Molecular Modeling Of Self-Assembled Cyclic Peptide Nanotube

Cyclic peptide nanotubes (SPNs) is composed of alternating D,L-amino acids, in which backbone ring prefer a plate-like conformation, and C=O and N-H group lie approximately perpendicular to the backbone plane. Such a conformation may facilitate the backbone-backbone antiparallelβ-sheet-like ring stacking arrangements through intermolecular hydrogen-bonding interactions.The inner and outer surface properties of peptide nanotubes can be modified by choosing different amino acid residues with specific side chain functionalities, and the ring size of peptide nanotubes can be changed by changing the numbers of peptide subunits employed. This flexible design and easy synthesis, has enabled these peptide nanotubes to be used as artificial trans-membrane ion channels, templates for nanoparticles, mimicing pore structures, nanoscale testing tubes and good biosensorsWhile SPNs are prone to congregate, it is difficult to characterize their structures and properties. We employed molecular modeling to investigate cyclic peptide monomer, dimer and nanotubes of three systems: cyclo-[D-Ala-L-Ala]_n (n=3,4,5,6,7,8), cyclo-[D-Phe-L-Ala]n (n=3,4,5,6,7,8) and cyclo-[(1R,3S)-γ-Acc-D-Phe]_n (n=3,4).Results show that cyclic peptide of n=7,8 also can adopt plate conformation and self-assemble into nanotubes.There are two different residue faces in one peptide ring due to steric and polarity difference of amino acid residues. In cyclo-[(1R,3S)-γ-Acc-D-Phe]_n (n=3,4),dimerα-αis more stable than dimerγ-γ. For dimers have different ability to adsorb CHCl₃,indicate it possible to alter the property of cyclic peptide nanotube.Inner and outer diameters of cyclic peptide nanotube are measured by analyzing the concentration of nanotube. the resulting internal diameters are 5.9 ?, 8.1 ?, 10.8 ? and 13.1 ? and the outer diameters are 18.2 ?, 21.7 ?, 23.4 ? and 25.9 ? for n=3, 4, 5 and 6 respectively. Molecular modeling results also show that H2O 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. Cooperated diffusion of H₂O molecules in cyclic peptide nanotube may bring this class nanotube specific character and it needs driving force for H₂O molecules to transport through the nanotube unilaterally.We designed anisotropic nanotube unilateral transportation of cyclic peptide nanotube...