The influence of geometry, surface character and flexibility on the permeation of ions and water through biological pores

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  • 25 February 2004
Abstract
Extended (ca. 0.1 micro seconds) molecular dynamics simulations are employed to test the hypothesis that a hydrophobic constriction site can act as an efficient barrier to ion and water permeation if its diameter is less than the diameter of an ion's first hydration shell. This hydrophobic gating mechanism is thought to operate in a number of ion channels, e.g. the nicotinic receptor, the bacterial mechanosensitive channels (MscL and MscS) and the potassium channels (KcsA, MthK, KvAP and KirBac). Simplified pore models allow one to investigate the primary characteristics of a conduction pathway, namely its geometry (shape, pore length and radius), the chemical character of the pore wall surface and its local flexibility and surface roughness. Our simulations show that a short hydrophobic pore is closed to water for radii smaller than 0.45 nm. By increasing the polarity of the pore wall (and thus reducing its hydrophobicity) the transition radius can be decreased until for hydrophilic pores liquid water is stable down to a radius comparable to a water molecule's radius. Ions behave similarly but the transition from conducting to non-conducting pores is even steeper and occurs at a radius of 0.65 nm for hydrophobic pores. The presence of water vapour in a constriction zone indicates a barrier for ion permeation. A thermodynamic model can explain the behaviour of water in nanopores in terms of the surface tensions, which leads to a simple measure of "hydrophobicity" in this context. Furthermore, increased local flexibility decreases the permeability of polar species. An increase in temperature has the same effect, and we hypothesise that both effects can be explained by a decrease of the effective solvent-surface attraction which in turn leads to an increase in the solvent-wall surface free energy.

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