Discrete molecular dynamics simulations of peptide aggregation

S Peng; F Ding; B Urbanc; S V Buldyrev; L Cruz; H E Stanley; N V Dokholyan

doi:10.1103/PhysRevE.69.041908

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Discrete molecular dynamics simulations of peptide aggregation

Journal article

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Discrete molecular dynamics simulations of peptide aggregation

S Peng, F Ding, B Urbanc, S V Buldyrev, L Cruz, H E Stanley and N V Dokholyan

Physical review. E, Statistical, nonlinear, and soft matter physics, v 69(4 Pt 1), pp 041908-041908

Apr 2004

DOI: https://doi.org/10.1103/PhysRevE.69.041908

PMID: 15169044

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Abstract

Colloids - chemistry

Temperature

Models, Chemical

Protein Structure, Secondary

Models, Molecular

Macromolecular Substances

Computer Simulation

Protein Denaturation

Protein Binding

Protein Conformation

Amyloid beta-Peptides - chemistry

Binding Sites

Dimerization

We study the aggregation of peptides using the discrete molecular dynamics simulations. Specifically, at temperatures above the alpha-helix melting temperature of a single peptide, the model peptides aggregate into a multilayer parallel beta-sheet structure. This structure has an interstrand distance of 4.8 A and an intersheet distance of 10 A, which agree with experimental observations. Our model explains these results as follows: hydrogen-bond interactions give rise to the interstrand spacing in beta sheets, while Gō interactions between side chains make beta strands parallel to each other and allow beta sheets to pack into layers. An important feature of our results is that the aggregates contain free edges, which may allow for further aggregation of model peptides to form elongated fibrils.

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Details

Title: Discrete molecular dynamics simulations of peptide aggregation
Creators: S Peng - Center for Polymer Studies and Department of Physics, Boston University, Boston, Massachusetts 02215, USA
F Ding
B Urbanc
S V Buldyrev
L Cruz
H E Stanley
N V Dokholyan
Publication Details: Physical review. E, Statistical, nonlinear, and soft matter physics, v 69(4 Pt 1), pp 041908-041908
Publisher: Cold Spring Harbor Press; United States
Resource Type: Journal article
Language: English
Academic Unit: Physics
Web of Science ID: WOS:000221252100045
Scopus ID: 2-s2.0-42749108544
Other Identifier: 991014877949504721

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Collaboration types: Domestic collaboration
Web of Science research areas: Physics, Fluids & Plasmas; Physics, Mathematical

Discrete molecular dynamics simulations of peptide aggregation

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Abstract

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UN Sustainable Development Goals (SDGs)

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