Replica exchange molecular dynamics simulations of amyloid peptide aggregation

TitleReplica exchange molecular dynamics simulations of amyloid peptide aggregation
Publication TypeJournal Article
Year of Publication2004
AuthorsCecchini M., Rao F., Seeber M., Caflisch A.
JournalJournal of Chemical Physics
Volume121
Issue21
Pagination10748-10756
Date Published2004 Dec 1
Type of ArticleResearch Article
ISSN0021-9606
KeywordsAmyloid, Binding Sites, Computer Simulation, Kinetics, Models, Chemical, Models, Molecular, Multiprotein Complexes, Protein Binding, Protein Conformation
Abstract

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

DOI10.1063/1.1809588
pubindex

0063

Alternate JournalJ Chem Phys
PubMed ID15549960
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