Replica exchange molecular dynamics simulations of amyloid peptide aggregation

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 aggregati...

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Bibliographic Details
Published in:The Journal of chemical physics 2004-12, Vol.121 (21), p.10748-10756
Main Authors: Cecchini, M, Rao, F, Seeber, M, Caflisch, A
Format: Article
Language:English
Subjects:
Amyloid - chemistry
Amyloid - ultrastructure
Binding Sites
Computer Simulation
Kinetics
Models, Chemical
Models, Molecular
Multiprotein Complexes - chemistry
Multiprotein Complexes - ultrastructure
Protein Binding
Protein Conformation
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Summary: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 beta-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
ISSN:0021-9606
1089-7690
DOI:10.1063/1.1809588