Molecular Modeling Investigation of Side Chain Structures of Self-Assembled Cyclic Peptide Nanotubes

摘要

In this paper, the effects of side chain conformation on the stability, diameter wall thickness, and outer surface matching of self-assembled cyclic peptide nanotube made of cyclo[(-D-Ala-L-AlaR)(n=6)(-)] (R = -C4H9) were investigated using molecular modeling methods. The results show that the side chains conformations have direct relationships with both the wall thickness and outer surface of the nanotube, while it has no influence on nanotube internal diameter. When dihedral angles C-C-C-C(0) of the single bond connected directly to the backbone ring rotated, the nanotubes have wall thicknesses of 8.35 angstrom, 7.55 angstrom, 8.05 angstrom and 8.05 angstrom, respectively. Energy and outer surface calculations suggest that the conformation with dihedral angle of 178 degrees and 179 degrees have a good match with dodecanethiol monolayer.