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

It has been suggested that the number and strength of local contacts are th e major factors governing conformation accessibility of model two ground-st ate polypeptide chains. This phenomenology has been posed as a possible fac tor influencing prion folding. To test this conjecture, recurrence quantifi cation analysis was applied to two model 36mers, and the Syrian hamster pri on protein. A unique divergence of the radius function for the recurrence q uantification variable %DET of hydrophobicity patterns was observed for bot h 36mers, and in a critical region of the hamster prion protein, This diver gence suggests a partition between strong short- and long-range hydrophobic ity patterns, and may be an important factor in prion phenomenology, along with other global thermodynamic factors.