Water Structure of the Central Hydrophobic Cavity of Mammalian Fructose 1,6‐bisphosphatase: a Potential Thermodynamic Determinant of Allowed Quaternary States

AMP and/or fructose‐2,6‐bisphosphate (F26BP) transform fructose‐1,6‐bisphosphatase (FBPase) from its active R‐state to an inactive T‐state. Intermediate states of FBPase observed in crystal structures (IR, IT and IF) lie sequentially in the R‐ to T‐state transition pathway. As many as 48 ordered water molecules are in the hydrophobic central cavity of FBPase tetramers. Indeed, water molecules in the cavity of the IR‐state show well‐defined clathrate structures. The objective here is the characterization of the structural, dynamic and thermodynamic properties of cavity water molecules in different states of FBPase. The presence of ordered water clusters in the central cavity of FBPase is confirmed by molecular dynamics (MD) simulations, but the size and stability of water clusters vary with the conformation of the tetramer. Clusters in the cavity of the IR‐ and IT‐states are more stable relative to other states by retention‐time and structure‐clustering analyses; whereas IF‐state water cluster shows the least stability. Water molecules in the central cavity could play a significant role in determining the free energy of intermediate states of FBPase by the formation of low‐entropy (high free‐energy) structures. The existence of well‐defined R‐ and T‐states of FBPase may be due in part to the stability‐modulation of water molecules in the central cavity. This research is supported by NIH grant NS 10546.