Modeling transient collapsed states of an unfolded protein to provide insights into early folding events

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Abstract
The primary driving force for protein folding is the sequestration of hydrophobic side chains from solvent water, but the means whereby the amino acid sequence directs the folding process to form the correct final folded state is not well understood. Measurements of NMR line broadening in spin-labeled samples of unfolded apomyoglobin at pH 2.3 have been used to derive a quantitative model for transient hydrophobic interactions between various sites in the polypeptide chain, as would occur during the initiation of protein folding. Local clusters of residues with high values for the parameter "average area buried upon folding" (AABUF) form foci not only for local contacts but for long-range interactions, the relative frequencies of which can be understood in terms of differences in the extent of reduction in chain configurational entropy that occurs upon formation of nonlocal contacts. These results complement the striking correlation previously observed between the kinetic folding process of apomyoglobin and the AABUF of its amino acid sequence [Nishimura C, Lietzow MA, Dyson HJ, Wright PE (2005) J Mol Biol 351:383-392]. For the acid-unfolded states of apomyoglobin, our approach identifies multiple distinct hydrophobic clusters of differing thermodynamic stability. The most structured of these clusters, although sparsely populated, have both native-like and nonnative character; the specificity of the transient long-range contacts observed in these states suggests that they play a key role in initiating chain collapse and folding.