The role of hydrophobicity patterns in prion folding as revealed by recurrence quantification analysis of primary structure

Protein Eng. 2000 Feb;13(2):99-104. doi: 10.1093/protein/13.2.99.

Abstract

It has been suggested that the number and strength of local contacts are the major factors governing conformation accessibility of model two ground-state polypeptide chains. This phenomenology has been posed as a possible factor influencing prion folding. To test this conjecture, recurrence quantification analysis was applied to two model 36mers, and the Syrian hamster prion protein. A unique divergence of the radius function for the recurrence quantification variable %DET of hydrophobicity patterns was observed for both 36mers, and in a critical region of the hamster prion protein. This divergence suggests a partition between strong short- and long-range hydrophobicity patterns, and may be an important factor in prion phenomenology, along with other global thermodynamic factors.

MeSH terms

  • Algorithms
  • Amino Acid Sequence
  • Animals
  • Computer Simulation
  • Cricetinae
  • Mesocricetus
  • Models, Chemical
  • Molecular Sequence Data
  • Prions / chemistry*
  • Protein Folding*
  • Recombinant Proteins / chemistry

Substances

  • Prions
  • Recombinant Proteins