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

Vinodhkumar Vijayakumar, Ramadoss Vijayaraj, Günther H.J. Peters

Research output: Contribution to journalJournal articleResearchpeer-review

Abstract

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.
Original languageEnglish
Article number264
JournalJournal of Molecular Modeling
Volume22
Issue number11
Number of pages12
ISSN1610-2940
DOIs
Publication statusPublished - 2016

Keywords

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

Fingerprint

Dive into the research topics of 'In silico study of amphiphilic nanotubes based on cyclic peptides in polar and non-polar solvent'. Together they form a unique fingerprint.

Cite this