Molecular dynamics study on the stability of peptide nanotubes placed in POPC phospholipid bilayer

The self-assembly and stacking of cyclic peptides form cyclic peptide nanotubes (CPNT). These nanotubes are able to transfer many substances such as drugs through the cell membrane. For this reason, they must maintain a stable structure in the phospholipid bilayer. Up to now the transfer of different molecules such as water, ions, glucose, glutamic acid, 5FU anticancer drug and so on through peptide nanotubes have been investigated theoretically and experimentally. In this study structure and stability of CPNT [(D-Ala-Glu-D-Ala-Gln)3] placed in POPC(1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) bilayer, is analyzed after 40ns molecular dynamic simulation. This nanotube has been previously synthesized experimentally. This analysis indicates the role of the nonbonded interaction between the side and main chains of cyclic peptide rings and their phospholipid environment, besides the role of non-bonded electrostatic interactions between neighboring cyclic peptide rings in CPNT’s stability. In addition, the number of rings placed in the lipid bilayer along with their arrangement so that similar charges wouldn’t sit on top of each other effect CPNT’s stability. The result of this study can help further experimental investigations in this field

Keywords:

Cyclic peptide nanotube , POPC membrane , Molecular dynamic simulation