Folding and Structural Transitions in Small Proteins

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DESCRIPTION (provided by applicant): This proposal represents an extended investigation into the application of the generalized-ensemble approach for protein-folding simulations. It is a continuation of the work that the PI did over the last few years. The PI intends to apply the novel techniques that were developed in his group a) to a study of folding transitions and the relation between secondary and tertiary structure formation in a few carefully selected proteins that have either only alpha-helices or beta-sheets as secondary structure elements. The following peptides will be considered: HP-36 (36 residues, all-helical), Beta3s (20 residues, all-beta-sheet), the B domain of staphylococcal protein A (45 residues, all-helical), and Anthopleurin A (49 residues, all-beta-sheet); b) to study the ensemble of low-energy structures, energy landscape and folding of the 62-residue IgG-binding domain of protein L and the 56-residue segment B1 of streptococcal protein G. These two small fast-folding proteins have both helix and beta-sheets and therefore allow one to probe results of the above investigation for complex examples of small proteins; c) and to research in some protein fragments, the transition from an alpha-helix to a beta-sheet, that is thought to be responsible for the outbreak of various neurodegenerative diseases. It is hoped that such research of the thermodynamic of folding and other structural transitions in proteins will lead to an improved understanding of the mechanism of folding. This would allow one to understand better the outbreak of various diseases associated with the malfunction of certain proteins and could lead to more efficient ways of drug design.