Predicting order and disorder for β-peptide foldamers in water

J Chem Inf Model. 2014 Oct 27;54(10):2776-83. doi: 10.1021/ci5003476. Epub 2014 Sep 15.

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 (3)J 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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Molecular Dynamics Simulation*
  • Peptides / chemistry*
  • Protein Folding
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Thermodynamics
  • Water / chemistry*

Substances

  • Peptides
  • Water