Monte Carlo studies on equilibrium globular protein folding. III. The four helix bundle.
The nature of the equilibrium conformational transition from the denatured state to a four-member alpha-helical bundle was studied employing a dynamic Monte Carlo algorithm in which the model protein chain was confined to a tetrahedral lattice. The model chain was allowed to hunt over all phase space, the target native state was not assumed a priori, and no site-specific interactions were introduced. The exterior vs the interior part of the protein is distinguished by the pattern of hydrophilic and hydrophobic interactions encoded into the primary sequence. The importance of a statistical preference for forming bends, as a function of bend location in the primary sequence, and helical wheel type cooperative interactions were examined, and the necessary conditions for collapse of the chain to the unique native structure were investigated. It was found that an amphipathic pattern of hydrophobic/hydrophilic interactions along with a statistical preference of the central residues for bend formation are sufficient to obtain the four-helix bundle. The transition to the native state has an all-or-none character.
Sikorski
A
A
Skolnick
J
J
D000465:Algorithms; D046911:Macromolecular Substances; D008962:Models, Theoretical; D009010:Monte Carlo Method; D011487:Protein Conformation; D011506:Proteins
D046911:Macromolecular Substances; D011506:Proteins