, Volume 17, Issue 5, pp 773-790
Date: 15 Apr 2012

Application of DFT methods to the study of the coordination environment of the VO2+ ion in V proteins

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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 F1-ATPase (CF1; 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 \( \left| {A_{\rm{iso}}^{\rm{N}} } \right| \) and \( \left| {A_{z}^{\rm{N}} } \right| \) 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 [ \( {\text{COO}}_{\text{Glu}}^{ - } \) , H2O, H2O, H2O] and [NHis(||), NHis(⊥), \( {\text{COO}}_{\text{Glu}}^{ - } \) , H2O], and that the donor set of site 3 of CF1-ATPase is [ \( {\text{COO}}_{\text{Asp}}^{ - } \) , OHThr, H2O, H2O, \( {\text{NH}}_{{ 2 {\text{Lys}}}}^{\text{ax}} \) ]. For VBrPO, the coordination modes [NHis(||), NHis(∠), OHSer, H2O, H2Oax] for the low-pH site and [NHis(||), NHis(∠), OHSer, OH, H2Oax] or [NHis(||), NHis(∠), \( {\text{O}}_{\text{Ser}}^{ - } \) , H2O] 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 ([NHis(||), \( {\text{COO}}_{\text{Glu}}^{ - } \) , H2O, H2O], [NHis(||), NHis(||), \( {\text{COO}}_{\text{Glu}}^{ - } \) , H2O], and [NHis(||), NHis(||), \( {\text{COO}}_{\text{Glu}}^{ - } \) , OH, \( {\text{N}}_{\text{His}}^{\text{ax}} \) ], respectively) seems to be the most plausible hypothesis.