Folding and form: Insights from lattice simulations
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.
- Publication:
-
Physical Review E
- Pub Date:
- May 2004
- DOI:
- 10.1103/PhysRevE.69.051917
- arXiv:
- arXiv:cond-mat/0312346
- Bibcode:
- 2004PhRvE..69e1917F
- Keywords:
-
- 87.15.Cc;
- 91.45.Ty;
- Folding and sequence analysis;
- Soft Condensed Matter
- E-Print:
- Submitted to Phys.Rev. E