Compactness determines protein folding type

J Bioinform Comput Biol. 2008 Aug;6(4):667-80. doi: 10.1142/s0219720008003618.


We have demonstrated here that protein compactness, which we define as the ratio of the accessible surface area of a protein to that of the ideal sphere of the same volume, is one of the factors determining the mechanism of protein folding. Proteins with multi-state kinetics, on average, are more compact (compactness is 1.49+/-0.02 for proteins within the size range of 101-151 amino acid residues) than proteins with two-state kinetics (compactness is 1.59+/-0.03 for proteins within the same size range of 101-151 amino acid residues). We have shown that compactness for homologous proteins can explain both the difference in folding rates and the difference in folding mechanisms.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computer Simulation
  • Models, Chemical*
  • Models, Molecular*
  • Protein Conformation
  • Protein Folding*
  • Proteins / chemistry*
  • Proteins / ultrastructure*


  • Proteins