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Exploring the early steps of aggregation of amyloid-forming peptide KFFE

Guanghong Wei1, Normand Mousseau1 and Philippe Derreumaux2

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It has been shown recently that even a tetrapeptide can form amyloid fibrils sharing all the characteristics of amyloid fibrils built from large proteins. Recent experimental studies also suggest that the toxicity observed in several neurodegenerative diseases, such as Alzheimer's disease and Creutzfeldt–Jakob disease, is not only related to the mature fibrils themselves, but also to the soluble oligomers formed early in the process of fibrillogenesis. This raises the interest in studying the early steps of the aggregation process. Although fibril formation follows the nucleation–condensation process, characterized by the presence of lag phase, the exact pathways remain to be determined. In this study, we used the activation–relaxation technique and a generic energy model to explore the process of self-assembly and the structures of the resulting aggregates of eight KFFE peptides. Our simulations show, starting from different states with a preformed antiparallel dimer, that eight chains can self-assemble to adopt, with various orientations, four possible distant oligomeric well-aligned structures of similar energy. Two of these structures show a double-layer β-sheet organization, in agreement with the structure of amyloid fibrils as observed by x-ray diffraction; another two are mixtures of dimers and trimers. Our results also suggest that octamers are likely to be below the critical size for nucleation of amyloid fibrils for small peptides.


PACS

87.14.E- Proteins

87.19.X- Diseases

36.20.Fz Constitution (chains and sequences)

87.19.L- Neuroscience

87.15.B- Structure of biomolecules

36.20.Hb Configuration (bonds, dimensions)

MSC

37N25 Dynamical systems in biology (See mainly 92-XX, but also 91-XX)

37M05 Simulation

92D20 Protein sequences, DNA sequences

Subjects

Soft matter, liquids and polymers

Atomic and molecular physics

Medical physics

Biological physics

Dates

Issue 44 (10 November 2004)

Received 30 September 2004

Published 22 October 2004



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