Correlated movements of ions and water in a nanochannel

Haan, Marcel Jan de; Gwan, J. F.; Baumgaertner, A.

doi:10.1080/08927020802433160

Cited by 7 publications

(3 citation statements)

References 36 publications

(17 reference statements)

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“…5 depend on the total number of interatomic distances and atoms involved in the calculation, and are used only for illustration purposes. Nonetheless, we are still able to indirectly conclude that the motion between the selected atoms must be highly correlated, confirming previous findings 17–21 in a completely novel and orthogonal way.…”

Section: Discussionsupporting

confidence: 89%

“…Importantly, there have been several reports on the correlated motion of ions and carbonyl groups inside the selectivity filter indicative of its flexibility. 17–21 Here, we demonstrate the potential mechanistic and biological significance of the distance corrections in the case of the selectivity filter of the KcsA ion channel and show that the type of motion in it can actually be determined indirectly through the calculated corrections.…”

Section: Introductionmentioning

confidence: 69%

See 1 more Smart Citation

Dynamics May Significantly Influence the Estimation of Interatomic Distances in Biomolecular X-ray Structures

Kuzmanic

Kruschel

Gunsteren

et al. 2011

Journal of Molecular Biology

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Atomic positions obtained by X-ray crystallography are time and space averages over many molecules in the crystal. Importantly, interatomic distances, calculated between such average positions and frequently used in structural and mechanistic analyses, can be substantially different from the more appropriate time-average and ensemble-average interatomic distances. Using crystallographic B-factors, one can deduce corrections, which have so far been applied exclusively to small molecules, to obtain correct average distances as a function of the type of atomic motion. Here, using 4774 high-quality protein X-ray structures, we study the significance of such corrections for different types of atomic motion. Importantly, we show that for distances shorter than 5 Å, corrections greater than 0.5 Å may apply, especially for noncorrelated or anticorrelated motion. For example, 14% of the studied structures have at least one pair of atoms with a correction of ≥ 0.5 Å in the case of noncorrelated motion. Using molecular dynamics simulations of villin headpiece, ubiquitin, and SH3 domain unit cells, we demonstrate that the majority of average interatomic distances in these proteins agree with noncorrelated corrections, suggesting that such deviations may be truly relevant. Importantly, we demonstrate that the corrections do not significantly affect stereochemistry and the overall quality of final refined X-ray structures, but can provide marked improvements in starting unrefined models obtained from low-resolution X-ray data. Finally, we illustrate the potential mechanistic and biological significance of the calculated corrections for KcsA ion channel and show that they provide indirect evidence that motions in its selectivity filter are highly correlated.

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Section: Discussionsupporting

confidence: 89%

Section: Introductionmentioning

confidence: 69%

Dynamics May Significantly Influence the Estimation of Interatomic Distances in Biomolecular X-ray Structures

Kuzmanic

Kruschel

Gunsteren

et al. 2011

Journal of Molecular Biology

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“…Given the great challenge that represents obtaining desalination nanomembranes, many molecular simulation works have been reported on water − and water and ions − confined at the nanoscale in hydrophobic pores. Besides the increasing number of molecular simulation studies published on the confinement of aqueous electrolyte solutions, other authors have also considered confinement and transport of ions in biological systems. ,, In what follows, we restrict ourselves to the review of the most recent but abundant theoretical and molecular simulation works published on the transport of aqueous electrolyte solutions in hydrophobic nanopores. Nicholson and Quirke reported one of the first molecular dynamics studies on the confinement of an aqueous solution of sodium chloride in a hydrophobic carbon nanotube.…”

Section: State Of the Artmentioning

confidence: 99%

Molecular Simulation of Ion-Specific Effects in Confined Electrolyte Solutions Using Polarizable Forcefields

et al. 2010

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This paper reports on a molecular dynamics study of aqueous electrolyte solutions confined in hydrophobic nanopores. We examined for the first time the effect of the size and polarizability of the ions on the structure and dynamics of the confined electrolyte solution by considering the series of sodium halides (NaX with X = F, Cl, Br, and I). We also address the effect of pore size by varying the diameter of the nanochannel. As far as structural properties are concerned, the behavior of the NaF electrolyte solution significantly differs from that of the other sodium halide solutions. Because of their small size, Na and F in NaF are found to be significantly solvated by water. In addition, due to steric and hydrophobic effects [ Chandler D. Chandler D. Nature2005437640.], Cl, Br, and I tend to be repelled from the regions where the density of water is larger. Ion-specific effects on the dynamics of water and ions are found to be minimized when the electrolyte solution is confined at the nanoscale in comparison to bulk water and the water−air interface. For instance, both the data for water and the ionic species indicate that the ratio of the self-diffusivity for the confined solution to that for the bulk is independent of the nature of the anion F, Cl, Br, and I. Moreover, while the average solvation times for Na in NaF and Na in NaX (X = Cl, Br, I) significantly differ for bulk electrolyte solutions, they turn out to be very similar for the confined solutions. Such a leveling of the dynamical properties of the electrolyte solutions due to confinement is also observed on the pairing of the anions and cations.

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Biomimetic Nanochannels: From Fabrication Principles to Theoretical Insights

Kan

Wen

et al. 2022

Small Methods

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Biological nanochannels which can regulate ionic transport across cell membranes intelligently play a significant role in physiological functions. Inspired by these nanochannels, numerous artificial nanochannels have been developed during recent years. The exploration of smart solid‐state nanochannels can lay a solid foundation, not only for fundamental studies of biological systems but also practical applications in various fields. The basic fabrication principles, functional materials, and diverse applications based on artificial nanochannels are summarized in this review. In addition, theoretical insights into transport mechanisms and structure–function relationships are discussed. Meanwhile, it is believed that improvements will be made via computer‐guided strategy in designing more efficient devices with upgrading accuracy. Finally, some remaining challenges and perspectives for developments in both novel conceptions and technology of this inspiring research field are stated.

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Correlated movements of ions and water in a nanochannel

Cited by 7 publications

References 36 publications

Dynamics May Significantly Influence the Estimation of Interatomic Distances in Biomolecular X-ray Structures

Dynamics May Significantly Influence the Estimation of Interatomic Distances in Biomolecular X-ray Structures

Molecular Simulation of Ion-Specific Effects in Confined Electrolyte Solutions Using Polarizable Forcefields

Biomimetic Nanochannels: From Fabrication Principles to Theoretical Insights

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