Energetics of Double-Ion Occupancy in the Gramicidin A Channel

Li, Yuhui; Andersen, Olaf S.; Roux, Benoı̂t

doi:10.1021/jp105820u

Cited by 16 publications

(23 citation statements)

References 54 publications

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“…The w(z) was offset to zero when the ion was in the bulk. Similarly, the equilibrium dissociation constant of a multiple occupancy state of the channel, K D (multiple), can be expressed as 51,52 ∫ ∫ …”

Section: ■ Methodsmentioning

confidence: 99%

Molecular Strategies to Achieve Selective Conductance in NaK Channel Variants

2014

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A recent crystallization of several ion channels has provided strong impetus for efforts aimed at understanding the different strategies employed by nature for selective ion transport. In this work, we used two variants of the selectivity filter of NaK channel to explore molecular mechanisms that give rise to K(+)-selectivity. We computed one-dimensional (1D) and two-dimensional (2D) potentials of mean force (PMFs) for ion permeation across the channel. The results indicate that the energies for Na(+) and K(+) permeation across the selectivity filter display significant differences in positions of the binding sites and barriers. One characteristic signature of a K(+)-selective channel is the apparent preservation of the site analogous to that of S2 in KcsA. The S2-bound ion can be almost ideally dehydrated and coordinated by 6 to 8 carbonyls. In a striking contrast, the PMFs controlling transport of ions in a nonselective variant show almost identical profiles for either K(+) or Na(+) and significant involvement of water molecules in ion coordination across the entire selectivity filter. An analysis of differences in 1D PMFs for Na(+) and K(+) suggests that coordination number alone is an insufficient predictor of site selectivity, while chemical composition (ratio of carbonyls and water molecules) correlates well with preference for K(+). Multi-ion effects such as dependence of the barriers and wells for permeant ion on the type of copermeant ion were found to play a significant role in the selectivity signature of the channel as well.

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Section: ■ Methodsmentioning

confidence: 99%

Molecular Strategies to Achieve Selective Conductance in NaK Channel Variants

2014

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“…The umbrella sampling method was recently used to determine a two-ion PMF, demonstrating that double occupancy in gramicidin A is not favorable. 46 …”

Section: Typical Questions Of Interestmentioning

confidence: 99%

Modeling and Simulation of Ion Channels

et al. 2012

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“…A series of extended simulations (~100 ns) on the voltage sensor domain of potassium channels revealed the importance of lipid phosphates in accommodating the significantly charged S4 helix [22]. Using umbrella sampling, potential of mean force has been calculated for permeation and effect of a potassium ion on the second ion passing through gramicidin A channel [23].…”

Section: Bioinformatics -Updated Features and Applications 86mentioning

confidence: 99%

Bioinformatics for Membrane Lipid Simulations: Models, Computational Methods, and Web Server Tools

Leong¹,

Lim²,

Choong³

2016

Bioinformatics - Updated Features and Applications

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Biological membranes are complex environments consisting of different types of lipids and membrane proteins. The structure of a lipid bilayer is typically difficult to study because the membrane liquid crystalline state is made up of multiple disordered lipid molecules. This complicates the description of the lipid membrane properties by the conformation of any single lipid molecule. Molecular dynamics (MD) simulations have been used extensively to investigate properties of membrane lipids, lipid vesicles, and membrane protein systems. All-atom membrane models can elucidate detailed contacts between membrane proteins and its surrounding lipids, while united-atom and coarsegrained description have allowed larger models and longer timescales up to microsecond mark to be probed. Additionally, membrane models with mixed phospholipids and lipopolysaccharide content have made it possible to model improved views of biological membranes. Here, we present an overview of commonly used lipid force fields by the biosimulation community, useful tools for membrane MD simulations, and recent advances in membrane simulations.

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Energetics of Double-Ion Occupancy in the Gramicidin A Channel

Cited by 16 publications

References 54 publications

Molecular Strategies to Achieve Selective Conductance in NaK Channel Variants

Molecular Strategies to Achieve Selective Conductance in NaK Channel Variants

Modeling and Simulation of Ion Channels

Bioinformatics for Membrane Lipid Simulations: Models, Computational Methods, and Web Server Tools

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