Folding and form: Insights from lattice simulations

Abstract

Monte Carlo simulations of a Miyazawa-Jernigan lattice-polymer model indicate that, depending on the native's structure 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 contact range and is characterised by progressive accumulation of structure towards the native fold. By contrast, folding to high contact order targets is largely dominated by intermediate stage contacts which are not present in the native fold, yielding a more cooperative folding process.