The proposed research is aimed at providing new insights on the conformational preferences of proteins, the generation of ligand-binding sites in proteins, and the recognition of protein surfaces. These studies should produce fundamental understanding of broad significance and generate tools that are valuable in basic research and, perhaps, in biomedical applications. The proposed program has four specific goals. (1) We will continue a productive examination of the sources of beta-sheet secondary structure stability. We have recently developed a model system for parallel beta-sheet that folds in water, and we will use this system to probe the origins of parallel beta-sheet folding preferences. In addition, we will use a new technique that we have recently developed, backbone thioester exchange (BTE), to answer fundamental questions regarding antiparallel beta-sheet stability. (2) We will use BTE and more traditional methods to examine factors that control tertiary structural stability. Several small proteins or protein fragments have been selected as platforms for these studies. (3) We will try to engineer binding sites for small molecules into minimum-length tertiary folding units, using both rational design and phage display. The peptides generated in this way might lead to fluorescent tags for proteins, allosteric modules for protein engineering or new sensors or catalysts. (4) We will explore the recognition of protein surfaces by unnatural oligomeric units. Principles identified in these experiments should support the development of antagonists for specific protein-protein interactions, an important goal in basic biological research and human medicine.
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