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Structure and dynamics of two β-peptides in solution from molecular dynamics simulations validated against experiment

Authors
  • Zagrovic, Bojan1, 2
  • Gattin, Zrinka1
  • Lau, Justin Kai-Chi1
  • Huber, Matthias1
  • van Gunsteren, Wilfred F.1
  • 1 Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, Zürich, 8093, Switzerland , Zürich (Switzerland)
  • 2 Mediterranean Institute for Life Sciences, Laboratory of Computational Biophysics, Mestrovicevo setaliste bb, Split, 21000, Croatia , Split (Croatia)
Type
Published Article
Journal
European Biophysics Journal
Publisher
Springer-Verlag
Publication Date
Mar 27, 2008
Volume
37
Issue
6
Pages
903–912
Identifiers
DOI: 10.1007/s00249-008-0307-y
Source
Springer Nature
Keywords
License
Yellow

Abstract

We have studied two different β-peptides in methanol using explicit solvent molecular dynamics simulations and the GROMOS 53A6 force field: a heptapeptide (peptide 1) expected to form a left-handed 314-helix, and a hexapeptide (peptide 2) expected to form a β-hairpin in solution. Our analysis has focused on identifying and analyzing the stability of the dominant secondary structure conformations adopted by the peptides, as well as on comparing the experimental NOE distance upper bounds and 3J-coupling values with their counterparts calculated on the basis of the simulated ensembles. Moreover, we have critically compared the present results with the analogous results obtained with the GROMOS 45A3 (peptide 1) and 43A1 (peptide 2) force fields. We conclude that within the limits of conformational sampling employed here, the GROMOS 53A6 force field satisfactorily reproduces experimental findings regarding the behavior of short β-peptides, with accuracy that is comparable to but not exceeding that of the previous versions of the force field.GCE legendConformational clustering analysis of the simulated ensemble of a ß-hexapeptide with two different simulation setups (a and b). The central members of all of the clusters populating more than 5% of all of the structures are shown, together with the most dominant hydrogen bonds and the corresponding percentages of cluster members containing them

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