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Self-organization in protein folding and the hydrophobic interaction
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Image of FIG. 1.
FIG. 1.

Schematic diagrams illustrating the hydrophobic interaction. (a) Hydrophobic energy of formation when nonpolar side chains interact in pairs and release some water molecules into the bulk solvent. (b) Hydrophobic energy of transfer when several side chains form a core and most clathrate bound water molecules are liberated.

Image of FIG. 2.
FIG. 2.

A display of the four-helix bundle used in the computer simulations. The backbone is lightly shaded and the hydrophobic side chains are darkly shaded.

Image of FIG. 3.
FIG. 3.

Time dependence of the nonequilibrium correlation function of the helicity for different hydrophobic interaction strengths .

Image of FIG. 4.
FIG. 4.

For each correlation curve of Fig. 3, is plotted as a function of the hydrophobic strength . The data points are fitted with the curve .

Image of FIG. 5.
FIG. 5.

Free energy, calculated from as a function of in kcal/mol. Self-organization is manifested in the dynamic strengthening of as the protein folds, which deepens the free-energy minimum of the native state (high ) and increases its stability relative to the unfolded configuration (low ).


Generic image for table
Table I.

Average stability times for a four-helix bundle as a function of the strength of the hydrophobic interaction, ( for one bond), calculated from Eq. (3).

Generic image for table
Table II.

Computer simulation results for the stability of a four-helix bundle. Unfolding is defined to have occurred when half of the residues in any of the four helices are no longer in the helix configuration.


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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Self-organization in protein folding and the hydrophobic interaction