Oxidation reaction by xanthine oxidase. Theoretical study of reaction mechanism

Journal of the American Chemical Society

Volumn 129, Issue 26, 2007, Pages 8131-8138

  Amano, Tatsuo ^a   Ochi, Noriaki ^a   Sato, Hirofumi ^a   Sakaki, Shigeyoshi ^a,b  

^a KYOTO UNIVERSITY   (Japan)

^b KYOTO UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; DEPROTONATION; HYDROGEN; LIGANDS; MOLYBDENUM; OPTIMIZATION; OXIDATION;

ACTIVATION BARRIERS; EXOTHERMICITY; FORMAMIDE; XANTHINE OXIDASES;

ENZYMES;

CARBON; FORMAMIDE; GLUTAMIC ACID; HYDROGEN; HYDROXIDE; LIGAND; MOLYBDENUM; PTERIN; XANTHINE OXIDASE;

ARTICLE; CHEMICAL REACTION; CHEMICAL STRUCTURE; COMPLEX FORMATION; DENSITY FUNCTIONAL THEORY; ENERGY; ENZYME ACTIVE SITE; ENZYME ACTIVITY; GEOMETRY; HYDROGEN BOND; OXIDATION;

BINDING SITES; COMPUTER SIMULATION; MODELS, CHEMICAL; MODELS, MOLECULAR; OXIDATION-REDUCTION; PROTEIN CONFORMATION; XANTHINE OXIDASE;

EID: 34447135008     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja068584d     Document Type: Article

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30. 6 The deprotonation of the Mo active center changes the anion form of Glu730 to the protonated neutral form. This means that the proton does not exist around the Mo active center. It is likely that the neutral carboxylic acid little influences the reaction of the active site when it is about 4 Å distant from the active site.
31. (a) The exothermicities of eqs 3 and 4 are evaluated to be 11.3 and 4.2 kcal/mol, respectively, with the PCM method, where the ε value of 4.0 was employed because this value is often used to mimic the atmosphere of protein in PCM calculations. These results indicate that eq 2 is still much more exothermic than eq 3, though the difference in exothermicity between eqs 2 and 3 considerably decreases in the PCM calculation. Thus, our conclusion does not change in the PCM calculation.
32. (b) The significant decrease in the exothermicity of eq 2 by the PCM calculation is understood by considering that the solvation induces a significantly larger stabilization energy of the product of eq 3 than that of eq 2 because the anionic O atom is exposed to solvent in the product of eq 3 but covered with the substrate in the product of eq 2.
33. Careful geometry optimization starting from TSc leads to PREc and PRODc.
34. 2-.