The twilight zone between protein order and disorder

Biophys J. 2008 Aug;95(4):1612-26. doi: 10.1529/biophysj.108.131151. Epub 2008 Apr 25.


The amino acid composition of intrinsically disordered proteins and protein segments characteristically differs from that of ordered proteins. This observation forms the basis of several disorder prediction methods. These, however, usually perform worse for smaller proteins (or segments) than for larger ones. We show that the regions of amino acid composition space corresponding to ordered and disordered proteins overlap with each other, and the extent of the overlap (the "twilight zone") is larger for short than for long chains. To explain this finding, we used two-dimensional lattice model proteins containing hydrophobic, polar, and charged monomers and revealed the relation among chain length, amino acid composition, and disorder. Because the number of chain configurations exponentially grows with chain length, a larger fraction of longer chains can reach a low-energy, ordered state than do shorter chains. The amount of information carried by the amino acid composition about whether a protein or segment is (dis)ordered grows with increasing chain length. Smaller proteins rely more on specific interactions for stability, which limits the possible accuracy of disorder prediction methods. For proteins in the "twilight zone", size can determine order, as illustrated by the example of two-state homodimers.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Computer Simulation
  • Models, Chemical*
  • Models, Molecular*
  • Molecular Sequence Data
  • Protein Conformation
  • Sequence Analysis, Protein / methods*
  • Structure-Activity Relationship