A quantum chemical study of the water-assisted mechanism in one-carbon unit transfer reaction catalyzed by glycinamide ribonucleotide transformylase

Theoretical study of the scavenging mechanism to 1,4-dicarbonyls by pyridoxamine: The water-assisted reaction

“…If not specially pointed out, the following analyses were referring to the energies obtained with MP2/6-31+G(d,p) method. To estimate the solvent effect of water, the single-point energies were calculated at the MP2/6-31+G(d,p) level with the Onsager self-consistent reaction field (SCRF) model [27] on the basis of the optimized geometries in the gas phase, and such treatment has been applied in many reaction systems [14,28,29]. What's more, the natural bond orbital (NBO) analysis was also performed to obtain reliable atomic charges [30].…”

Molecule dynamics and combined QM/MM study on one-carbon unit transfer reaction catalyzed by GAR transformylase

“…This one-carbon transfer process incorporates the C-8 carbon of the purines, and is the first of two formyl transfer reactions; the other widely investigated is aminoimidazole carboxamide ribonucleotide transformylase (AICAR Tfase). Because of its association with DNA synthesis, GAR Tfase has become the target of anti-neoplasitc agents and much effort has been done on its catalytic mechanism [2][3][4][5][6][7][8][9][10][11]. In the catalytic system, the apoenzyme crystal structure has revealed a proposed binding pocket lined by side chains of 13 strictly conserved residues [2].…”