RULES FOR HELIX TERMINATION, THE C CAPPING BOX

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The long term objective of this project is to understand quantitatively the stereochemical and physico-chemical basis of alpha-helix termination. This means better understanding the mechanism of protein folding, one of the most basic problems in biomedical research. The health-related significance of this work is that the information obtained could be used for the design of new protein structures and the improvement of stabilities of biologically active proteins. The following questions will be answered: 1) Which residues in the C-capping box are important for the formation of the alphal helix termination motif? 2) What are the thermodynamic propensities of different residues at solvent exposed (C2, C1, Ccap & C ) positions of the C-capping box in an alpha-helix? 3) Do these propensities correlate with thermodynamic propensity scales obtained in other systems (alpha-helix propensities, beta-sheet propensities) or structural parameters (peptide backbone amide hydrogen exchange factors, buried and exposed surface area, etc.)? 4) What is the role of the bracketing hydrophobic interactions in formation and stabilization of the alphal motif? These questions will be answered by study of specific mutations in the C-capping box of the alpha-helix of ubiquitin using a combination of experimental methods, providing both structural (CD, fluorescence, and NMR spectroscopies and X-ray crystallography) and thermodynamic (microcalorimetry,) information on the system. From these data, we will evaluate the structural and energetic contributions of various amino acid residues at different positions of C-capping box.