In silico study of amphiphilic nanotubes based on cyclic peptides in polar and non-polar solvent

Vinodhkuma Vijayakumar, Ramadoss Vijayaraj, Günther H. Peters

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The stability of cyclic peptide assemblies (CPs) forming a macromolecular nanotube structure was investigated in solvents of different polarity using computational methods. The stability and structure of the complexes were studied using traditional molecular dynamics (MD). Energy of dissociation was estimated from steered MD in combination with umbrella sampling simulations. A cyclic peptide nanotube (CPNT) was constructed by stacking of eight cyclo[(d-Trp-l-Gln-d-Trp-l-Glu)2], and hereafter is referred to as (WQWE)8. Its dissociation was studied by pulling 1, 2, or 3 subunits from the nanotube. The crucial point in the dissociation event of the CP subunit(s) is the breaking of backbone–backbone hydrogen bonds and consecutive annihilation of side chain interactions. Gibbs free energy calculations to estimate the binding affinity of CP subunit(s) reveal that the (WQWE)8 nanotube is significantly more stable in non-polar environments than in polar environments. The presently investigated nanotube, (WQWE)8, displays a higher stability in polar solvent than the previously studied nanotube, (QAEA)8. It appears that tryptophan contributes favorable to the improved stability by forming side chain–side chain hydrogen bonds.
TidsskriftJournal of Molecular Modeling
StatusUdgivet - 2016


  • Cyclic peptide nanotubes
  • Free energy calculations
  • In silico modelling
  • Peptide conformation
  • Simulation techniques
  • Steered molecular dynamics simulations

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