Combined Effect of Pore Radius and Protein Dielectric Coefficient on the Selectivity of a Calcium Channel

Boda, Dezső; Valiskó, Mónika; Eisenberg, Robert S.; Nonner, Wolfgang; Henderson, Douglas; Gillespie, Dirk

doi:10.1103/physrevlett.98.168102

Cited by 88 publications

(156 citation statements)

References 13 publications

(18 reference statements)

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“…For a typical SF geometry condition (P b = 1) corresponds to the concentration [Ca] 0 ≈200mM/l. The dependence of the resonance point's position on V c coincides with both simulations and with earlier analytic results [13], [14].…”

Section: Se Qsupporting

confidence: 90%

Effect of local binding on stochastic transport in ion channels

Kaufman¹,

Gibby²,

Luchinsky³

et al. 2017

2017 International Conference on Noise and Fluctuations (ICNF)

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Abstract-Ionic Coulomb blockade is an electrostatic phenomenon recently discovered in low-capacitance ion channels/nanopores. Depending on the fixed charge that is present, Coulomb blockade strongly and selectively influences the ease with which a given type of ion can permeate the pore. The phenomenon arises from the discreteness of the charge-carriers and it manifests itself strongly for divalent ions (e.g. Ca 2+ ). Ionic Coulomb blockade is closely analogous to electronic Coulomb blockade in quantum dots. In addition to the non-local 1D Coulomb interaction considered in the standard Coulomb blockade approach, we now propose a correction to take account of the singular part of the attraction to the binding site (i.e. local site binding). We show that this correction leads to a geometrydependent shift of the single-ion barrierless resonant conduction points M0. We also show that local ion-ion repulsion accounts for a splitting of Ca 2+ profiles observed earlier in Brownian dynamics simulations.

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Section: Se Qsupporting

confidence: 90%

Effect of local binding on stochastic transport in ion channels

Kaufman¹,

Gibby²,

Luchinsky³

et al. 2017

2017 International Conference on Noise and Fluctuations (ICNF)

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“…We also plan to introduce the finite size of ions, which will be especially important for pores characterized by extremely high surface charges densities and possible resulting crowding of ions. Considering size of ions will also be crucial for the description of even shorter pores whose length approaches the pore opening diameter, as it is the case of biological channels 60,61 . To this end, we also refer to a non-linear variant of the PNP-Equations 62 , which have already been applied in the context of ion channels 63 .…”

Section: Resultsmentioning

confidence: 99%

Rectification properties of conically shaped nanopores: consequences of miniaturization

Pietschmann

Wolfram

Burger

et al. 2013

Phys. Chem. Chem. Phys.

116

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Nanopores attracted a great deal of scientific interest as templates for biological sensors as well as model systems to understand transport phenomena at the nanoscale. The experimental and theoretical analysis of nanopores has been so far focused on understanding the effect of the pore opening diameter on ionic transport. In this article we present systematic studies on the dependence of ion transport properties on the pore length. Particular attention was given to the effect of ion current rectification exhibited for conically shaped nanopores with homogeneous surface charges. We found that reducing the length of conically shaped nanopores significantly lowered their ability to rectify ion current. However, rectification properties of short pores can be enhanced by tailoring the surface charge and the shape of the narrow opening. Furthermore we analyze the relationship of the rectification behavior and ion selectivity for different pore lengths. All simulations were performed using MsSimPore, a software package for solving the Poisson-Nernst-Planck (PNP) equations. It is based on a novel finite element solver and allows for simulations up to surface charge densities of -2 e/nm 2 . MsSimPore is based on 1D reduction of the PNP model, but allows for a direct treatment of the pore with bulk electrolyte reservoirs, a feature which was previously used in higher dimensional models only. MsSimPore includes these reservoirs in the calculations; a property especially important for short pores, where the ionic concentrations and the electric potential vary strongly inside the pore as well as in the regions next to pore entrance.

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“…[1][2][3][4][5][6][7][8][9][10][11][12][13][14][15][16][17] The dielectric boundaries usually were hard impenetrable walls or ions were excluded from their vicinity by other walls or some repulsion potential. Even when the possibility of ions crossing dielectric boundaries is otherwise a physical reality, authors decided to avoid such events in their simulations in one way or other.…”

Section: Introductionmentioning

confidence: 99%

“…Various boundary element methods (BEM) in apparent surface charge (ASC) calculations were widely used to compute induced charges. 32,33 A variational formalism has been proposed by Allen et al 34 Inspired by this paper, a method called the induced charge computation (ICC) method was proposed by us 8,11 and used to study DLs 9 and ion channels 11,12,14,17 with Monte Carlo (MC) simulations. In all these studies, the ions stayed in their native dielectric; they did not cross dielectric boundaries.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

A method for treating the passage of a charged hard sphere ion as it passes through a sharp dielectric boundary

Boda

Henderson

Eisenberg

et al. 2011

The Journal of Chemical Physics

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In the implicit solvent models of electrolytes (such as the primitive model (PM)), the ions are modeled as point charges in the centers of spheres (hard spheres in the case of the PM). The surfaces of the spheres are not polarizable which makes these models appropriate to use in computer simulations of electrolyte systems where these ions do not leave their host dielectrics. The same assumption makes them inappropriate in simulations where these ions cross dielectric boundaries because the interaction energy of the point charge with the polarization charge induced on the dielectric boundary diverges. In this paper, we propose a procedure to treat the passage of such ions through dielectric interfaces with an interpolation method. Inspired by the "bubble ion" model (in which the ion's surface is polarizable), we define a space-dependent effective dielectric coefficient, eff (r), for the ion that overlaps with the dielectric boundary. Then, we replace the "bubble ion" with a point charge that has an effective charge q/ eff (r) and remove the portion of the dielectric boundary where the ion overlaps with it. We implement the interpolation procedure using the induced charge computation method [D. Boda, D. Gillespie, W. Nonner, D. Henderson, and B. Eisenberg, Phys. Rev. E 69, 046702 (2004)]. We analyze the various energy terms using a spherical ion passing through an infinite flat dielectric boundary as an example.

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Combined Effect of Pore Radius and Protein Dielectric Coefficient on the Selectivity of a Calcium Channel

Cited by 88 publications

References 13 publications

Effect of local binding on stochastic transport in ion channels

Effect of local binding on stochastic transport in ion channels

Rectification properties of conically shaped nanopores: consequences of miniaturization

A method for treating the passage of a charged hard sphere ion as it passes through a sharp dielectric boundary

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