title: Aggregate geometry in amyloid fibril nucleation.
abstract: We present and study a minimal structure-based model for the self-assembly of peptides into ordered β-sheet-rich fibrils. The peptides are represented by unit-length sticks on a cubic lattice and interact by hydrogen bonding and hydrophobicity forces. Using Monte Carlo simulations with >10(5) peptides, we show that fibril formation occurs with sigmoidal kinetics in the model. To determine the mechanism of fibril nucleation, we compute the joint distribution in length and width of the aggregates at equilibrium, using an efficient cluster move and flat-histogram techniques. This analysis, based on simulations with 256 peptides in which aggregates form and dissolve reversibly, shows that the main free-energy barriers that a nascent fibril has to overcome are associated with changes in width.
authors: Computational Biology and Biological Physics, Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, SE-223 62 Lund, Sweden.
authors: Anders
authors: A
authors: Irbäck
authors: Sigurður Æ
authors: SÆ
authors: Jónsson
authors: Niels
authors: N
authors: Linnemann
authors: Björn
authors: B
authors: Linse
authors: Stefan
authors: S
authors: Wallin
mesh_terms: D000682:Amyloid / Q000737:chemistry* / Q000378:metabolism*; D057927:Hydrophobic and Hydrophilic Interactions; D007700:Kinetics; D008956:Models, Chemical; D009010:Monte Carlo Method; D013329:Structure-Activity Relationship; D013816:Thermodynamics
chemical_list: D000682:Amyloid