Predicting folded protein structure from the primary amino acid sequence remains one of the great unsolved problems in biochemistry. In turn, an understanding of the molecular dynamics of folded proteins is imperative for understanding their biological function. In recent years it has become clear that protein structure, folding patterns and dynamics all depend upon the interplay among a number of subtle interactions. To understand this interplay, biochemists must develop a deeper physical insights into these various interactions. A recent major advance towards understanding the forces that control protein structure is the discovery of short alanine-based peptides, 16-mers and 17-mers, that form stable alpha-helices in aqueous solution. These helices exhibit a thermal unfolding transition between 0 degrees C and 60 degrees C. They are constructed from naturally-occurring amino acids and, therefore, serve as excellent models of helical structures in natural proteins. These helices further serve as a testing ground for theories of protein molecular dynamics. We propose to greatly advance the understanding of these peptides by using Electron Spin Resonance (ESR) to study spin labeled peptide analogs. Using such techniques, our lab is the first to have demonstrated an ability to experimentally measure local position dependent peptide dynamics and these measurements are now providing a reference point for computer molecular dynamics studies. In past work we have shown that helical peptides can be spin labeled with a minimal perturbation of their alpha-helix -> coil equilibrium. We have further shown that the dynamic details extracted from a combination of ESR experiments and Circular Dichroism (CD) experiments can be used to provide a detailed description of peptide dynamics throughout the folding process. Our research plan is to now combine our ESR technology with peptide design technology and systematically probe the physical aspects that control helix formation, stability and local motions. The chief goals of the proposed research are: 1) Determine a mobility profile along the alpha-helix backbone;2) Localize the influence of helix-breaking residues; 3) Detect the interactions among large residue side chains that are located close to each other on the helix surface; 4) Determine the actual winding geometry of these helical peptides to distinguish 3(10) helix from alpha-helix.
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