A minimal physically realistic protein-like lattice model: designing an energy landscape that ensures all-or-none folding to a unique native state.
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.
Pokarowski
Piotr
P
Institute of Applied Mathematics and Mechanics, Warsaw University, Banacha 2, Poland.
Kolinski
Andrzej
A
Skolnick
Jeffrey
J
D020816:Amino Acid Motifs; D003198:Computer Simulation; D003461:Crystallography / Q000379:methods*; D004735:Energy Transfer; D019277:Entropy; D008958:Models, Molecular; D009010:Monte Carlo Method; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D055672:Static Electricity; D013314:Stress, Mechanical
D010455:Peptides; D011506:Proteins