Replica exchange molecular dynamics simulations of amyloid peptide aggregation

M Cecchini; F Rao; M Seeber; A Caflisch

doi:10.1063/1.1809588

Replica exchange molecular dynamics simulations of amyloid peptide aggregation

J Chem Phys. 2004 Dec 1;121(21):10748-56. doi: 10.1063/1.1809588.

Authors

M Cecchini¹, F Rao, M Seeber, A Caflisch

Affiliation

¹ Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.

PMID: 15549960
DOI: 10.1063/1.1809588

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 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

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Amyloid / chemistry*
Amyloid / ultrastructure*
Binding Sites
Computer Simulation
Kinetics
Models, Chemical*
Models, Molecular*
Multiprotein Complexes / chemistry
Multiprotein Complexes / ultrastructure
Protein Binding
Protein Conformation

Substances

Amyloid
Multiprotein Complexes