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- Title
Validation of the GROMOS 54A7 Force Field Regarding Mixed α/ β-Peptide Molecules.
- Authors
Wang, Dongqi; Freitag, Fabian; Gattin, Zrinka; Haberkern, Hannah; Jaun, Bernhard; Siwko, Magdalena; Vyas, Rounak; van Gunsteren, Wilfred F.; Dolenc, Jožica
- Abstract
A molecular-dynamics (MD) simulation study of two heptapeptides containing α- and β-amino acid residues is presented. According to NMR experiments, the two peptides differ in dominant fold when solvated in MeOH: peptide 3 adopts predominantly β-hairpin-like conformations, while peptide 8 adopts a 14/ 15-helical fold. The MD simulations largely reproduce the experimental data. Application of NOE atomatom distance restraining improves the agreement with experimental data, but reduces the conformational sampling. Peptide 3 shows a variety of conformations, while still agreeing with the NOE and 3 J-coupling data, whereas the conformational ensemble of peptide 8 is dominated by one helical conformation. The results confirm the suitability of the GROMOS 54A7 force field for simulation or structure refinement of mixed α/ β-peptides in MeOH.
- Subjects
PEPTIDES; MOLECULAR dynamics; AMINO acids; CONFORMATIONAL analysis; ORGANIC compounds
- Publication
Helvetica Chimica Acta, 2012, Vol 95, Issue 12, p2562
- ISSN
0018-019X
- Publication type
Article
- DOI
10.1002/hlca.201200534