In the last several years, our group has studied the folding behavior of small single domain proteins, including cyt c, Rd-apocyt b562, barnase, PDZ domain, and FAT domain. We found that these proteins fold through partially unfolded intermediates that exist after the rate-limiting step. We called them hidden intermediates since they can not be detected in conventional kinetic experiments. Further, we have developed a native-state hydrogen exchange-directed protein engineering method for populating the intermediates and determined the first high-resolution structures of the intermediates by multi-dimensional NMR methods. Recently, we have extended our studies to include multi-domain proteins such as T4 lysozyme and a redesigned protein by coupling protein A B-domain with Rd-apocyt b562. The results obtained from these studies provide strong support for the hypothesis that the kinetic principle of protein folding is the step-wise folding of cooperative structure units (foldons) (see pictures in the Gallery). We also provided theoretical arguments on why proteins should fold in a step-wise manner and why the current funnel-like energy landscape view is inadequate to describe the folding behavior of proteins, i.e., desolvation during folding leads to energy barrier on the energy landscape, random search, and coopertive formation of partially unfolded intermediates.
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