A simple model predicts experimental folding rates and a hub-like topology

J Phys Chem B. 2012 Jun 14;116(23):6764-74. doi: 10.1021/jp212332c. Epub 2012 Apr 11.


A simple model is presented that describes general features of protein folding, in good agreement with experimental results and detailed all-atom simulations. Starting from microscopic physics, and with no free parameters, this model predicts that protein folding occurs remarkably quickly because native-like states are kinetic hubs. A hub-like network arises naturally out of microscopic physical concerns, specifically the kinetic longevity of native contacts during a search of globular conformations. The model predicts folding times scaling as τ(f) ~ e(ξN) in the number of residues, but because the model shows ξ is small, the folding times are much faster than Levinthal's approximation. Importantly, the folding time scale is found to be small due to the topology and structure of the network. We show explicitly how our model agrees with generic experimental features of the folding process, including the scaling of τ(f) with N, two-state thermodynamics, a sharp peak in C(V), and native-state fluctuations.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Kinetics
  • Models, Chemical*
  • Protein Conformation
  • Protein Folding
  • Proteins / chemistry*
  • Thermodynamics*


  • Proteins