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Potential of mean force calculations of ligand binding to ion channels from Jarzynski’s equality and umbrella sampling
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10.1063/1.2904461
/content/aip/journal/jcp/128/15/10.1063/1.2904461
http://aip.metastore.ingenta.com/content/aip/journal/jcp/128/15/10.1063/1.2904461
View: Figures

Figures

Image of FIG. 1.
FIG. 1.

Lateral views of the carbon nanotube (left) and the gramicidin A channel (right) systems. The nanotube is surrounded by a layer of capped nanotubes (only two are shown for clarity). Gramicidin A is embedded in a lipid bilayer (only the head groups of the lipid molecules are depicted by large balls). The ion is at the pore center surrounded by single-file water molecules (little balls) in both cases. The systems are hydrated with water on both sides.

Image of FIG. 2.
FIG. 2.

Bound configuration of the HERG potassium channel with CnErg1 toxin. The toxin is peripherally bound to a subunit as depicted. Only two of the four subunits of the potassium channel are displayed for clarity. One ion is in the cavity and two others are in the S2–S4 sites of the selectivity filter.

Image of FIG. 3.
FIG. 3.

PMF of a ion along the central axis of the carbon nanotube calculated by using umbrella sampling (us) and Jarzynski’s equality with a pulling velocity of (je-10) and (je-5).

Image of FIG. 4.
FIG. 4.

Similar to Fig. 3 but for the gramicidin A channel. The symmetric PMF is obtained using umbrella sampling (us) and the asymmetric one using Jarzynski’s equality (je). The histogram in the inset shows the distribution of work at .

Image of FIG. 5.
FIG. 5.

PMFs for binding of a ion to the gramicidin A channel along the channel axis. The umbrella sampling (us) result is compared those obtained from Jarzynski’s equality (je) using different steering forces (indicated on the left-hand side in units of ).

Image of FIG. 6.
FIG. 6.

Similar to Fig. 5 but showing the effect of reducing the pulling velocity (indicated on the right-hand side in units of Å/ns) on the PMFs calculated from Jarzynski’s equality. The top figure (a) shows the results for a soft spring with and the bottom figure (b) for a stiff spring with .

Image of FIG. 7.
FIG. 7.

The effect of increasing the number of steering simulations progressively from 5 to 20 (indicated on the left-hand side) on the PMFs calculated from Jarzynski’s equality. The umbrella sampling result from Fig. 5 is also shown for reference (us).

Image of FIG. 8.
FIG. 8.

PMF’s for binding of organic cations, ethylammonium (EA) and tetraethylammonium (TEA), to the gramicidin A channel. PMFs that are obtained from Jarzynski’s equality (je) again yield binding pockets that are much deeper in energy compared to those of umbrella sampling (us).

Image of FIG. 9.
FIG. 9.

Similar to Fig. 8 but for binding of the toxin CnErg1 to the HERG potassium channel. The histogram in the inset shows the distribution of work at .

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/content/aip/journal/jcp/128/15/10.1063/1.2904461
2008-04-17
2014-04-16
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Potential of mean force calculations of ligand binding to ion channels from Jarzynski’s equality and umbrella sampling
http://aip.metastore.ingenta.com/content/aip/journal/jcp/128/15/10.1063/1.2904461
10.1063/1.2904461
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