dorsal/arxiv
View SchemaThe influence of geometry, surface character and flexibility on the permeation of ions and water through biological pores
| Authors | Oliver Beckstein, Mark S. P. Sansom |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0402041 |
| URL | https://arxiv.org/abs/q-bio/0402041 |
| DOI | 10.1088/1478-3967/1/1/005 |
| Journal | Physical Biology 1 (2004), 43-53 |
Abstract
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, bacterial mechanosensitive channels (MscL and MscS) and perhaps in some potassium channels (e.g. KcsA, MthK, and KvAP). 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 extended (ca. 0.1 \mu s) molecular dynamic 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 in the effective solvent-surface attraction which in turn leads to an increase in the solvent-wall surface free energy.
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"abstract": "A hydrophobic constriction site can act as an efficient barrier to ion and\nwater permeation if its diameter is less than the diameter of an ion\u0027s first\nhydration shell. This hydrophobic gating mechanism is thought to operate in a\nnumber of ion channels, e.g. the nicotinic receptor, bacterial mechanosensitive\nchannels (MscL and MscS) and perhaps in some potassium channels (e.g. KcsA,\nMthK, and KvAP). Simplified pore models allow one to investigate the primary\ncharacteristics of a conduction pathway, namely its geometry (shape, pore\nlength, and radius), the chemical character of the pore wall surface, and its\nlocal flexibility and surface roughness. Our extended (ca. 0.1 \\mu s) molecular\ndynamic simulations show that a short hydrophobic pore is closed to water for\nradii smaller than 0.45 nm. By increasing the polarity of the pore wall (and\nthus reducing its hydrophobicity) the transition radius can be decreased until\nfor hydrophilic pores liquid water is stable down to a radius comparable to a\nwater molecule\u0027s radius. Ions behave similarly but the transition from\nconducting to non-conducting pores is even steeper and occurs at a radius of\n0.65 nm for hydrophobic pores. The presence of water vapour in a constriction\nzone indicates a barrier for ion permeation. A thermodynamic model can explain\nthe behaviour of water in nanopores in terms of the surface tensions, which\nleads to a simple measure of \"hydrophobicity\" in this context. Furthermore,\nincreased local flexibility decreases the permeability of polar species. An\nincrease in temperature has the same effect, and we hypothesise that both\neffects can be explained by a decrease in the effective solvent-surface\nattraction which in turn leads to an increase in the solvent-wall surface free\nenergy.",
"arxiv_id": "q-bio/0402041",
"authors": [
"Oliver Beckstein",
"Mark S. P. Sansom"
],
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"q-bio.SC",
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],
"doi": "10.1088/1478-3967/1/1/005",
"journal_ref": "Physical Biology 1 (2004), 43-53",
"title": "The influence of geometry, surface character and flexibility on the permeation of ions and water through biological pores",
"url": "https://arxiv.org/abs/q-bio/0402041"
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