title: Application of DFT methods to the study of the coordination environment of the VO2+ ion in V proteins.
abstract: Density functional theory (DFT) methods were used to simulate the environment of vanadium in several V proteins, such as vanadyl-substituted carboxypeptidase (sites A and B), vanadyl-substituted chloroplast F(1)-ATPase (CF(1); site 3), the reduced inactive form of vanadium bromoperoxidase (VBrPO; low- and high-pH sites), and vanadyl-substituted imidazole glycerol phosphate dehydratase (IGPD; sites α, β, and γ). Structural, electron paramagnetic resonance, and electron spin echo envelope modulation parameters were calculated and compared with the experimental values. All the simulations were performed in water within the framework of the polarizable continuum model. The angular dependence of [Formula: see text] and [Formula: see text] on the dihedral angle θ between the V=O and N-C bonds and on the angle φ between the V=O and V-N bonds, where N is the coordinated aromatic nitrogen atom, was also found. From the results it emerges that it is possible to model the active site of a vanadium protein through DFT methods and determine its structure through the comparison between the calculated and experimental spectroscopic parameters. The calculations confirm that the donor sets of sites B and A of vanadyl-substituted carboxypeptidase are [[Formula: see text], H(2)O, H(2)O, H(2)O] and [N(His)(||), N(His)(⊥), [Formula: see text], H(2)O], and that the donor set of site 3 of CF(1)-ATPase is [[Formula: see text], OH(Thr), H(2)O, H(2)O, [Formula: see text]]. For VBrPO, the coordination modes [N(His)(||), N(His)(∠), OH(Ser), H(2)O, H(2)O(ax)] for the low-pH site and [N(His)(||), N(His)(∠), OH(Ser), OH(-), H(2)O(ax)] or [N(His)(||), N(His)(∠), [Formula: see text], H(2)O] for the high-pH site, with an imidazole ring of histidine strongly displaced from the equatorial plane, can be proposed. Finally, for sites α, β, and γ of IGPD, the subsequent deprotonation of one, two, and three imidazole rings of histidine and the participation of a carboxylate group of a glutamate residue ([N(His)(||), [Formula: see text], H(2)O, H(2)O], [N(His)(||), N(His)(||), [Formula: see text], H(2)O], and [N(His)(||), N(His)(||), [Formula: see text], OH(-), [Formula: see text]], respectively) seems to be the most plausible hypothesis.
authors.affiliation: Istituto CNR di Chimica Biomolecolare, Trav. La Crucca 3, 07040, Sassari, Italy.
authors.forename: Daniele
authors.initials: D
authors.lastname: Sanna
authors.forename: Vincent L
authors.initials: VL
authors.lastname: Pecoraro
authors.forename: Giovanni
authors.initials: G
authors.lastname: Micera
authors.forename: Eugenio
authors.initials: E
authors.lastname: Garribba
mesh_terms: D044646:Ascophyllum / Q000201:enzymology; D002268:Carboxypeptidases / Q000737:chemistry; D002413:Cations, Divalent / Q000737:chemistry; D025222:Chloroplast Proton-Translocating ATPases / Q000737:chemistry; D004578:Electron Spin Resonance Spectroscopy; D006836:Hydro-Lyases / Q000737:chemistry; D008958:Models, Molecular; D010544:Peroxidases / Q000737:chemistry; D010944:Plants / Q000201:enzymology; D011506:Proteins / Q000737:chemistry*; D011789:Quantum Theory; D012441:Saccharomyces cerevisiae / Q000201:enzymology; D014639:Vanadium / Q000737:chemistry*
chemical_list: D002413:Cations, Divalent; D011506:Proteins; D014639:Vanadium; D010544:Peroxidases; C026195:bromide peroxidase; D002268:Carboxypeptidases; D025222:Chloroplast Proton-Translocating ATPases; D006836:Hydro-Lyases; C021434:imidazoleglycerolphosphate dehydratase