Hydrophobic collapse

AM Gutm, VI Abkevich, El Shakhnovich. Is burst hydrophobic collapse necessary for protein folding Biochemistry 34 3066-3076, 1995. 

Mok KH, Kuhn LT, Goez M, Day IJ, Lin JC, Andersen NH, Hore PJ (2007) A pre-existing hydrophobic collapse in the unfolded state of an ultrafast folding protein. Nature 447 106-109. 

Concomitant Hydrophobic Collapse and Partial Helix Formation... 

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. 

The spirobenzoxazepine 28 was studied by 2-D and nuclear Overhauser enhancement Spectroscopy (NOESY) NMR and X-ray crystallography, and in both cases the same chair conformation, 28, was formed (See Figure 5). The authors conclude that this compound 28 is a semirigid scaffold, able to present various substituents without undergoing hydrophobic collapse, and 28 behaves structurally as a privileged structure <2004TL1051>. 

Once formed, a bubble nucleus is exceedingly stable.. ..There appears to be no time limit beyond which it is not possible to regenerate a bubble from a hydrophobic collapse site. In these experiments as much as 48 hours were permitted to elapse between bubble collapse and regeneration (ref. 84 cf. synthetic microbubble disappearance and formation in Section 10.4). 

The preorganised macrocycle binding sites remain effective at all dendrimer generation levels and hence binding is not inhibited by hydrophobic collapse of the dendritic branches. 

Aromatic groups are suggested to interact with each other both polar and nonpolar conformation, indeed, can undergo to hydrophobic collapse of C2 and one of C3 - phenyl rings [70],... 

The decreased degree of hydrophobic collapse with the default dielectric screening (AGBNP) as compared with additional dielectric screening (AGBNP+) is due to a salt bridge forming between the side chains of K50... 

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