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• W4212876709 abstract "The second step in the de novo biosynthetic pathway of purine is catalyzed by PurD, which consumes an ATP molecule to produce glycinamide ribonucleotide (GAR) from glycine and phosphoribosylamine (PRA). PurD initially reacts with ATP to produce an intermediate, glycyl-phosphate, which then reacts with PRA to produce GAR. The structure of the glycyl-phosphate intermediate bound to PurD has not been determined. Therefore, the detailed reaction mechanism at the molecular level is unclear. Here, we developed a computational protocol to analyze the free-energy profile for the glycine phosphorylation process catalyzed by PurD, which examines the free-energy change along a minimum energy path based on a perturbation method combined with the quantum mechanics and molecular mechanics hybrid model. Further analysis revealed that during the formation of glycyl-phosphate, the partial atomic charge distribution within the substrate molecules was not localized according to the formal charges, but was delocalized overall, which contributed significantly to the interaction with the charged amino acid residues in the ATP-grasp domain of PurD." @default.
• W4212876709 created "2022-02-24" @default.
• W4212876709 creator A5009526340 @default.
• W4212876709 creator A5022771107 @default.
• W4212876709 creator A5032544713 @default.
• W4212876709 date "2022-02-14" @default.
• W4212876709 modified "2023-10-14" @default.
• W4212876709 title "Free-Energy Profile Analysis of the Catalytic Reaction of Glycinamide Ribonucleotide Synthetase" @default.
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• W4212876709 doi "https://doi.org/10.3390/life12020281" @default.
• W4212876709 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/35207568" @default.
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