Denatured State Bias toward the Topology of Alpha-helical Folds

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This project will investigate how a linear sequence of amino acids encodes the three-dimensional structure of a protein. The folding code is of fundamental importance and has clear practical value for the pharmaceutical and biotech industries. Solving the folding code will ultimately allow reliable design of proteins with a desired structure and function. A primary barrier to cracking the folding code is that the code is highly redundant. Two amino acid sequences with little resemblance can yield proteins with similar three-dimensional shapes. This project will test the hypothesis that short segments of a protein?s amino acid sequence act like punctuation marks that bias the protein chain to change direction. Placing these punctuation marks in the right places is thus sufficient to establish a protein?s shape. This project will also provide training for one undergraduate student and two graduate students in a broad array of biochemical and biophysical methods. As part of this project, Dr. Bowler will work with the spectrUM Discovery Area, an interactive science center located in downtown Missoula, Montana. The Discovery Area provides hands-on activities to spark excitement about science in K-12 students. Combining computer graphics and physical models of proteins produced with a 3D printer, Dr. Bowler will develop educational modules for the Discovery Area to demonstrate the link between protein structure and function. The focus of this research will be a set of small proteins containing two to four alpha-helices in compact bundles. Each protein contains sequences that permit the protein chain to turn. This project will test the hypothesis that the turn sequences bias the shape of a protein even under solution conditions that disrupt protein structure. The project will employ NMR and fluorescence methods, a thermodynamic approach involving formation of histidine-heme loops and computer simulations to test this hypothesis. The research will also test whether protein shape can be evolved by inserting turn sequences into a 42 residue polyalanine sequence known to form a single long α-helix. Finally, the research will test whether protein structure can be devolved by replacing turn sequences with polyalanine segments. Thus, this project will provide important new insights into the role of turn sequences in the folding code.