Replica exchange molecular dynamics simulations of amyloid peptide aggregation

Details Replica exchange molecular dynamics simulations of amyloid peptide aggregation Replica exchange molecular dynamics simulations of amyloid peptide aggregation

2004-09-17

arxiv.org/abs/q-bio/0409021v1

Biology

Quantitative Biology

Biomolecules

11 pages, 8 figures, Revtex4

Scientific paper

10.1063/1.1809588

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.

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