Libraries of alpha-helical peptides may prove to be useful sources of DNA binding ligands and provide insight into the requirements for selective DNA recognition. Knowledge of protein structure-function relationships and their impact on protein-DNA interactions can be augmented by concentrating on the basic region/leucine zipper (bZIP) motif, in which a pair of short, basic alpha-helices recognizes the DNA major groove with sequence-specificity and high affinity. This proposal targets the aryl hydrocarbon receptor/nuclear translocator heterodimeric system, suspected of mediating the deleterious health effects f environmental pollutants and interfering with endocrine disruptor pathways. Based on sequence homology, the aryl hydrocarbon receptor (AhR) and the aryl hydrocarbon nuclear translocator (Arnt) are believed to be basic region/helix-loop-helix proteins (bHLH), and alpha-helical DNA-binding motif similar to the bZIP. The goal is to explore the universality of the protein alpha-helix as a scaffold for design of sequence-specific DNA-binding proteins by reducing Nature's constructs to a minimal, approximately 60 amino-acid helix that serves as an ideal a molecular recognition scaffold (structure). Quantitative examination of how these proteins recognize specific DMA sequences will contribute to our understanding of the determinants of binding specificity in protein-DNA interactions (function). Designed proteins are bacterially expressed and extensively purified. Structure is characterized by circular dichroism; DNA-binding function is characterized by Dnase I footprinting. Thermodynamics of cocomplexation is dissected by fluorescence anisotropy and calorimetry, and structural information is obtained by x-ray crystallography and molecular modeling.
