title: Theoretical insights into [NiFe]-hydrogenases oxidation resulting in a slowly reactivating inactive state.
abstract: [NiFe]-hydrogenases catalyse the relevant H2→ 2H++ 2e-reaction. Aerobic oxidation or anaerobic oxidation of this enzyme yields two inactive states called Ni-A and Ni-B. These states differ for the reactivation kinetics which are slower for Ni-A than Ni-B. While there is a general consensus on the structure of Ni-B, the nature of Ni-A is still controversial. Indeed, several crystallographic structures assigned to the Ni-A state have been proposed, which, however, differ for the nature of the bridging ligand and for the presence of modified cysteine residues. The spectroscopic characterization of Ni-A has been of little help due to small differences of calculated spectroscopic parameters, which does not allow to discriminate among the various forms proposed for Ni-A. Here, we report a DFT investigation on the nature of the Ni-A state, based on systematic explorations of conformational and configurational space relying on accurate energy calculations, and on comparisons of theoretical geometries with the X-ray structures currently available. The results presented in this work show that, among all plausible isomers featuring various protonation patterns and oxygenic ligands, the one corresponding to the crystallographic structure recently reported by Volbeda et al. (J Biol Inorg Chem 20:11-22, 19)-featuring a bridging hydroxide ligand and the sulphur atom of Cys64 oxidized to bridging sulfenate-is the most stable. However, isomers with cysteine residues oxidized to terminal sulfenate are very close in energy, and modifications in the network of H-bond with neighbouring residues may alter the stability order of such species.
authors.affiliation: Department of Earth and Environmental Science, University of Milano-Bicocca, Piazza Della Scienza 1, 20126, Milan, Italy.
authors.forename: Raffaella
authors.initials: R
authors.lastname: Breglia
authors.affiliation: Departamento de Ingeniería Química y Bioquímica, Instituto Tecnológico de Durango, Felipe Pescador Ote, Durango, Mexico.
authors.forename: Manuel Antonio
authors.initials: MA
authors.lastname: Ruiz-Rodriguez
authors.affiliation: Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy.
authors.forename: Alessandro
authors.initials: A
authors.lastname: Vitriolo
authors.affiliation: Departamento de Ingeniería Química y Bioquímica, Instituto Tecnológico de Durango, Felipe Pescador Ote, Durango, Mexico.
authors.forename: Rubén Francisco
authors.initials: RF
authors.lastname: Gonzàlez-Laredo
authors.affiliation: Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy.
authors.forename: Luca
authors.initials: L
authors.lastname: De Gioia
authors.affiliation: Department of Earth and Environmental Science, University of Milano-Bicocca, Piazza Della Scienza 1, 20126, Milan, Italy.
authors.forename: Claudio
authors.initials: C
authors.lastname: Greco
authors.affiliation: Department of Earth and Environmental Science, University of Milano-Bicocca, Piazza Della Scienza 1, 20126, Milan, Italy. maurizio.bruschi@unimib.it.
authors.forename: Maurizio
authors.initials: M
authors.lastname: Bruschi
mesh_terms: D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D003545:Cysteine; D006864:Hydrogenase / Q000737:chemistry* / Q000378:metabolism*; D008958:Models, Molecular; D010084:Oxidation-Reduction; D010100:Oxygen / Q000378:metabolism; D011789:Quantum Theory
chemical_list: C043296:nickel-iron hydrogenase; D006864:Hydrogenase; D003545:Cysteine; D010100:Oxygen
keywords: Density functional theory; Ni-A state; Oxidative inactivation; Protein S-sulfenation; [NiFe]-hydrogenase