Transient intermediate units in protein folding

How a polypeptide chain folds into its final native structure as it comes off the ribosome is the final step in the Central Dogma of biology. A better understanding of this fundamental process may have implications for structure prediction, folding diseases and protein design. Cytochrome c is a well-studied protein folding model. Cytochrome c structure can be broken down into cooperative units of secondary structure, detectable by hydrogen exchange. Cytochrome c folds through the sequential acquisition of these structural units. In two-state folding, these units fail to accumulate and are normally undetectable. This work describes the development of a technique that detects not only the transient population of these units but also the “hidden” kinetic barriers that separate them. The folding pathway of cytochrome c seems to have functional importance. Major conformational changes, such as the alkaline transition, appear to occur through the folding pathway. To facilitate further studies, a recombinant cytochrome c was expressed with high yields in E. coli. Initial hydrogen exchange studies of the modified recombinant protein are described. The last section discusses the generalization of the nucleation-sequential stabilization model