|
The energy surface of apomyoglobin appears to have a sizable
energy trap that very early condenses the protein into a topology
with a very small cooperative unit (the AGH core), found in the
totally folded protein, which remains during the rest of the folding
process, perhaps serving as a template. It seems likely that the
presence of secondary structure is required before the 'nucleation'
of this tertiary structure can take place, and the required helical
structure has, indeed, already formed. The helical structure can
be viewed as a 'framework' for the formation of the small cooperative
unit. The next stage is further growth of ordered structure on
top of the small AGH core in both the amount of residues in helices
and an extension of tertiary contacts spreading out from the small
core area. Perhaps surprisingly for a small protein like apomyoglobin,
a second kinetic phase whereby other residues condense into a
native fold occurs much later, on relatively slow time scales.
Hence, two folding units describe the folding of this protein.
From this degree of detail, it is fairly easy to see how the early
structures, even if local and fluctuating in nature, result in
the required constriction in conformational space that accelerates
and directs the folding process.
|