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

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Abstract

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 H2O 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 Å, 8.1 Å, 10.8 Å and 13.1 Å and outer diameters of 18.2 Å, 21.7 Å, 23.4 Å and 25.9 Å respectively. Modeling results demonstrate 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.

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Authors and Affiliations

  1. School of Materials Science and Engineering, Harbin Institute of Technology, Box 433, No. 92 West Dazhi Street, Harbin, 150001, P.R. China

    Jingchuan Zhu, Jie Cheng, Zhouxiong Liao & Zhonghong Lai

  2. School of Chemical and Environmental Engineering, Harbin University of Science and Technology, No. 52, Xuefu Road, Box 128, Harbin, 150040, P.R. China

    Bo Liu

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  1. Jingchuan Zhu
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Correspondence to Jie Cheng.

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Zhu, J., Cheng, J., Liao, Z. et al. Investigation of structures and properties of cyclic peptide nanotubes by experiment and molecular dynamics. J Comput Aided Mol Des 22, 773–781 (2008). https://doi.org/10.1007/s10822-008-9212-9

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