Search for folding initiation sites from amino acid sequence

J Bioinform Comput Biol. 2008 Aug;6(4):681-91. doi: 10.1142/s021972000800362x.


A crucial event in protein folding is the formation of a folding nucleus, which is a structured part of the protein chain in the transition state. We demonstrate a correlation between locations of residues involved in the folding nuclei and locations of predicted amyloidogenic regions. The average Phi-values are significantly greater inside amyloidogenic regions than outside them. We have found that fibril formation and normal folding involve many of the same key residues, giving an opportunity to outline the folding initiation site in protein chains. The search for folding initiation sites for apomyoglobin and ribonuclease. A coincides with the predictions made by other approaches.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Amyloid / chemistry*
  • Amyloid / ultrastructure*
  • Binding Sites
  • Computer Simulation
  • Models, Chemical*
  • Models, Molecular*
  • Molecular Sequence Data
  • Protein Binding
  • Protein Folding
  • Sequence Analysis, Protein / methods*


  • Amyloid