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Replica exchange molecular dynamics simulations of amyloid peptide aggregation

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M. Cecchini; F. Rao; M. Seeber; A. Caflisch

Journal: J Chem Phys
Year: 2004
Volume: 121
Issue: 21
Pages: 10748-10756
DOI: 10.1063/1.1809588
Type of Publication: Journal Article

Amyloid; Binding Sites; Computer Simulation; Kinetics; Models, Chemical; Models, Molecular; Multiprotein Complexes; Protein Binding; Protein Conformation


The replica exchange molecular dynamics (REMD) approach is applied to four oligomeric peptide systems. At physiologically relevant temperature values REMD samples conformation space and aggregation transitions more efficiently than constant temperature molecular dynamics (CTMD). During the aggregation process the energetic and structural properties are essentially the same in REMD and CTMD. A condensation stage toward disordered aggregates precedes the β-sheet formation. Two order parameters, borrowed from anisotropic fluid analysis, are used to monitor the aggregation process. The order parameters do not depend on the peptide sequence and length and therefore allow to compare the amyloidogenic propensity of different peptides