Analysis of FBPase-AMP Interactions

Consistent with the experimental data, mutation of the purine base nitrogens, i.e. N, 3N, 7N and 9N, showed that replacement of N, 3N and 9N with CH had little effect on binding affinity whereas a similar replacement of 7N led to a loss of 2.8 kcal/mol. The 0.6 kcal/mol gain in affinity for the 1-deaza and 3-deaza AMP analogues was consistent with the hydrophobic nature of this portion of the binding site cavity and the absence of hydrogen bond donors in the vicinity of either heteroatom. 

Less apparent from the X-ray structure were the calculated results for the mutations of the 6NH2 group, 7N and 9N. Mutation of the 6NH2 group to hydrogen led to a loss of only 2.3 kcal/mol, which was in agreement with the experimental result of 2.8 kcal/mol. The results indicate that despite 

2 Scan of Residues in the Purine Base Binding Region 

Computational mutation of Tyrl 13 to Phe resulted in a 700-fold decrease in the binding affinity of AMP relative to wild-type FBPase. The calculated results were consistent with earlier experimental data.28 Since Tyrl 13 hydrogen bonds to both the 5 oxygen and the 3 hydroxyl, it is unclear how much each hydrogen bond contributes to AMP binding affinity. 

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