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Molecular dynamics simulation of amyloid beta dimer formation
Journal article   Open access   Peer reviewed

Molecular dynamics simulation of amyloid beta dimer formation

B Urbanc, L Cruz, F Ding, D Sammond, S Khare, S V Buldyrev, H E Stanley and N V Dokholyan
Biophysical journal, v 87(4), pp 2310-2321
Oct 2004
DOI: https://doi.org/10.1529/biophysj.104.040980
PMID: 15454432
Featured in Collection :   UN Sustainable Development Goals @ Drexel
url
https://doi.org/10.1529/biophysj.104.040980View
Published, Version of Record (VoR) Open

Abstract

Protein Structure, Tertiary Motion Multiprotein Complexes - chemistry Models, Chemical Computer Simulation Models, Molecular Protein Binding Protein Conformation Amyloid beta-Peptides - chemistry Binding Sites Dimerization
Recent experiments with amyloid beta (Abeta) peptide indicate that formation of toxic oligomers may be an important contribution to the onset of Alzheimer's disease. The toxicity of Abeta oligomers depends on their structure, which is governed by assembly dynamics. Due to limitations of current experimental techniques, a detailed knowledge of oligomer structure at the atomic level is missing. We introduce a molecular dynamics approach to study Abeta dimer formation. 1), We use discrete molecular dynamics simulations of a coarse-grained model to identify a variety of dimer conformations; and 2), we employ all-atom molecular mechanics simulations to estimate thermodynamic stability of all dimer conformations. Our simulations of a coarse-grained Abeta peptide model predicts 10 different planar beta-strand dimer conformations. We then estimate the free energies of all dimer conformations in all-atom molecular mechanics simulations with explicit water. We compare the free energies of Abeta(1-42) and Abeta(1-40) dimers. We find that 1), dimer conformations have higher free energies compared to their corresponding monomeric states; and 2), the free-energy difference between the Abeta(1-42) and the corresponding Abeta(1-40) dimer conformation is not significant. Our results suggest that Abeta oligomerization is not accompanied by the formation of thermodynamically stable planar beta-strand dimers.

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Collaboration types
Domestic collaboration
Web of Science research areas
Biophysics
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