Discrete intermediates versus molten globule models for protein folding: characterization of partially folded intermediates of apomyoglobin

Background: Although small proteins may fold in an apparent two-state manner, most studies of protein folding reveal transient intermediates. The ‘molten globule’ has been proposed to be a general intermediate in protein folding. Relatively little is known about the structure of partially folded intermediates, however.

Results: Three different partially folded intermediates of apomyoglobin, having 35%, 50% and 60% helix, were characterized at low pH in the presence of different anions. It was found that increasing helical structure correlated with decreasing size and increasing stability to urea. Similar intermediates have been observed transiently during the folding of apomyoglobin.

Conclusions: The results are consistent with a model for folding in which structural units coalesce to form a core of relatively native-like structure, the remainder of the protein being relatively disordered. For a given protein there will be certain partially folded conformations of particularly low free energy that are preferentially populated under both equilibrium and transient folding conditions. The conformation and topology of the intermediates will be specific to a given protein, so there are no ‘general’ intermediates, such as the molten globule, in folding.