The hepatocyte nuclear factor 3 (HNF-3) and Drosophila forkhead (fkh) homologues constitute a large family of proteins and utilize a winged helix"""""""" motif to recognize their cognate DNA sites. The family members are present in a wide range of tissues and ply important roles in cell- type-specific gene expression. Interestingly, although the HNF-3/fkh homologues have almost invariable amino acid sequences in their principal DNA recognition helix (H3), they exhibit divergent DNA binding specificity. Previous data have demonstrated that the amino acid sequence immediately prior to H3 can adopt alternative conformations among different HNF-3/fkh family members, and that these alternative conformations regulate the presentation of H3 as well as DNA binding specificity. However, how these alternative conformations can change DNA contact patterns among different HNF-3/fkh family members are not fully understood. Thus, a combination of molecular biology and modern NMR techniques will be applied to investigate this question. HNF-3/fkh homologues are highly dynamic DNA binding proteins. However how their dynamic properties are related to their DNA binding process is not clear. Thus, a systematic investigation of internal motions among different HNF-3/fkh proteins and their DNA complexes are necessary. Relaxation NMR techniques will be used for this study. Previous results indicated that most DNA contacts made by an HNF-3/fkh family member are on one strand of a double stranded AT rich sequence. Thus, a question is whether this unique DNA contact mode is another reason for nature to keep the highly conserved principal DNA contact helix? A combination of molecular biology and NMR techniques will be used to study the relationship between the DNA contact residues and binding specificity in HNF-3/fkh members. The information obtained from this research will help us to understand the roles of the HNF-3/fkh proteins in tissue specific gene regulation and developmental regulation.
