Collapse cooperativity

Miranker, A., Dobson, C.M. Collapse and cooperativity in protein folding. Curr. Opin. Struct. Biol. 

A low AH for a cooperative cluster rotation allows excitation of a cluster of atoms from normal to saddle-point positions. Such an excitation may, in turn, lower the energy of the saddle-point sites relative to the normal sites, thus effectively introducing a AHg(T) that collapses in a smooth transition. At temperatures T> T, the mobile ions become disordered over the normal and saddle-point sites. Such a situation appears to be illustrated by stoichiometric LijN and PbFj (Goodenough, 1984). 

The two examples of adsorbed side chain substituted macromolecules, i.e., the poly(n-butyl acrylate) brush and the tris(p-undecyloxybenzyloxo) benzoate jacketed polystyrene, demonstrate two rather complementary aspects of the interaction of such molecules with a planar surface. In the first case the two-dimension to three-dimension transition results in a cooperative collapse of an extended coil conformation to a globule. The second case shows a rather high degree ordering with a distinct orientation of the backbone in the substrate plane. Combination of both effects and partial desorption can lead to a repta-tion-hke directed motion as depicted schematically in Fig. 36. 

Fig. 5. Protein folding. The unfolded polypeptide chain collapses and assembles to form simple structural motifs such as p-sheets and a-helices by nucleation-condensation mechanisms involving the formation of hydrogen bonds and van der Waal s interactions. Small proteins (eg, chymotrypsin inhibitor 2) attain their final (tertiary) structure in this way. Larger proteins and multiple protein assemblies aggregate by recognition and docking of multiple domains (eg, p-barrels, a-helix bundles), often displaying positive cooperativity. Many noncovalent interactions, including hydrogen bonding, van der Waal s and electrostatic interactions, and the hydrophobic effect are exploited to create the final, compact protein assembly. Further structural...

As a rule, the distortion of the water lattice that is found in water without a solute (1) can easily take place in cooperation with the accompanying cation except in the cases of potassium, rubidium, and cesium. These ions are large enough to fill the cavities of the water lattice and to attenuate the lattice vibrations, thus preventing a local collapse of the structure and an increase in the number of interstitial water molecules. The normal water structure is essentially retained, and the lattice, stabilized by cations of the proper size, rejects the complex nonfitting ion (2). 

The first two stages observed in the folding trajectories corresponded to a fast entropic recoil of the extended polymer, followed by a cooperative collapse that reduces the length of the protein back to its folded length [10]. To further... 

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