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Biophys J. 2003 Mar;84(3):1518-26.

A minimal physically realistic protein-like lattice model: designing an energy landscape that ensures all-or-none folding to a unique native state.

Pokarowski P, Kolinski A, Skolnick J.

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Institute of Applied Mathematics and Mechanics, Warsaw University, Banacha 2, Poland.

Abstract

A simple protein model restricted to the face-centered cubic lattice has been studied. The model interaction scheme includes attractive interactions between hydrophobic (H) residues, repulsive interactions between hydrophobic and polar (P) residues, and orientation-dependent P-P interactions. Additionally, there is a potential that favors extended beta-type conformations. A sequence has been designed that adopts a native structure, consisting of an antiparallel, six-member Greek-key beta-barrel with protein-like structural degeneracy. It has been shown that the proposed model is a minimal one, i.e., all the above listed types of interactions are necessary for cooperative (all-or-none) type folding to the native state. Simulations were performed via the Replica Exchange Monte Carlo method and the numerical data analyzed via a multihistogram method.

PMID:: 12609858; [PubMed - indexed for MEDLINE]
PMCID:: PMC1302725

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