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Protein Engineering, Vol. 13, No. 2, 99-104, February 2000
© 2000 Oxford University Press

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

Joseph P. Zbilut1, Charles L. Webber, Jr2, Alfredo Colosimo3 and Alessandro Giuliani4

Department of Molecular Biophysics and Physiology, Rush Medical College, 1653 W. Congress, Chicago, IL 60612, 2 Department of Physiology, Loyola University, Stritch School of Medicine, 2160 S. First Avenue, Maywood, IL 60153, USA, 3 Department of Biochemical Sciences, University of Rome `La Sapienza', P.le A. Moro, 5, 00185 Rome and 4 Istituto Superiore di Sanità, Lab. TCE, Viale Regina Elena, 299, 00161 Rome, Italy

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.


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