title: Isocyanide in biochemistry? A theoretical investigation of the electronic effects and energetics of cyanide ligand protonation in [FeFe]-hydrogenases.
abstract: The presence of Fe-bound cyanide ligands in the active site of the proton-reducing enzymes [FeFe]-hydrogenases has led to the hypothesis that such Brønsted-Lowry bases could be protonated during the catalytic cycle, thus implying that hydrogen isocyanide (HNC) might have a relevant role in such crucial microbial metabolic paths. We present a hybrid quantum mechanical/molecular mechanical (QM/MM) study of the energetics of CN(-) protonation in the enzyme, and of the effects that cyanide protonation can have on [FeFe]-hydrogenase active sites. A detailed analysis of the electronic properties of the models and of the energy profile associated with H(2) evolution clearly shows that such protonation is dysfunctional for the catalytic process. However, the inclusion of the protein matrix surrounding the active site in our QM/MM models allowed us to demonstrate that the amino acid environment was finely selected through evolution, specifically to lower the Brønsted-Lowry basicity of the cyanide ligands. In fact, the conserved hydrogen-bonding network formed by these ligands and the neighboring amino acid residues is able to impede CN(-) protonation, as shown by the fact that the isocyanide forms of [FeFe]-hydrogenases do not correspond to stationary points on the enzyme QM/MM potential-energy surface.
authors.affiliation: Department of Biotechnology and Biosciences, University of Milan-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy. Claudio.greco@unimib.it
authors.forename: Claudio
authors.initials: C
authors.lastname: Greco
authors.forename: Maurizio
authors.initials: M
authors.lastname: Bruschi
authors.forename: Piercarlo
authors.initials: P
authors.lastname: Fantucci
authors.forename: Ulf
authors.initials: U
authors.lastname: Ryde
authors.forename: Luca
authors.initials: L
authors.lastname: De Gioia
mesh_terms: D045285:Desulfovibrio desulfuricans / Q000201:enzymology*; D006860:Hydrogen Bonding; D006864:Hydrogenase / Q000737:chemistry / Q000378:metabolism*; D007506:Iron-Sulfur Proteins / Q000737:chemistry / Q000378:metabolism*; D008024:Ligands; D008958:Models, Molecular; D015394:Molecular Structure; D009570:Nitriles / Q000737:chemistry* / Q000378:metabolism; D011522:Protons; D013816:Thermodynamics
chemical_list: D007506:Iron-Sulfur Proteins; D008024:Ligands; D009570:Nitriles; D011522:Protons; C118830:iron hydrogenase; D006864:Hydrogenase