Water and ion permeability of a claudin model: A computational study

Proteins. 2016 Mar;84(3):305-15. doi: 10.1002/prot.24969. Epub 2016 Feb 1.


At present, the three-dimensional structure of the multimeric paracellular claudin pore is unknown. Using extant biophysical data concerning the size of the pore and permeation of water and cations through it, two three-dimensional models of the pore are constructed in silico. Molecular Dynamics (MD) calculations are then performed to compute water and sodium ion permeation fluxes under the influence of applied hydrostatic pressure. Comparison to experiment is made, under the assumption that the hydrostatic pressure applied in the simulations is equivalent to osmotic pressure induced in experimental measurements of water/ion permeability. One model, in which pore-lining charged is distributed evenly over a selectivity filter section 10-16 Å in length, is found to be generally consistent with experimental data concerning the dependence of water and ion permeation on channel pore diameter, pore length, and the sign and magnitude of pore lining charge. The molecular coupling mechanism between water and ion flow under conditions where hydrostatic pressure is applied is computationally elucidated.

Keywords: claudin; claudin-2; graphene; ion channels; ion permeation; nanotube; water permeation.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Claudins / chemistry*
  • Hydrostatic Pressure
  • Molecular Dynamics Simulation
  • Osmolar Concentration
  • Permeability
  • Protein Structure, Quaternary
  • Sodium / chemistry*
  • Water / chemistry*


  • Claudins
  • Water
  • Sodium