Sequence Determinants of a Protein Folding Pathway

Local hydrophobic collapse of the polypeptide chain and transient long-range interactions in unfolded states of apomyoglobin appear to occur in regions of the amino acid sequence which, upon folding, bury an above-average area of hydrophobic surface. To explore the role of these interactions in protein folding, we prepared and characterized apomyoglobins with compensating point mutations designed to change the average buried surface area in local regions of the sequence, while conserving as much as possible the constitution of the hydrophobic core. The behavior of the mutants in quench-flow experiments to determine the folding pathway was exactly as predicted by the changes in the buried surface area parameter calculated from the amino acid sequence. In addition, spin label experiments with acid-unfolded mutant apomyoglobin showed that the transient long-range contacts that occur in the wild-type protein are abolished in the mutant, while new contacts are observed between areas that now have above-average buried surface area. We conclude that specific groupings of amino acid side-chains, which can be predicted from the sequence, are responsible for early hydrophobic interactions in the first phase of folding in apomyoglobin, and that these early interactions determine the subsequent course of the folding process.