Self-organization in protein folding and the hydrophobic interaction

J Chem Phys. 2005 Aug 1;123(5):054901. doi: 10.1063/1.1990110.


Self-organization is a critical aspect of living systems. During the folding of protein molecules, the hydrophobic interaction plays an important role in the collapse of the peptide chain to a compact shape. As the hydrophobic core tightens and excludes water, not only does the number of hydrophobic side chain contacts increase, but stabilization is further enhanced by an increase in strength of each hydrophobic interaction between side chains in the core. Thus, the self-organization of the protein folding process augments itself by enhancing the stability of the core against large-scale motions that would unfold the protein. Through calculations and computer simulations on a model four-helix bundle protein, we show how the strengthening of the hydrophobic interaction is crucial for stabilizing the core long enough for completion of the folding process and quantitatively manifests self-organizing dynamical behavior.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Computer Simulation
  • Hydrophobic and Hydrophilic Interactions
  • Models, Statistical
  • Models, Theoretical
  • Molecular Conformation
  • Monte Carlo Method
  • Probability
  • Protein Binding
  • Protein Conformation
  • Protein Folding*
  • Protein Structure, Secondary
  • Proteins / chemistry*
  • Thermodynamics
  • Water / chemistry


  • Proteins
  • Water