Folding and form: Insights from lattice simulations

2003/12/31 by Patrícia F. N. Faísca, P. F. N. Faisca, M. M. Telo da Gama +1 · 4 citations
Engineering · Materials Science · Physics and Astronomy · #Adhesion, Friction, and Surface Interactions #Block Copolymer Self-Assembly #Theoretical and Computational Physics #cond-mat.soft

paper · pdf · doi:10.1103/physreve.69.051917

published as Physical Review E 69, 051917 (2004) · Submitted to Phys.Rev. E

arxiv created 2004/02/05 · openalex publication_date 2004/05/28 · arxiv updated 2009/12/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28

Abstract

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.

Citations

• Topological complexity, contact order, and protein folding rates

Cited by

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

Related

• On the relation between native geometry and conformational plasticity
• Native geometry and the dynamics of protein folding
• Non‐native interactions play an effective role in protein folding dynamics
• Introducing Protein Folding Using Simple Models
• Looking for packing units of the protein structure