This project continues to focus on understanding the role of early structural events in the transition from the unfolded to the native state of a protein, which is one of the most challenging and critical aspects of the protein folding problem. Rapid accumulation of partially folded intermediates may be important for directing the protein toward its unique native conformation. Despite intense study, important questions remain to be answered concerning the nature and origin of the barriers and the structural properties of the intermediates encountered during early stages of folding. Are compact states the result of a non- specific chain collapse or more specific folding events? What is the relative importance of local vs. long- range interactions? Do intermediates contain native-like tertiary interactions? For many proteins, intermediates are populated even at equilibrium, which raises further questions concerning the origin of structural co-operativity, the relationship between kinetic and thermodynamic intermediates, and any residual interactions remaining in the denatured state. These fundamental questions are addressed by coupling advanced mixing techniques for rapid initiation of folding reactions with a variety of detection methods, including intrinsic and extrinsic fluorescence probes and H/D exchange labeling experiments with NMR detection. These techniques, in conjunction with protein engineering and chemical modification methods for introducing spectroscopic marker, will be used to gain detailed insight into the folding mechanism of model proteins, including staphylococcal nuclease and horse cytochrome c.
The Specific Aims are: (1) to monitor the formation of long-range and specific tertiary contacts during folding of these proteins by coupling fluorescence labeling and microsecond mixing techniques;(2) to observe formation of hydrogen-bonded structure on the microsecond time scale by H/D exchange and NMR;(3) to elucidate the structure of equilibrium intermediates;(4) to study the conformational properties of denatured protein states by fluorescence and hydrodynamic methods. Insight into the structural, thermodynamic and kinetic properties of protein folding intermediates is critical for understanding and treating a wide range of diseases that can be linked to aggregation of partially denatured or misfolded forms of proteins. Issues related to protein stability and folding also play a central role in understanding the biological consequences of mutations, and in de novo protein design. Studies of protein folding in vitro further provide the necessary framework for protein structure prediction, and for understanding cellular protein folding, trafficking and degradation.
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