Theoretical study of a vanadate peptide complex

Bühl, Michæl

doi:10.1002/(sici)1096-987x(199909)20:12<1254::aid-jcc5>3.0.co;2-f

Cited by 21 publications

(15 citation statements)

References 51 publications

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“…17, 18, 23, 24, 32, 38–42 Table 1 contains the results of calculations performed on the HIDA and HIDPA complexes using three functionals, b3lyp, PBE1PBE, and PBEPBE, and three basis sets, 6–311++G(d,p), 6–311++G, and tzvp as available in the Gaussian03 program. 43 The results obtained for the quadrupolar coupling constant and the asymmetry parameters of the EFG tensor for the HIDPA complex are in good agreement with experiment.…”

Section: Resultsmentioning

confidence: 99%

51V solid-state NMR and density functional theory studies of eight-coordinate non-oxo vanadium complexes: oxidized amavadin

et al. 2009

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SUMMARY Using 51V magic angle spinning solid-state NMR spectroscopy and Density Functional Theory calculations we have characterized the chemical shift and quadrupolar coupling parameters for two eight-coordinate vanadium complexes, [PPh4][V(V)(HIDPA)2] and [PPh4][V(V)(HIDA)2]; HIDPA = 2,2′-(hydroxyimino)dipropionate and HIDA = 2,2′-(hydroxyimino)diacetate. The coordination geometry under examination is the less common non-oxo eight coordinate distorted dodecahedral geometry that has not been previously investigated by solid-state NMR spectroscopy. Both complexes were isolated by oxidizing their reduced forms: [V(IV)(HIDPA)2]2- and [V(IV)(HIDA)2]2-. V(IV)(HIDPA)22- is also known as amavadin, a vanadium-containing natural product present in the Amanita muscaria mushroom and responsible for vanadium accumulation in nature. The quadrupolar coupling constants, CQ, are found to be moderate, 5.0 to 6.4 MHz while the chemical shift anisotropies are relatively small for vanadium complexes, −420 and 360 ppm. The isotropic chemical shifts in the solid state are −220 and −228 ppm for the two compounds, and near the chemical shifts observed in solution. Presumably this is a consequence of the combined effects of the increased coordination number and the absence of oxo groups. Density Functional Theory calculations of the electric field gradient parameters are in good agreement with the NMR results while the chemical shift parameters show some deviation from the experimental values. Future work on this unusual coordination geometry and a combined analysis by solid-state NMR and Density Functional Theory should provide a better understanding of the correlations between experimental NMR parameters and the local structure of the vanadium centers.

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Section: Resultsmentioning

confidence: 99%

51V solid-state NMR and density functional theory studies of eight-coordinate non-oxo vanadium complexes: oxidized amavadin

et al. 2009

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“…Computational studies of this enzyme complement and correlate well to available experimental techniques. Michael Bühl and co-workers have carried out an extensive series of DFT calculations in which 51 V NMR chemical shift values were calculated. − Valeria Conte and co-workers have carried out calculations for small models of each catalytic intermediate. These calculations, done on vanadate models of fewer than 10 atoms, provided some insight into the order and location of peroxide 28 and bromide binding 29 and reactivity .…”

Section: Introductionmentioning

confidence: 99%

Quantum Mechanics/Molecular Mechanics Calculations of the Vanadium Dependent Chloroperoxidase

Kravitz

Pecoraro

Carlson

2005

J. Chem. Theory Comput.

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Large quantum mechanics/molecular mechanics (QM/MM) calculations are used to probe the resting and initial protonated states of the vanadium dependent chloroperoxidase from the pathogenic fungus Curvularia inaequalis. QSite was used to model 433 residues and 24 structural waters with molecular mechanics, while 8 active-site residues and the vanadate cofactor (161 atoms) were represented at the B3LYP/lacvp* level of theory. Our previous study of small model systems implied that the resting state of the enzyme contains a trigonal bipyramidal vanadate with one hydroxyl group in the equatorial plane and another in the axial position. This study uses a much larger model of the biological system at a higher level of theory to identify the location of the equatorial hydroxo group with respect to the enzyme active site. We also identify a second resting-state configuration with an axial water and three equatorial oxo moieties that is nearly isoenergetic with the previously identified state. We propose that the resting state is a hybrid of these two configurations, stabilized by the long-range electrostatic field of the protein environment. The first step in catalysis is believed to be protonation of the vanadate. Our previous small models indicated that there were two protonated configurations, but this study shows that the configuration containing an axial water and one hydroxo group in the equatorial plane is significantly lower in energy than any other configuration. Additionally, we can now assign an important role for lysine 353 in the catalytic cycle. Based on our calculations and other model studies, we provide an updated catalytic cycle for vanadium dependent haloperoxidase activity. Further, we demonstrate the importance of system set up. In particular, maintaining the proper electrostatic field at the active site is crucial for identifying the correct minima in a truncated protein model.

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“…[12] For a more conclusive estimate of the solvent effect, additional water molecules would have to be included. Attempts to optimize correspondingly hydrated (or, in general, solvated) cluster geometries, however, are compromised by the large number of possible minima, which would have to be located.…”

Section: Introductionmentioning

confidence: 99%

Medium Effects on51V NMR Chemical Shifts: A Density Functional Study

2001

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Car-Parrinello molecular dynamics simulations were performed for [H2VO4], [VO2(OH2)4]+, and [VO(O2)2(OH2)]- in periodic boxes with 30, 28, and 29 water molecules, respectively, employing the BLYP density functional. On the timescale of the simulations, up to 2 ps, well-structured first solvation spheres are discernible for [H2VO4]- and [VO(O2)2(OH2)]- containing, on average, eight and ten water molecules, respectively. One of the four water molecules directly attached to the metal in [VO2(OH2)4]+ is only loosely bound, and the average coordination number of vanadium in aqueous VO2+ is between five and six. 51V chemical shifts were evaluated at the B3LYP level for representative snapshots along the trajectories, including the water molecules of the solvent by means of point charges. The resulting averaged delta(51V) values are proposed to model the combined effects of temperature (dynamic averaging) and solvent (charge polarization). Both effects are shown to be rather small, of the order of a few dozen ppm. The observed shielding of 51V in the bis(peroxo) complex with respect to the vanadate species is not reproduced computationally.

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Theoretical study of a vanadate peptide complex

Cited by 21 publications

References 51 publications

51V solid-state NMR and density functional theory studies of eight-coordinate non-oxo vanadium complexes: oxidized amavadin

51V solid-state NMR and density functional theory studies of eight-coordinate non-oxo vanadium complexes: oxidized amavadin

Quantum Mechanics/Molecular Mechanics Calculations of the Vanadium Dependent Chloroperoxidase

Medium Effects on51V NMR Chemical Shifts: A Density Functional Study

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