CHROMOPHORE-CHROMOPHORE INTERACTIONS IN UNFOLDED LABELED PROTEINS/NATIVE COND

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This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. The commonly held view that unfolded proteins are random coils without any residual structure is being rigorously scrutinized currently. Some recent NMR studies have indicated that the unfolded state has a significant amount of residual structure that encodes the native topology. At the same time a number of small angle x-ray scattering (SAXS) and light scattering measurements have indicated that the average dimensions of the unfolded state correspond to that expected for random coils. Understanding the structure of the unfolded state is critical to many protein-folding studies. The unfolded state and partially unfolded intermediates have also been implicated in the aggregation of many proteins. There have been only relatively few SAXS studies on the unfolded state under native like conditions and our proposed experiments on two model systems are specifically designed to address this issue. Another conflicting issue that has emerged from investigations of the unfolded state is the discrepancy in results observed between SAXS and FRET measurements on a variety of different proteins. To further investigate this apparent discrepancy, which is critical to the interpretation of a multitude of ensemble and single molecule FRET studies, it would be extremely beneficial if both techniques were applied to a non-folding polypeptide with and without a FRET pair.