title: The role of hydrophobicity patterns in prion folding as revealed by recurrence quantification analysis of primary structure.
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.
authors.affiliation: Department of Molecular Biophysics and Physiology, Rush Medical College, 1653 W. Congress, Chicago, IL 60612, USA. jzbilut@rush.edu
authors.forename: J P
authors.initials: JP
authors.lastname: Zbilut
authors.forename: C L
authors.initials: CL
authors.lastname: Webber
authors.forename: A
authors.initials: A
authors.lastname: Colosimo
authors.forename: A
authors.initials: A
authors.lastname: Giuliani
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D000818:Animals; D003198:Computer Simulation; D006224:Cricetinae; D008647:Mesocricetus; D008956:Models, Chemical; D008969:Molecular Sequence Data; D011328:Prions / Q000737:chemistry*; D017510:Protein Folding; D011994:Recombinant Proteins / Q000737:chemistry
chemical_list: D011328:Prions; D011994:Recombinant Proteins