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Monte carlo studies on equilibrium globular protein folding. III. The four helix bundle
Author(s) -
Sikorski Andrzej,
Skolnick Jeffrey
Publication year - 1989
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.360280605
Subject(s) - chemistry , monte carlo method , lattice protein , helix bundle , protein folding , crystallography , bundle , globular protein , native state , folding (dsp implementation) , contact order , sequence (biology) , chemical physics , statistical physics , protein structure , physics , mathematics , materials science , biochemistry , statistics , composite material , electrical engineering , engineering
The nature of the equilibrium conformational transition from the denatured state to a four‐member α‐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.