Investigation of structures and properties of cyclic peptide nanotubes by experiment and molecular dynamics

In order to investigate the structures and properties of cyclic peptide nanotubes of cyclo[(-D-Phe-L-Ala)(n = 3,4,5,6)-], cyclo[(-D-Phe-L-Ala)(n = 4)-] was synthesized and self-assembled to nanotubes, and its structure and morphology of the nanotube were characterized by mass spectrometry (MS), fourier transform infrared spectroscopy (FT-IR) and scanning electron microscopy (SEM). On the basis of these experimental results, the structures of cyclo[(-D-Phe-L-Ala)(n = 3,4,5,6)-] were characterized by molecular dynamics. In addition, the motion behaviors of H(2)O molecules in nanotubes were investigated by molecular dynamics using a COMPASS force field. Experimental results show that cyclo[(-D-Phe-L-Ala)(n = 4)-] peptides self-assemble into nanotube bundles. Molecular modeling results indicate that cyclic peptide nanotubes with n = 3, 4, 5 and 6 are very stable; these nanotubes have internal diameters of 5.9 angstrom, 8.1 angstrom, 10.8 angstrom and 13.1 angstrom and outer diameters of 18.2 angstrom, 21.7 angstrom, 23.4 angstrom and 25.9 angstrom respectively. Modeling results demonstrate that H(2)O molecules move in cooperation in single nanotube and they diffuse in one dimension, but they did not diffuse unilaterally due to the antiparallel ring stacking arrangement.