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A Minimal Physically Realistic Protein-Like Lattice Model: Designing an Energy Landscape that Ensures All-Or-None Folding to a Unique Native State

Piotr Pokarowski^*, Andrzej Kolinski^, and Jeffrey Skolnick

^* Institute of Applied Mathematics and Mechanics, Warsaw University, Banacha 2, 02-097 Warsaw, Poland; Laboratory of Theory of Biopolymers, Faculty of Chemistry, Warsaw University, Pasteura 1, 02-093 Warsaw, Poland; and Donald Danforth Plant Science Center, Bioinformatics and Computational Genomics, 975 N. Warson Rd., Saint Louis, Missouri 63141 USA

Correspondence: Address reprint requests to Andrzej Kolinski, E-mail: Kolinski{at}chem.uw.edu.pl or Skolnick{at}danforthcenter.org.

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 ß-type conformations. A sequence has been designed that adopts a native structure, consisting of an antiparallel, six-member Greek-key ß-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.