Entropic barriers, transition states, funnels, and exponential protein folding kinetics: a simple model

Protein Sci. 2000 Mar;9(3):452-65. doi: 10.1110/ps.9.3.452.

Abstract

This paper presents an analytically tractable model that captures the most elementary aspect of the protein folding problem, namely that both the energy and the entropy decrease as a protein folds. In this model, the system diffuses within a sphere in the presence of an attractive spherically symmetric potential. The native state is represented by a small sphere in the center, and the remaining space is identified with unfolded states. The folding temperature, the time-dependence of the populations, and the relaxation rate are calculated, and the folding dynamics is analyzed for both golf-course and funnel-like energy landscapes. This simple model allows us to illustrate a surprising number of concepts including entropic barriers, transition states, funnels, and the origin of single exponential relaxation kinetics.

MeSH terms

  • Algorithms
  • Kinetics
  • Models, Molecular
  • Protein Conformation
  • Protein Folding*
  • Temperature