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Computational Methods in Nanostructure Design

Replica Exchange Simulations of Self-Assembling Peptides
  • Giovanni Bellesia
  • Sotiria Lampoudi
  • Joan-Emma Shea
Protocol
Part of the Methods in Molecular Biology™ book series (MIMB, volume 474)

Summary

Self-assembling peptides can serve as building blocks for novel biomaterials. Replica exchange molecular dynamics simulations are a powerful means to probe the conformational space of these peptides. We discuss the theoretical foundations of this enhanced sampling method and its use in biomolecular simulations. We then apply this method to determine the monomeric conformations of the Alzheimer amyloid-β(12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28) peptide that can serve as initiation sites for aggregation.

Key Words

Alzheimer amyloid-β peptide biomaterials conformational space sampling molecular dynamics simulations replica exchange algorithm 

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Copyright information

© Humana Press, a part of Springer Science + Business Media, LLC 2008

Authors and Affiliations

  • Giovanni Bellesia
    • 1
  • Sotiria Lampoudi
    • 2
  • Joan-Emma Shea
    • 1
  1. 1.Department of Chemistry and BiochemistryUniversity of CaliforniaSanta Barbara
  2. 2.Department of Computer ScienceUniversity of CaliforniaSanta Barbara

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