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, ribonuclease H, 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 co-opertive formation of partially unfolded intermediates.
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