Hydrophobic collapse model

The nucleation-condensation mechanism can be accommodated in modified framework and hydrophobic-collapse models the framework model must be modified so that formation of secondary structure is linked to the formation of tertiary interactions and the hydrophobic collapse model must have the formation of tertiary interactions linked to the formation of secondary structure. Another variation of concerted structure formation is the hydrophobic zipper. 68 Whatever the distinctions of names, stable tertiary and secondary structural interactions must form concurrently. 

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. 

Regardless of the view of the folding process as discrete steps with defined intermediates or as an energetic fiinnel, one of the interesting questions that still remains open is the order of events during the folding pathways. The three major hypotheses for the order of events are (f) the framework model (22-24), (2) the nucleation-growth mechanism (25), and (3) the hydrophobic collapse model (3,4). 

As indicated above for napsagatran, hydrophobic collapse is a powerful driving force. Models that placed the Pl piperidine in the rather hydrophilic SI region did not take this into account. 

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 ... 

As the water-ethanol mixture has lower permittivity ( = 50) than water (e 80), while the water-N-methylpropionamide mixture has higher permittivity (e 140), it is somewhat surprising that ESR spectra for FS counterions in an aqueous solution of PDADMAC are not consistent with the charged cylindrical cell model. The most likely cause for the failure of the model for pure water are differences in solvation of the polyelectrolyte chain compared to the mixed solvents. The organic components of both solvent mixtures feature ethyl groups that are better suited than water for solvating the hydrophobic parts of the PDADMAC chains. They may thus prevent a local hydrophobic collapse of the chain. 

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