1
|
Stiebritz MT. MetREx: A protein design approach for the exploration of sequence-reactivity relationships in metalloenzymes. J Comput Chem 2015; 36:553-63. [DOI: 10.1002/jcc.23831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 12/12/2014] [Accepted: 12/16/2014] [Indexed: 01/10/2023]
Affiliation(s)
- Martin T. Stiebritz
- Laboratorium für Physikalische Chemie, ETH Zürich; Vladimir-Prelog-Weg 2 CH-8093 Zürich Switzerland
| |
Collapse
|
2
|
Murray KA, Wodrich MD, Hu X, Corminboeuf C. Toward functional type III [Fe]-hydrogenase biomimics for H2 activation: insights from computation. Chemistry 2015; 21:3987-96. [PMID: 25649221 DOI: 10.1002/chem.201405619] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Indexed: 11/06/2022]
Abstract
The chemistry of [Fe]-hydrogenase has attracted significant interest due to its ability to activate molecular hydrogen. The intriguing properties of this enzyme have prompted the synthesis of numerous small molecule mimics aimed at activating H2. Despite considerable effort, a majority of these compounds remain nonfunctional for hydrogenation reactions. By using a recently synthesized model as an entry point, seven biomimetic complexes have been examined through DFT computations to probe the influence of ligand environment on the ability of a mimic to bind and split H2. One mimic, featuring a bidentate diphosphine group incorporating an internal nitrogen base, was found to have particularly attractive energetics, prompting a study of the role played by the proton/hydride acceptor necessary to complete the catalytic cycle. Computations revealed an experimentally accessible energetic pathway involving a benzaldehyde proton/hydride acceptor and the most promising catalyst.
Collapse
Affiliation(s)
- Kevin A Murray
- Laboratory for Computational Molecular Design, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne (Switzerland)
| | | | | | | |
Collapse
|
3
|
Swanson KD, Ratzloff MW, Mulder DW, Artz JH, Ghose S, Hoffman A, White S, Zadvornyy OA, Broderick JB, Bothner B, King PW, Peters JW. [FeFe]-Hydrogenase Oxygen Inactivation Is Initiated at the H Cluster 2Fe Subcluster. J Am Chem Soc 2015; 137:1809-16. [DOI: 10.1021/ja510169s] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Kevin D. Swanson
- Department
of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Michael W. Ratzloff
- Biosciences
Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - David W. Mulder
- Biosciences
Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Jacob H. Artz
- Department
of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Shourjo Ghose
- Department
of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Andrew Hoffman
- Department
of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Spencer White
- Department
of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Oleg A. Zadvornyy
- Department
of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Joan B. Broderick
- Department
of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Brian Bothner
- Department
of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Paul W. King
- Biosciences
Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - John W. Peters
- Department
of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| |
Collapse
|
4
|
Almazahreh LR, Imhof W, Talarmin J, Schollhammer P, Görls H, El-khateeb M, Weigand W. Ligand effects on the electrochemical behavior of [Fe2(CO)5(L){μ-(SCH2)2(Ph)PO}] (L = PPh3, P(OEt)3) hydrogenase model complexes. Dalton Trans 2015; 44:7177-89. [DOI: 10.1039/c5dt00064e] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
In this paper we study the influence of substituting one CO ligand in [Fe2(CO)6{μ-(SCH2)2(Ph)PO}] (1) by better σ-donors (PPh3(2) and P(OMe)3(3)) in relation to the electrochemical behavior.
Collapse
Affiliation(s)
- Laith R. Almazahreh
- Institut für Anorganische und Analytische Chemie
- Friedrich-Schiller-Universität Jena
- D-07743 Jena
- Germany
| | - Wolfgang Imhof
- Institut für Integrierte Naturwissenschaften
- Universität Koblenz-Landau
- D-56070 Koblenz
- Germany
| | - Jean Talarmin
- UMR CNRS 6521
- Université de Bretagne Occidentale
- 29238 Brest-Cedex
- France
| | | | - Helmar Görls
- Institut für Anorganische und Analytische Chemie
- Friedrich-Schiller-Universität Jena
- D-07743 Jena
- Germany
| | - Mohammad El-khateeb
- Chemistry Department
- Jordan University of Science and Technology
- 22110 Irbid
- Jordan
| | - Wolfgang Weigand
- Institut für Anorganische und Analytische Chemie
- Friedrich-Schiller-Universität Jena
- D-07743 Jena
- Germany
| |
Collapse
|
5
|
Finkelmann AR, Stiebritz MT, Reiher M. Activation Barriers of Oxygen Transformation at the Active Site of [FeFe] Hydrogenases. Inorg Chem 2014; 53:11890-902. [DOI: 10.1021/ic501049z] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Arndt R. Finkelmann
- Laboratorium
für Physikalische
Chemie, ETH Zürich, Valdimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Martin T. Stiebritz
- Laboratorium
für Physikalische
Chemie, ETH Zürich, Valdimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Markus Reiher
- Laboratorium
für Physikalische
Chemie, ETH Zürich, Valdimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| |
Collapse
|
6
|
Kubas A, De Sancho D, Best RB, Blumberger J. Aerobic damage to [FeFe]-hydrogenases: activation barriers for the chemical attachment of O2. Angew Chem Int Ed Engl 2014; 53:4081-4. [PMID: 24615978 PMCID: PMC4143129 DOI: 10.1002/anie.201400534] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Indexed: 11/11/2022]
Abstract
[FeFe]-hydrogenases are the best natural hydrogen-producing enzymes but their biotechnological exploitation is hampered by their extreme oxygen sensitivity. The free energy profile for the chemical attachment of O2 to the enzyme active site was investigated by using a range-separated density functional re-parametrized to reproduce high-level ab initio data. An activation free-energy barrier of 13 kcal mol(-1) was obtained for chemical bond formation between the di-iron active site and O2, a value in good agreement with experimental inactivation rates. The oxygen binding can be viewed as an inner-sphere electron-transfer process that is strongly influenced by Coulombic interactions with the proximal cubane cluster and the protein environment. The implications of these results for future mutation studies with the aim of increasing the oxygen tolerance of this enzyme are discussed.
Collapse
Affiliation(s)
- Adam Kubas
- Department of Physics and Astronomy, University College LondonGower Street, London WC1E 6BT (UK)
| | - David De Sancho
- Department of Chemistry, Cambridge UniversityLensfield Road, Cambridge CB2 1EW (UK)
| | - Robert B Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesda, MD 20892-0520 (USA)
| | - Jochen Blumberger
- Department of Physics and Astronomy, University College LondonGower Street, London WC1E 6BT (UK)
| |
Collapse
|
7
|
Kubas A, De Sancho D, Best RB, Blumberger J. Aerobic Damage to [FeFe]-Hydrogenases: Activation Barriers for the Chemical Attachment of O2. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201400534] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
|
8
|
Finkelmann AR, Stiebritz MT, Reiher M. Inaccessibility of the μ-hydride species in [FeFe] hydrogenases. Chem Sci 2014. [DOI: 10.1039/c3sc51700d] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
|
9
|
Bergeler M, Stiebritz MT, Reiher M. Structure-Property Relationships of Fe4S4Clusters. Chempluschem 2013; 78:1082-1098. [DOI: 10.1002/cplu.201300186] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Indexed: 11/08/2022]
|
10
|
Bruska MK, Stiebritz MT, Reiher M. Analysis of differences in oxygen sensitivity of Fe-S clusters. Dalton Trans 2013; 42:8729-35. [PMID: 23632881 DOI: 10.1039/c3dt50763g] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Many but not all iron-sulphur clusters in metalloproteins are known to be sensitive to molecular oxygen with dramatic consequences for their biological function. We performed a systematic quantum chemical investigation that sheds light on the differences in oxygen sensitivity depending on charge and spin states of these clusters as well as on their spatial fixation by the enzyme's scaffold. We find that significant structural distortions are required to bind O2 exothermically to [Fe2S2] and [Fe3S4] clusters, while only small conformational changes allow for the thermodynamically favorable coordination of molecular oxygen to [Fe4S4] cubanes and [Fe4S3] clusters.
Collapse
Affiliation(s)
- Marta K Bruska
- ETH Zurich, Laboratorium für Physikalische Chemie, Wolfgang-Pauli-Strasse 10, 8093 Zürich, Switzerland
| | | | | |
Collapse
|
11
|
Wodrich MD, Hu X. Electronic Elements Governing the Binding of Small Molecules to a [Fe]-Hydrogenase Mimic. Eur J Inorg Chem 2013. [DOI: 10.1002/ejic.201300081] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
12
|
Finkelmann AR, Stiebritz MT, Reiher M. Kinetic modeling of hydrogen conversion at [Fe] hydrogenase active-site models. J Phys Chem B 2013; 117:4806-17. [PMID: 23560849 DOI: 10.1021/jp312662y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
By means of density functional theory, we investigate the catalytic cycle of active-site model complexes of [Fe] hydrogenase and study how ligand substitutions in the first coordination sphere of the reactive Fe center affect the free-energy surface of the whole reaction pathway. Interestingly, dispersion interactions between the active site and the hydride acceptor MPT render the hydride transfer step less endergonic and lower its barrier. Substitution of CO by CN(-), which resembles [FeFe] hydrogenase-like coordination, inverts the elementary steps H(-) transfer and H2 cleavage. A simplified kinetic model reveals the specifics of the interplay between active-site composition and catalysis. Apparently, the catalytic efficiency of [Fe] hydrogenase can be attributed to a flat energy profile throughout the catalytic cycle. Intermediates that are too stable, as they occur, e.g., when one CO ligand is substituted by CN(-), significantly slow down the turnover rate of the enzyme. The catalytic activity of the wild-type form of the active-site model could, however, be enhanced by a PH3 ligand substitution of the CO ligand.
Collapse
Affiliation(s)
- Arndt R Finkelmann
- Laboratorium für Physikalische Chemie, ETH Zurich, Wolfgang-Pauli-Str. 10, 8093 Zurich, Switzerland
| | | | | |
Collapse
|
13
|
Oxygen tolerance of an in silico-designed bioinspired hydrogen-evolving catalyst in water. Proc Natl Acad Sci U S A 2013; 110:2017-22. [PMID: 23341607 DOI: 10.1073/pnas.1215149110] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Certain bacterial enzymes, the diiron hydrogenases, have turnover numbers for hydrogen production from water as large as 10(4)/s. Their much smaller common active site, composed of earth-abundant materials, has a structure that is an attractive starting point for the design of a practical catalyst for electrocatalytic or solar photocatalytic hydrogen production from water. In earlier work, our group has reported the computational design of [FeFe](P)/FeS(2), a hydrogenase-inspired catalyst/electrode complex, which is efficient and stable throughout the production cycle. However, the diiron hydrogenases are highly sensitive to ambient oxygen by a mechanism not yet understood in detail. An issue critical for practical use of [FeFe](P)/FeS(2) is whether this catalyst/electrode complex is tolerant to the ambient oxygen. We report demonstration by ab initio simulations that the complex is indeed tolerant to dissolved oxygen over timescales long enough for practical application, reducing it efficiently. This promising hydrogen-producing catalyst, composed of earth-abundant materials and with a diffusion-limited rate in acidified water, is efficient as well as oxygen tolerant.
Collapse
|
14
|
Ciaccafava A, Hamon C, Infossi P, Marchi V, Giudici-Orticoni MT, Lojou E. Light-induced reactivation of O2-tolerant membrane-bound [Ni–Fe] hydrogenase from the hyperthermophilic bacterium Aquifex aeolicus under turnover conditions. Phys Chem Chem Phys 2013; 15:16463-7. [DOI: 10.1039/c3cp52596a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
15
|
|
16
|
Abstract
The H(2)-evolving potential of [FeFe] hydrogenases is severely limited by the oxygen sensitivity of this class of enzymes. Recent experimental studies on hydrogenase from C. reinhardtii point to O(2)-induced structural changes in the [Fe(4)S(4)] subsite of the H cluster. Here, we investigate the mechanistic basis of this observation by means of density functional theory. Unexpectedly, we find that the isolated H cluster shows a pathological catalytic activity for the formation of reactive oxygen species such as O(2)(-) and HO(2)(-). After protonation of O(2)(-), an OOH radical may coordinate to the Fe atoms of the cubane, whereas H(2)O(2) specifically reacts with the S atoms of the cubane-coordinating cysteine residues. Both pathways are accompanied by significant structural distortions that compromise cluster integrity and thus catalytic activity. These results explain the experimental observation that O(2)-induced inhibition is accompanied by distortions of the [Fe(4)S(4)] moiety and account for the irreversibility of this process.
Collapse
Affiliation(s)
- Marta K. Bruska
- Laboratorium für Physikalische Chemie, ETH Zurich, Wolfgang-Pauli-Strasse 10 8093 Zürich, Switzerland
| | - Martin T. Stiebritz
- Laboratorium für Physikalische Chemie, ETH Zurich, Wolfgang-Pauli-Strasse 10 8093 Zürich, Switzerland
| | - Markus Reiher
- Laboratorium für Physikalische Chemie, ETH Zurich, Wolfgang-Pauli-Strasse 10 8093 Zürich, Switzerland
| |
Collapse
|