The long term objective of this research is to understand the structural principles of beta-sheet folding using a small protein that folds by a two state mechanism. We utilize sequences of the Pin WW domain, a 34 residue 3-stranded antiparallel Beta-sheet, incorporating both natural and unnatural amino acid mutations to understand the structural features that are critical for the transition state formation and ground state stability. Our ability to chemically synthesize WW domains with varied backbone connectivity and a constant Beta-sheet core structure allows us to understand what aspect of topology (structure) is important for predicting folding rates-a prediction that is accurate within an order of magnitude or so. Synthetic accessibility also allows us to make subtle changes in WW domain structure to better understand how these changes influence the range of folding rates exhibited by WW domain variants. Thermodynamic and kinetic data for mutations at nearly every position in the sequence can be processed to afford a Phi (phi) analysis (phi) = deltadeltaG++/deltadeltaG) to discern the extent to which a perturbation in the free energy of folding is mirrored in the transition state. We make predictions about the importance of certain structural features including hydrogen bonding, hydrophobic interactions, conformational preferences, chain connectivity (topology), etc. in both the ground state and transition states that can be tested experimentally using a phi analysis. Understanding Beta-sheet folding is important to improve fold predictions from sequence and to begin to understand the balance between 13-sheet folding and misfolding-the latter process affords aggregates that appear to cause neurodegeneration.
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