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 of 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), an 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, ~60 amino-acid helix that serves as an ideal a molecular recognition scaffold (structure). Quantitative examination of how these proteins recognize specific DNA 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.
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