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Molecular dynamics study of Na+ transportation in a cyclic peptide nanotube and its influences on water behaviors in the tube

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Abstract

The dynamics of Na+ transportation in a transmembrane cyclic peptide nanotube of 8 × (WL)4/POPE has been simulated. The curve of PMF (potential of mean force) for Na+ moving through the tube, based on ABF (adaptive biasing force) method, indicates that Na+ possesses lower free energy in an α-plane region than in a mid-plane one. It was found that Na+ would desorb one or two water molecules in the first solvation shell when entering the tube and later maintain in a solvation state. The average numbers of water molecules around Na+ are 4.50, 4.09 in the first solvation shell, and 3.10, 4.08 in the second one for Na+ locating in an α-plane zone and a mid-plane region, respectively. However, water molecules far away from Na+ location still nearly arrange in a form of 1-2-1-2 file. The dipole orientations of water molecules in the regions of gaps 1 and 7 display “D-defects”, resulted from the simultaneous electrostatic potentials generated by Na+ and the bare carbonyls at the tube mouths. Such “D-defects” accommodate the energetically favorable water orientations thereby.

The PMF profile of Na+ transportation in an octa-CPNT and D-defects emerging in the tube.

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Acknowledgments

This work has been supported by the National Natural Science Foundation of China (Grant No. 21173154) and the Priority Academic Program Development of Jiangsu Higher Education Institutions. The authors are sincerely thankful to Mr. Jian Liu from Shanghai Institute of Applied Physics, Chinese Academy of Sciences for his insightful suggestions, and indebted to Mr. Zhao Liu and Dr. Jianfeng Yan, School of computer Science & Technology of Soochow University for providing generous amounts of computer facilities assignment on High-performance computing cluster system.

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Authors and Affiliations

  1. Faculty of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou, 215123, People’s Republic of China

    Xuezeng Song, Jianfen Fan, Dongyan Liu, Hui Li & Rui Li

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  1. Xuezeng Song
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  2. Jianfen Fan
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  3. Dongyan Liu
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  4. Hui Li
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Correspondence to Jianfen Fan.

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Song, X., Fan, J., Liu, D. et al. Molecular dynamics study of Na+ transportation in a cyclic peptide nanotube and its influences on water behaviors in the tube. J Mol Model 19, 4271–4282 (2013). https://doi.org/10.1007/s00894-013-1899-4

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  • DOI: https://doi.org/10.1007/s00894-013-1899-4

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