Folding and form: insights from lattice simulations.
Monte Carlo simulations of a Miyazawa-Jernigan lattice-polymer model indicate that, depending on the native structure's geometry, the model exhibits two broad classes of folding mechanisms for two-state folders. Folding to native structures of low contact order is driven by backbone distance and is characterized by a progressive accumulation of structure towards the native fold. By contrast, folding to high contact order targets is dominated by intermediate stage contacts not present in the native fold, yielding a more cooperative folding process.
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D000465:Algorithms; D003198:Computer Simulation; D007700:Kinetics; D015233:Models, Statistical; D009010:Monte Carlo Method; D011487:Protein Conformation; D017510:Protein Folding; D013816:Thermodynamics; D013997:Time Factors