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.

Submitted to Phys.Rev. E

References in corpus (3)

• Statistical Analysis of Native Contact Formation in the Folding of Designed Model Proteins
• Thermodynamic control and dynamical regimes in protein folding
• Topological complexity, contact order and protein folding rates

Cited by in corpus (5)

• Entropic rigidity of a crumpling network in a randomly folded thin sheet
• Identifying critical residues in protein folding: Insights from phi-value and Pfold analysis
• Native geometry and the dynamics of protein folding
• The Go model revisited: Native structure and the geometric coupling between local and long-range contacts
• Folding of small proteins: A matter of geometry?