The mechanism by which proteins acquire their native, biologically relevant structures is not yet known. While the three dimensional structures of many proteins have now been solved, very little is known about the structures of protein denatured state ensembles. These ensembles, however, are equally important to the native states in determining protein stability and, presumably, the rates at which proteins fold. We propose to undertake a systematic study of protein denatured states. We will focus on three different small proteins all of which fold by simple, two-state mechanisms. The structures of the denatured states of these proteins will be explored by small angle x-ray scattering. We will compare the effects of different denaturants and also investigate the structures of mutants that have altered denatured state ensembles. The results of these studies will provide new information on the structure of denatured states that will be useful to the development of theoretical models of protein folding. Furthermore, we will for the first time be able to examine 1) the assumed correlation between folding cooperativity and denatured state compactness and 2) any correlation between compactness and folding rate.
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