HETERONUCLEAR 3D NMR-STUDIES OF WATER BOUND TO AN FK506 BINDING-PROTEIN IMMUNOSUPPRESSANT COMPLEX

From a series of N-15-resolved 3D ROESY-HMQC and C-13-resolved 3D NOESY-HMQC spectra of the FK506 binding protein (FKBP)/ascomycin complex in H2O, the locations of three tightly bound water molecules were identified. These waters are all buried within the interior of the complex and form an integral part of its structure via a network of hydrogen bonds. Water molecules in identical locations exhibiting a similar hydrogen bonding pattern were also observed in the X-ray crystal structures of FKBP/FK506 [Van Duyne, G. D., Standaert, R. F., Karplus, P. A., Schreiber, S. L., & Clardy, J. (1991) Science 252, 839-842] and FKBP/rapamycin [Van Duyne, G. D., Standaert, R. F., Schreiber, S. L., & Clardy, J. (1991) J. Am. Chem. Soc. 113, 7433-7434]. However, none of the surface waters observed in the X-ray structures were detected in the NMR experiments due to their fast exchange with bulk water. In order to examine the effects of the three, internal water molecules on NMR structure determinations of the FKBP/ascomycin complex, two sets of NMR structures were calculated either with or without the waters. By including the three internal waters in the structure calculations, a decrease in the root mean square deviation and improved angular order parameters was observed for FKBP residues in the vicinity of the water molecules. In addition, subtle conformational differences were observed between NMR structures generated either with or without the waters. These differences not only are caused by the added distance restraints involving water but also may be due to the bulk of the water and ability of the water to bridge otherwise distant regions of the protein through water-mediated hydrogen bonds. These results suggest that in some cases internal water molecules are important to include in three-dimensional structure determinations of proteins by NMR.