Hydrophobic collapse protein folding model

In addition to the histogram methodology, this chapter has also described and applied overlap functions to analyze the structural behavior of the protein model during the cooling process. When applied in concert with the histogram calculations, the results indicate the system folds in two transitions. The first occurs at Tm 242 K, where the system undergoes a hydrophobic collapse to what could be referred to as a molten globule ... 

Hydrophobic collapse model The formation of hydrophobic clusters drives compaction of the protein so that the polypeptide chain folds in a confined volume narrowing the conformational search to the native state (Kim and Baldwin, 1990). The expulsion of water from the burial of nonpolar surfaces provides the hydrophobic driving force and the secondary structures are formed during hydrophobic collapse. 

Optimal rates of folding occur when there is not an initial collapse of structure, hydrophobic or otherwise, but when there is a specific and extended nucleus in the transition state model proteins evolve toward nucleation mechanisms with extended nuclei.45,47... 

---