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European Biophysics Journal

, Volume 37, Issue 6, pp 903–912 | Cite as

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

  • Bojan Zagrovic
  • Zrinka Gattin
  • Justin Kai-Chi Lau
  • Matthias Huber
  • Wilfred F. van GunsterenEmail author
Original Paper

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 legend

Conformational 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

Keywords

GROMOS 53A6 β-peptides Molecular dynamics Force field validation 

Notes

Acknowledgments

B.Z acknowledges support from an EMBO postdoctoral fellowship. This work was financially supported by grants from the National Center of Competence in Research (NCCR) in Structural Biology of the Swiss National Science Foundation, which is gratefully acknowledged.

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Copyright information

© EBSA 2008

Authors and Affiliations

  • Bojan Zagrovic
    • 1
    • 2
  • Zrinka Gattin
    • 1
  • Justin Kai-Chi Lau
    • 1
  • Matthias Huber
    • 1
  • Wilfred F. van Gunsteren
    • 1
    Email author
  1. 1.Laboratory of Physical ChemistrySwiss Federal Institute of TechnologyZürichSwitzerland
  2. 2.Laboratory of Computational BiophysicsMediterranean Institute for Life SciencesSplitCroatia

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