 PMCID: PMC2721637 DOI: 10.1021/bi900574h] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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Nickel-containing carbon monoxide dehydrogenases (CODHs) reversibly catalyze the oxidation of carbon monoxide to carbon dioxide and are of vital importance in the global carbon cycle. The unusual catalytic CODH C-cluster has been crystallographically characterized as either a NiFe4S4 or a NiFe4S5 metal center, the latter containing a fifth, additional sulfide that bridges Ni and a unique Fe site. To determine whether this bridging sulfide is catalytically relevant and to further explore the mechanism of the C-cluster, we obtained crystal structures of the 310 kDa bifunctional CODH/acetyl-CoA synthase complex from Moorella thermoacetica bound both with a substrate H2O/OH− molecule and with a cyanide inhibitor. X-ray diffraction data were collected from native crystals and from identical crystals soaked in a solution containing potassium cyanide. In both structures, the substrate H2O/OH− molecule exhibits binding to the unique Fe site of the C-cluster. We also observe cyanide binding in a bent conformation to Ni of the C-cluster, adjacent the substrate H2O/OH− molecule. Importantly, the bridging sulfide is not present in either structure. As these forms of the C-cluster represent the coordination environment immediately before the reaction takes place, our findings do not support a fifth, bridging sulfide playing a catalytic role in the enzyme mechanism. The crystal structures presented here, along with recent structures of CODHs from other organisms, have led us toward a unified mechanism for CO oxidation by the C-cluster, the catalytic center of an environmentally important enzyme.
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Affiliation(s)
- Yan Kung
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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Jeoung JH, Dobbek H. Structural Basis of Cyanide Inhibition of Ni, Fe-Containing Carbon Monoxide Dehydrogenase. J Am Chem Soc 2009; 131:9922-3. [DOI: 10.1021/ja9046476] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Jae-Hun Jeoung
- Labor für Bioanorganische Chemie, Universität Bayreuth, Universitätsstrasse 30, 95447 Bayreuth, Germany
| | - Holger Dobbek
- Labor für Bioanorganische Chemie, Universität Bayreuth, Universitätsstrasse 30, 95447 Bayreuth, Germany
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Ragsdale SW, Pierce E. Acetogenesis and the Wood-Ljungdahl pathway of CO(2) fixation. BIOCHIMICA ET BIOPHYSICA ACTA 2008; 1784:1873-98. [PMID: 18801467 PMCID: PMC2646786 DOI: 10.1016/j.bbapap.2008.08.012] [Citation(s) in RCA: 714] [Impact Index Per Article: 44.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2008] [Revised: 08/12/2008] [Accepted: 08/13/2008] [Indexed: 01/04/2023]
Abstract
Conceptually, the simplest way to synthesize an organic molecule is to construct it one carbon at a time. The Wood-Ljungdahl pathway of CO(2) fixation involves this type of stepwise process. The biochemical events that underlie the condensation of two one-carbon units to form the two-carbon compound, acetate, have intrigued chemists, biochemists, and microbiologists for many decades. We begin this review with a description of the biology of acetogenesis. Then, we provide a short history of the important discoveries that have led to the identification of the key components and steps of this usual mechanism of CO and CO(2) fixation. In this historical perspective, we have included reflections that hopefully will sketch the landscape of the controversies, hypotheses, and opinions that led to the key experiments and discoveries. We then describe the properties of the genes and enzymes involved in the pathway and conclude with a section describing some major questions that remain unanswered.
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Affiliation(s)
- Stephen W Ragsdale
- Department of Biological Chemistry, MSRB III, 5301, 1150 W. Medical Center Drive, University of Michigan, Ann Arbor, MI 48109-0606, USA.
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