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Title: Energetic and dynamic analysis of transport of Na + and K + through a cyclic peptide nanotube in water and in lipid bilayers

Potential of mean force (PMF) profiles and position-dependent diffusion coefficients of Na + and K + are calculated to elucidate the translocation of ions through a cyclic peptide nanotube, composed of 8 × cyclo[-(D-Leu-Trp) 4-] rings, in water and in hydrated DMPC bilayers. The PMF profiles and PMF decomposition analysis for the monovalent cations show that favorable interactions of the cations with the CPN as well as the lipid bilayer and dehydration free energy penalties are two major competing factors which determine the free energy surface for ion transport through CPNs both in water and lipid bilayers, and that the selectivity of CPNs to cations mainly arises from favorable interaction energies of cations with CPNs and lipid bilayers that are more dominant than the dehydration penalties. Calculations of the position-dependent diffusion coefficients and dynamic friction kernels of the cations indicate that the dehydration process along with the molecular rearrangements occurring outside the channel and the coupling of the ion motions with the chain-structured water movements inside the channel lead to decrease of the diffusion coefficients far away from the channel entrance and also reduced coefficients inside the channel. Here the PMF and diffusivity profiles for Na + and K +more » reveal that the energetics of ion transport through the CPN are governed by global interactions of ions with all the components in the system while the diffusivity of ions through the channel is mostly determined by local interactions of ions with the confined water molecules inside the channel. Comparison of Na + and K + ion distributions based on overdamped Brownian dynamics simulations based on the PMF and diffusivity profiles with the corresponding results from molecular dynamics shows good agreement, indicating accuracy of the Bayesian inference method for determining diffusion coefficients in this application. In addition this work shows that position-dependent diffusion coefficients of ions are required to explain the dynamics and conductance of ions through the CPN properly.« less
 [1] ;  [1] ;  [1] ;  [2] ;  [1]
  1. Kangwon National Univ., Gangwon-do (Republic of Korea)
  2. Northwestern Univ., Evanston, IL (United States)
Publication Date:
Grant/Contract Number:
Accepted Manuscript
Journal Name:
Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces and Biophysical Chemistry
Additional Journal Information:
Journal Volume: 120; Journal Issue: 46; Journal ID: ISSN 1520-6106
American Chemical Society
Research Org:
Northwestern Univ., Evanston, IL (United States)
Sponsoring Org:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)
Contributing Orgs:
This research was supported by Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education, Science and Technology (No. NRF-2014R1A1A2059300). This study was also supported by Research Grant from Kangwon National University (No. 120110130).
Country of Publication:
United States
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; 36 MATERIALS SCIENCE; 77 NANOSCIENCE AND NANOTECHNOLOGY; ion transport; cyclic peptide nanotube; potential of mean force; diffusivity
OSTI Identifier: