THERMODYNAMICS OF WATER MEDIATING PROTEIN-LIGAND INTERACTIONS IN CYTOCHROME P450CAM - A MOLECULAR-DYNAMICS STUDY

Ordered water molecules are observed by crystallography and nuclear ma gnetic resonance to mediate protein-ligand interactions. Here, we exam ine the energetics of hydrating cavities formed at protein-ligand inte rfaces using molecular dynamics simulations. The free energies of hydr ating two cavities in the active site of two liganded complexes of cyt ochrome P450cam were calculated by multiconfigurational thermodynamic integration. The complex of cytochrome P450cam with 2-phenyl-imidazole contains a crystallographically well defined water molecule mediating hydrogen bonds between the protein and the inhibitor. We calculate th at this water molecule is stabilized by a binding free energy of -11.6 +/- 6.6 kJ/mol. The complex of cytochrome P450cam with its natural su bstrate, camphor, contains a cavity that is empty in the crystal struc ture although a water molecule in it could make a hydrogen bond to cam phor. Here, solvation of this cavity is calculated to be unfavorable b y +15.8 +/- 5.0 kJ/mol. The molecular dynamics simulations can thus di stinguish a hydrated interfacial cavity from an empty one. They also p rovide support for the notion that protein-ligand complexes can accomm odate empty interfacial cavities and that such cavities are likely to be unhydrated unless more than one hydrogen bond can be made to a wate r molecule in the cavity.