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Investigating the mechanism of peptide aggregation: Insights from mixed Monte Carlo-Molecular dynamics simulations

by: Massimiliano Meli, Giulia Morra, and Giorgio Colombo

In: BIOPHYSICAL JOURNAL, Vol. 94, Nr. 11 9650 ROCKVILLE PIKE, BETHESDA, MD 20814-3998 USA: BIOPHYSICAL SOC (June 2008) , p. 4414-4426.

Abstract

The early stages of peptide aggregation are currently not accessible by experimental techniques at atomic resolution. In this article, we address this problem through the application of a mixed simulation scheme in which a preliminary coarse-grained Monte Carlo analysis of the free-energy landscape is used to identify representative conformations of the aggregates and subsequent all-atom molecular dynamics simulations are used to analyze in detail possible pathways for the stabilization of oligomers. This protocol was applied to systems consisting of multiple copies of the model peptide GNNQQNY, whose detailed structures in the aggregated state have been recently solved in another study. The analysis of the various trajectories provides dynamical and structural insight into the details of aggregation. In particular, the simulations suggest a hierarchical mechanism characterized by the initial formation of stable parallel beta-sheet dimers and identify the formation of the polar zipper motif as a fundamental feature for the stabilization of initial oligomers. Simulation results are consistent with experimentally derived observations and provide an atomically detailed view of the putative initial stages of fibril formation.

BibTeX record

@article{ISI:000255904300027,
  abstract = {{The early stages of peptide aggregation are currently not accessible by
   experimental techniques at atomic resolution. In this article, we
   address this problem through the application of a mixed simulation
   scheme in which a preliminary coarse-grained Monte Carlo analysis of
   the free-energy landscape is used to identify representative
   conformations of the aggregates and subsequent all-atom molecular
   dynamics simulations are used to analyze in detail possible pathways
   for the stabilization of oligomers. This protocol was applied to
   systems consisting of multiple copies of the model peptide GNNQQNY,
   whose detailed structures in the aggregated state have been recently
   solved in another study. The analysis of the various trajectories
   provides dynamical and structural insight into the details of
   aggregation. In particular, the simulations suggest a hierarchical
   mechanism characterized by the initial formation of stable parallel
   beta-sheet dimers and identify the formation of the polar zipper motif
   as a fundamental feature for the stabilization of initial oligomers.
   Simulation results are consistent with experimentally derived
   observations and provide an atomically detailed view of the putative
   initial stages of fibril formation.}},
  added-at = {2009-01-11T01:42:11.000+0100},
  address = {{9650 ROCKVILLE PIKE, BETHESDA, MD 20814-3998 USA}},
  affiliation = {{Colombo, G (Reprint Author), CNR, Ist Chim \& Ricoscimento Mol, Via Mario Bianco 9, I-20131 Milan, Italy.
   {[}Meli, Massimiliano; Morra, Giulia; Colombo, Giorgio] CNR, Ist Chim \& Ricoscimento Mol, I-20131 Milan, Italy.}},
  author = {Meli, Massimiliano and Morra, Giulia and Colombo, Giorgio},
  author-email = {{giorgio.colombo@icrm.cnr.it}},
  biburl = {http://www.bibsonomy.org/bibtex/24cf4d5345264bbdaadc1a0d714c06f84/huiyangsfsu},
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  doc-delivery-number = {{301OA}},
  doi = {{10.1529/biophysj.107.121061}},
  interhash = {a8a58cda7310bf4b211fee16e62e4ac6},
  intrahash = {4cf4d5345264bbdaadc1a0d714c06f84},
  issn = {{0006-3495}},
  journal = {{BIOPHYSICAL JOURNAL}},
  journal-iso = {{Biophys. J.}},
  keywords = {formation hierarchical},
  keywords-plus = {{AMYLOID FIBRIL FORMATION; CROSS-BETA-SPINE; FOLDING SIMULATIONS; VILLIN
   HEADPIECE; ENERGY LANDSCAPE; FORMING PEPTIDE; EARLY STEPS; IN-VITRO;
   PROTEIN; OLIGOMERS}},
  language = {{English}},
  month = {{JUN 1}},
  number = {{11}},
  number-of-cited-references = {{62}},
  pages = {{4414-4426}},
  publisher = {{BIOPHYSICAL SOC}},
  subject-category = {{Biophysics}},
  times-cited = {{1}},
  timestamp = {2009-01-11T01:42:11.000+0100},
  title = {{Investigating the mechanism of peptide aggregation: Insights from mixed
   Monte Carlo-Molecular dynamics simulations}},
  type = {{Article}},
  unique-id = {{ISI:000255904300027}},
  volume = {{94}},
  year = {{2008}}
}

Endnote record

%0 Journal Article
%1 ISI:000255904300027
%A Meli, Massimiliano
%A Morra, Giulia
%A Colombo, Giorgio
%C {9650 ROCKVILLE PIKE, BETHESDA, MD 20814-3998 USA}
%D {2008}
%I {BIOPHYSICAL SOC}
%J {BIOPHYSICAL JOURNAL}
%K 
%N {11}
%P {4414-4426}
%T {Investigating the mechanism of peptide aggregation: Insights from mixed
   Monte Carlo-Molecular dynamics simulations}
%R {10.1529/biophysj.107.121061}
%V {94}
%X {The early stages of peptide aggregation are currently not accessible by
   experimental techniques at atomic resolution. In this article, we
   address this problem through the application of a mixed simulation
   scheme in which a preliminary coarse-grained Monte Carlo analysis of
   the free-energy landscape is used to identify representative
   conformations of the aggregates and subsequent all-atom molecular
   dynamics simulations are used to analyze in detail possible pathways
   for the stabilization of oligomers. This protocol was applied to
   systems consisting of multiple copies of the model peptide GNNQQNY,
   whose detailed structures in the aggregated state have been recently
   solved in another study. The analysis of the various trajectories
   provides dynamical and structural insight into the details of
   aggregation. In particular, the simulations suggest a hierarchical
   mechanism characterized by the initial formation of stable parallel
   beta-sheet dimers and identify the formation of the polar zipper motif
   as a fundamental feature for the stabilization of initial oligomers.
   Simulation results are consistent with experimentally derived
   observations and provide an atomically detailed view of the putative
   initial stages of fibril formation.}