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Biophysical Journal 85:3544-3557 (2003)
© 2003 The Biophysical Society

Protein Aggregation/Folding: The Role of Deterministic Singularities of Sequence Hydrophobicity as Determined by Nonlinear Signal Analysis of Acylphosphatase and Aß(1–40)

Joseph P. Zbilut *, Alfredo Colosimo {dagger}, Filippo Conti {ddagger}, Mauro Colafranceschi {dagger} ¶, Cesare Manetti {ddagger}, MariaCristina Valerio {ddagger}, Charles L. Webber, Jr. § and Alessandro Giuliani ¶

* Department of Molecular Biophysics and Physiology, Rush Medical College, Chicago, Illinois; {dagger} Department of Human Physiology and Pharmacology, University of Rome "La Sapienza," Rome, Italy; {ddagger} Department of Chemistry, University of Rome "La Sapienza," Rome, Italy; § Department of Physiology, Loyola University Medical Center, Maywood, Illinois; and Health and Environment Department, Istituto Superiore di Sanitá, Rome, Italy

Correspondence: Address reprint requests to Joseph P. Zbilut. Tel.: 312-942-6008; Fax: 312-942-8711; E-mail: joseph_p_zbilut{at}rush.edu.

The problem of protein folding vs. aggregation was investigated in acylphosphatase and the amyloid protein Aß(1–40) by means of nonlinear signal analysis of their chain hydrophobicity. Numerical descriptors of recurrence patterns provided the basis for statistical evaluation of folding/aggregation distinctive features. Static and dynamic approaches were used to elucidate conditions coincident with folding vs. aggregation using comparisons with known protein secondary structure classifications, site-directed mutagenesis studies of acylphosphatase, and molecular dynamics simulations of amyloid protein, Aß(1–40). The results suggest that a feature derived from principal component space characterized by the smoothness of singular, deterministic hydrophobicity patches plays a significant role in the conditions governing protein aggregation.




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