Predicting order and disorder for β-peptide foldamers in water

Lukács J. Németh, Zsófia Hegedüs, Tamás A. Martinek

Research output: Contribution to journalArticle

8 Citations (Scopus)

Abstract

Following a quantitative validation approach, we tested the AMBER ff03 and GAFF force fields with the TIP3P explicit water model in molecular dynamic simulations of β-peptide foldamers. The test sequences were selected to represent a wide range of folding behavior in water: compact helix, strand mimetic geometry, and the state of disorder. The combination AMBER ff03-TIP3P successfully predicted the experimentally observed conformational properties and reproduced the NOE distances and backbone 3J coupling data at a good level. GAFF was unable to produce folded structures correctly due to its biased torsion potentials. We can recommend AMBER ff03-TIP3P for simulations involving β-peptide sequences in aqueous media including ordered and disordered structures.

Original languageEnglish
Pages (from-to)2776-2783
Number of pages8
JournalJournal of Chemical Information and Modeling
Volume54
Issue number10
DOIs
Publication statusPublished - Oct 27 2014

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ASJC Scopus subject areas

  • Chemistry(all)
  • Chemical Engineering(all)
  • Computer Science Applications
  • Library and Information Sciences

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