Molecular dynamics study of a V2O5 crystal

Chiba, Hideyuki; Nishidate, Kazume; Baba, Mamoru; Kumagai, Naoya; Satō, Tsutomu; Nishikawa, Kiyoshi

doi:10.1016/s0038-1098(99)00102-7

Cited by 5 publications

(1 citation statement)

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“…The Amber force field was used for the protein, water, and counterions. Atom−atom parameters for vanadate and peroxovanadate cofactors were taken according to ref , whereas atomic point charges were calculated using the RESP scheme adopted in Amber for the imidazole/vanadate and imidazole/peroxo cofactor complexes. Charges for different protonation states were calculated.…”

Section: Computational Detailsmentioning

confidence: 99%

Structure and Function of Vanadium Haloperoxidases

Raugei

Carloni

2005

J. Phys. Chem. B

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A quantum mechanics/molecular mechanics study of the resting state of the vanadium dependent chloroperoxidase from fungi Curvularia inaequalis and of the early intermediates of the halide oxidation is reported. The investigation of different protonation states indicates that the enzyme likely consists of an anionic H2VO4- vanadate moiety where one hydroxo group is in axial position. The calculations suggest that the hydrogen peroxide binding may not involve an initial protonation of the vanadate cofactor. A low free energy reactive path is found where the hydrogen peroxide directly attacks the axial hydroxo group, resulting in the formation of an hydrogen peroxide intermediate. This intermediate is promptly protonated to yield a peroxo species. The free energy barrier for the formation of the peroxo species does not depend significantly upon the protonation state of the cofactor. The most likely protonation states of the peroxo cofactor are neutral forms HVO2(O2) with a hydroxo group either H-bonded to Ser402 or coordinated to Arg360. The peroxo cofactor is also coordinated to an axial water molecule, which could be important for the stability of the peroxovanadate/His496 adduct. Our calculations strongly suggest that the halide oxidation may take place with the preliminary formation of a peroxovanadate/halogen adduct. Subsequently, the halogen reacts with the peroxo moiety yielding a hypohalogen vanadate. The most reactive protonation state of peroxovanadate is the neutral HVO2(O2) with the hydroxo group H-bonded to Ser402. The important role of Lys353 in determining the catalytic activity is also confirmed.

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Section: Computational Detailsmentioning

confidence: 99%