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Prediction of aggregation rate and aggregation-prone segments in polypeptide sequences

Department of Biochemistry, University of Zürich, CH-8057 Zürich, Switzerland

(RECEIVED March 23, 2005; FINAL REVISION June 23, 2005; ACCEPTED July 4, 2005)

The reliable identification of -aggregating stretches in protein sequences is essential for the development of therapeutic agents for Alzheimer’s and Parkinson’s diseases, as well as other pathological conditions associated with protein deposition. Here, a model based on physicochemical properties and computational design of -aggregating peptide sequences is shown to be able to predict the aggregation rate over a large set of natural polypeptide sequences. Furthermore, the model identifies aggregation-prone fragments within proteins and predicts the parallel or anti-parallel -sheet organization in fibrils. The model recognizes different -aggregating segments in mammalian and nonmammalian prion proteins, providing insights into the species barrier for the transmission of the prion disease.

Keywords: Alzheimer’s disease; amyloid; protein aggregation rate; prion protein; species barrier; genetic algorithm; molecular dynamics

Article and publication are at http://www.proteinscience.org/cgi/doi/10.1110/ps.051471205.

Reprint requests to: Amedeo Caflisch, Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland; e-mail: caflisch{at}bioc.unizh.ch; fax: +41-44-635-68-62.

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