Location of ion-binding sites in the gramicidin channel by X-ray diffraction

Olah, Glenn A.; Huang, Huey W.; Liu, Wenhan; Wu, Yinghao

doi:10.1016/0022-2836(91)90272-8

Cited by 111 publications

(121 citation statements)

References 32 publications

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“…In microscopic terms, this just means that the divalent ion is bound to its hydrating water more strongly than monovalent ions. A number of modeling [43], X-ray scattering [44] and NMR [24] studies suggest that divalent cations bind further from the center of the channel (~13 Å) than monovalent cations (~9-10 Å), consistent with them encountering a large energetic barrier beyond the mouth of the channel. In this position the ion can still be surrounded by the majority of its hydrating water, which would have to be removed if it were to permeate further.…”

Section: Gramicidin Channelmentioning

confidence: 99%

Mechanisms of valence selectivity in biological ion channels

Corry

Chung

2006

Cell. Mol. Life Sci.

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Transmembrane ion channels play a crucial role in the existence of all living organisms. They partition the exterior from the interior of the cell, maintain the proper ionic gradient across the cell membrane and facilitate signaling between cells. To perform these functions, ion channels must be highly selective, allowing some types of ions to pass while blocking the passage of others. Here we review a number of studies that have helped to elucidate the mechanisms by which ion channels discriminate between ions of differing charge, focusing on four channel families as examples: gramicidin, ClC chloride, voltage-gated calcium and potassium channels. The recent availability of high-resolution structural data has meant that the specific inter-atomic interactions responsible for valence selectivity can be pinpointed. Not surprisingly, electrostatic considerations have been shown to play an important role in ion specificity, although many details of the origins of this discrimination remain to be determined.

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Section: Gramicidin Channelmentioning

confidence: 99%

Mechanisms of valence selectivity in biological ion channels

Corry

Chung

2006

Cell. Mol. Life Sci.

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“…Experimental [49][50][51][52] and BD simulations [10] data for the gA channel and theoretical results for functionalized nanotubes [35] have proposed two large concentration peaks at the binding sites separated by a cation-depleted region. This is exactly what we observe in our simulations, as shown in Fig.…”

Section: Resultsmentioning

confidence: 99%

Ion fluxes through nanopores and transmembrane channels

et al. 2012

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We introduce an implicit solvent Molecular Dynamics approach for calculating ionic fluxes through narrow nanopores and transmembrane channels. The method relies on a dual-control-volume grand-canonical molecular dynamics (DCV-GCMD) simulation and the analytical solution for the electrostatic potential inside a cylindrical nanopore recently obtained by Levin [Europhys. Lett. 76, 163 (2006)]. The theory is used to calculate the ionic fluxes through an artificial transmembrane channel which mimics the antibacterial gramicidin A channel. Both current-voltage and current-concentration relations are calculated under various experimental conditions. We show that our results are comparable to the characteristics associated to the gramicidin A pore, especially the existence of two binding sites inside the pore and the observed saturation in the current-concentration profiles.

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“…F u rth e rm o re O lah e t al. [46] give binding sites for T l+ at a b o u t 9.6 Ä an d for Ba2+ at about 13.0 A, w hereby the location o f the T l+-binding site is surprising because it w as generally thought th a t m onovalent cations bind at the first turn o f the helix [47,48], Finkelstein and A ndersen [49] found experim entally that gram icidin shows w ater perm eability even w ith a sodium ion at the channel entrance. They concluded, consistent with the sim ulation results, the existence o f a binding site in the open region o f the helix.…”

Section: E Nergy Profiles Fo R Cationsmentioning

confidence: 99%

Ion Transport through Gramicidin A. Water Structure and Functionality

Poxleitner

Seitz-Beywl

Heinzinger

1993

Zeitschrift Für Naturforschung C

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Ion Transport, G ram icidin A, M olecular Dynamics, Functionality, W ater Structure M olecular Dynamics (M D) simulations were performed on a gramicidin A dimer model representing a transm em brane channel. Different from previous simulations the peptide was in contact with bulk water at both ends of the dimer to guarantee a realistic description o f the hydration of the biomolecule. The flexible BJH model for water was employed in the sim ula tions and the gramicidin-water, gramicidin-ion and ion-water potentials used are based on molecular orbital calculations. The water structure near the gramicidin was investigated first by a simulation w ithout ions, while for the energy profiles of the ion transport through the channel a potassium or a sodium ion was added. These investigations provide a detailed and conclusive picture on a molecular level of the role of water in the ion transport through a gramicidin A channel and can explain the experimental results on the selectivity between alkali ions, their double or even triple occupancy, the exclusion or permeability of anions depending upon cation concentration and the consequences of differences in the ionic charge. The investi gation dem onstrate that the water molecules around the gramicidin behave as an integral part of the peptide and the functionality is the result o f the whole complex biomolecule-water.

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Location of ion-binding sites in the gramicidin channel by X-ray diffraction

Cited by 111 publications

References 32 publications

Mechanisms of valence selectivity in biological ion channels

Mechanisms of valence selectivity in biological ion channels

Ion fluxes through nanopores and transmembrane channels

Ion Transport through Gramicidin A. Water Structure and Functionality

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