title: Predicting order and disorder for β-peptide foldamers in water.
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.
authors.affiliation: SZTE-MTA Lendulet Foldamer Research Group, Institute of Pharmaceutical Analysis, University of Szeged , Somogyi u. 6, H-6720 Szeged, Hungary.
authors.forename: Lukács J
authors.initials: LJ
authors.lastname: Németh
authors.forename: Zsófia
authors.initials: Z
authors.lastname: Hegedüs
authors.forename: Tamás A
authors.initials: TA
authors.lastname: Martinek
mesh_terms: D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000737:chemistry*; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D013816:Thermodynamics; D014867:Water / Q000737:chemistry*
chemical_list: D010455:Peptides; D014867:Water