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. 1996 Dec;71(6):3177–3185. doi: 10.1016/S0006-3495(96)79511-5

Valence selectivity of the gramicidin channel: a molecular dynamics free energy perturbation study.

B Roux 1
PMCID: PMC1233806  PMID: 8968588

Abstract

The valence selectivity of the gramicidin channel is examined using computer simulations based on atomic models. The channel interior is modeled using a gramicidin-like periodic poly (L,D)-alanine beta-helix. Free energy perturbation calculations are performed to obtain the relative affinity of K+ and Cl- for the channel. It is observed that the interior of the gramicidin channel provides an energetically favorable interaction site for a cation but not for an anion. Relative to solvation in bulk water, the carbonyl CO oxygens can provide a favorable interaction to stabilize K+, whereas the amide NH hydrogens are much less effective in stabilizing Cl-. The results of the calculations demonstrate that, as a consequence of the structural asymmetry of the backbone charge distribution, a K+ cation can partition spontaneously from bulk water to the interior of the gramicidin channel, whereas a Cl- anion cannot.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

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