Mechanism of nitrate reduction by Desulfovibrio desulfuricans nitrate reductase--a theoretical investigation.
The oxidative half-reaction of oxygen atom transfer from nitrate to an Mo(IV) complex has been investigated at various levels of theory. Two models have been used to simulate the enzyme active site. In the second, more advanced model, additional amino acid residues capable of significantly affecting the catalytic efficiency of the enzyme were included. B3LYP/6-31+G*, ONIOM, and orbital-free embedding approaches have been used to construct the potential energy profile and to qualitatively compare the results of a QM/MM study with those obtained by a full quantum mechanical strategy. The study has confirmed the utility of the orbital-free embedding method in the description of enzymatic processes.
Leopoldini
Monica
M
Dipartimento di Chimica and Centro di Calcolo ad Alte Prestazioni per Elaborazioni Parallele e Distribuite, Centro d'Eccellenza MIUR, Università della Calabria, 87030 Arcavacata di Rende (CS), Italy.
Russo
Nino
N
Toscano
Marirosa
M
Dulak
Marcin
M
Wesolowski
Tomasz Adam
TA
D001665:Binding Sites; D002384:Catalysis; D045285:Desulfovibrio desulfuricans / Q000201:enzymology*; D008958:Models, Molecular; D008982:Molybdenum; D050901:Nitrate Reductase / Q000378:metabolism*; D009566:Nitrates / Q000378:metabolism*; D010084:Oxidation-Reduction; D011789:Quantum Theory
D009566:Nitrates; D008982:Molybdenum; D050901:Nitrate Reductase