The role of the high potential [3Fe-4S]1+,0 cluster of [NiFe] hydrogenase from Desulfovibrio species located halfway between the proximal and distal low potential [4Fe-4S]2+,1+ clusters has been investigated by using site-directed mutagenesis. Proline 238 of Desulfovibrio fructosovorans [NiFe] hydrogenase, which occupies the position of a potential ligand of the lacking fourth Fe-site of the [3Fe-4S] cluster, was replaced by a cysteine residue. The properties of the mutant enzyme were investigated in terms of enzymatic activity, EPR, and redox properties of the iron-sulfur centers and crystallographic structure. We have shown on the basis of both spectroscopic and x-ray crystallographic studies that the [3Fe-4S] cluster of D. fructosovorans hydrogenase was converted into a [4Fe-4S] center in the P238 mutant. The [3Fe-4S] to [4Fe-4S] cluster conversion resulted in a lowering of approximately 300 mV of the midpoint potential of the modified cluster, whereas no significant alteration of the spectroscopic and redox properties of the two native [4Fe-4S] clusters and the NiFe center occurred. The significant decrease of the midpoint potential of the intermediate Fe-S cluster had only a slight effect on the catalytic activity of the P238C mutant as compared with the wild-type enzyme. The implications of the results for the role of the high-potential [3Fe-4S] cluster in the intramolecular electron transfer pathway are discussed.
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http://dx.doi.org/10.1073/pnas.95.20.11625 | DOI Listing |
J Chem Theory Comput
January 2025
Max-Planck-Institute for Solid State Research, Heisenbergstraße 1, 70569 Stuttgart, Germany.
A new method to perform complete active space second-order perturbation theory on top of large active spaces optimized with full configuration quantum Monte Carlo is presented. Computing the three- and Fock-contracted four-particle density matrix from imaginary-time-averaged wave functions is found to resolve fermionic positivity violations and to ensure numerical stability. The protocol is applied to [NiFe]-hydrogenase, [CuO]-oxidase and Fe-porphyrin model systems up to 26 electrons in 27 orbitals and benchmarked against DMRG-CASPT2.
View Article and Find Full Text PDFJ Chem Inf Model
January 2025
Institute of Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, Berlin 10623, Germany.
Machine learning (ML) is a powerful tool for the automated data analysis of molecular dynamics (MD) simulations. Recent studies showed that ML models can be used to identify protein-ligand unbinding pathways and understand the underlying mechanism. To expedite the examination of MD simulations, we constructed PathInHydro, a set of supervised ML models capable of automatically assigning unbinding pathways for the dissociation of gas molecules from [NiFe] hydrogenases, using the unbinding trajectories of CO and H from [NiFe] hydrogenase as a training set.
View Article and Find Full Text PDFProc Natl Acad Sci U S A
December 2024
Department of Pharmaceutical Analysis, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, People's Republic of China.
Inflammatory bowel disease (IBD) is often associated with excessive inflammatory response and highly dysregulated gut microbiota. Traditional treatments utilize drugs to manage inflammation, potentially with probiotic therapy as an adjuvant. However, current standard practices often suffer from detrimental side effects, low bioavailability, and unsatisfactory therapeutic outcomes.
View Article and Find Full Text PDFChem Commun (Camb)
November 2024
Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford, OX1 3QR, UK.
The ability of hydrogenase enzymes to activate H with excellent selectivity leads to many interesting possibilities for biotechnology driven by H as a clean reductant. Here, we review examples where hydrogenase enzymes have been used to drive native and non-native hydrogenation reactions in solution or as part of a redox cascade on a conductive support, with a focus on the developments we have contributed to this field. In all of the examples discussed, hydrogenation reactions are enabled by coupled redox reactions: the oxidation of H at a hydrogenase active site, linked electronically ( relay clusters in the enzyme and/or conductive support) to the site of a reduction reaction, and we note how this parallels developments in site-separated reactivity in heterogeneous catalysis.
View Article and Find Full Text PDFJ Am Chem Soc
November 2024
Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany.
[NiFe]-hydrogenases catalyze the reversible activation of H using a unique NiFe(CN)CO metal site, which is assembled by a sophisticated multiprotein machinery. The [4Fe-4S] cluster-containing HypCD complex, which possesses an ATPase activity with a hitherto unknown function, serves as the hub for the assembly of the Fe(CN)CO subfragment. HypCD is also thought to be responsible for the subsequent transfer of the iron fragment to the apo-form of the catalytic hydrogenase subunit, but the underlying mechanism has remained unexplored.
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