Ionic channels in biological membranes- electrostatic analysis of a natural nanotube

Eisenberg, Robert S.

doi:10.1080/001075198181775

Cited by 98 publications

(68 citation statements)

References 125 publications

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“…The PNP model suffers from at least three difficulties, even in three dimensions (Eisenberg, 1998a;Eisenberg, 1998b;Eisenberg, 1996b;Horn, 1998): it lacks chemistry and single filing, it lacks spatial resolution, and it does not deal with protein conformation changes thought to underlie gating.…”

Section: Brief History Of Diffusion Theory Of Chemical Reactions Thementioning

confidence: 99%

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From Structure to Function in Open Ionic Channels

Eisenberg

1999

Journal of Membrane Biology

158

131

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We consider a simple working hypothesis that all permeation properties of open ionic channels can be predicted by understanding electrodiffusion in fixed structures, without invoking conformation changes, or changes in chemical bonds. We know, of course, that ions can bind to specific protein structures, and that this binding is not easily described by the traditional electrostatic equations of physics textbooks, that describe average electric fields, the so-called `mean field'. The question is which specific properties can be explained just by mean field electrostatics and which cannot. I believe the best way to uncover the specific chemical properties of channels is to invoke them as little as possible, seeking to explain with mean field electrostatics first. Then, when phenomena appear that cannot be described that way, by the mean field alone, we turn to chemically specific explanations, seeking the appropriate tools (of electrochemistry, Langevin, or molecular dynamics, for example) to understand them. In this spirit, we turn now to the structure of open ionic channels, apply the laws of electrodiffusion to them, and see how many of their properties we can predict just that way.Comment: Nearly final version of publicatio

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Section: Brief History Of Diffusion Theory Of Chemical Reactions Thementioning

confidence: 99%

“…(Otherwise, the simulations could not be used to design real transistors, which require bias potentials to function usefully.) Physicists familiar with these methods might find them revealing if applied to systems of ions and channels (Eisenberg, 1998a).…”

Section: Brief History Of Diffusion Theory Of Chemical Reactions Thementioning

confidence: 99%

From Structure to Function in Open Ionic Channels

Eisenberg

1999

Journal of Membrane Biology

158

131

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“…Within the framework our data, the observed increase of the overall conductance of the alamethicin channel when cholesterol is part of the biomembrane composition, can be viewed as a consequence of a dipole moment decrease caused by cholesterol. In order to qualitatively check the influence of dipole potential alterations on the overall conductance of an over-simplified conducting pore embedded into a model biomembrane, we have conducted a simulation based on the Poisson-Nernst-Planck theory [23]. We found that in the case of the alamethicin pore, which shows modest selectivity for monovalent cations (P + /P − = 4) [31], a simulated decrease of the dipole potential leads to an increase in the electric conductivity, which is in agreement with the experimental data.…”

Section: Discussionmentioning

confidence: 99%

“…When cholesterol-containing asymmetric bilayer membranes were to be used, one of the lipid leaflets contained growing amounts (10 %, 20 % and 50 % w/w -with respect to the total mass achieved) of cholesterol (Sigma-Aldrich). In order to simulate the effect of bilayer's dipole potential modification induced by cholesterol on the electrical conductance through alamethicin oligomers, we resorted to the use of the Poisson-Nernst-Planck theory [23]. The perturbing effect of cholesterol on the magnitude of the biomembrane dipole moment was modelled as a relative decrease of the electrical dipole field within the polar region of the biomembrane.…”

Section: Methodsmentioning

confidence: 99%

Biophysical changes induced by cholesterol on phosphatidylcholine artificial biomembranes containing alamethicin oligomers

Cernescu

Luchian

2006

Open Physics

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Abstract:Cholesterol is an important constituent of eukaryotic cell membranes, whose interaction with phospholipids leads to a broad range of biological roles, such as: maintenance of proper fluidity, formation of raft domains, reduction of passive permeability of various chemical species through the bilayer (e.g., glucose, glycerol, K + , Na + and Cl − ions), and increased mechanical strength of the membrane. In this work we studied an interesting paradigm, as to whether cholesterol-containing phosphatidylcholine biomembranes influence the kinetics and transport features of alamethicin oligomers embedded into it. We demonstrate that moderate relative amounts of cholesterol increase the electrical conductance of various sub-conductance states of the alamethicin oligomer, caused probably by a non-monotonic change in the lumped dipole moment of the biomembrane. Our data suggest that biomembrane stiffness caused by cholesterol, visibly modifies the association-dissociation rates of alamethicin oligomerization in the biomembrane. Moreover, increasing concentrations of cholesterol seem to lead to more stable intermediate alamethicin oligomers. We show that in the presence of cholesterol, as the diameter of the alamethicin oligomer increases, so does the time of another monomer to get picked up. These results brings into focus the interesting issue of how oligomerization of proteins affects their interaction affinities for membrane-based lipids.

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“…The PNP equations were suggested as the basic continuum model for open ion channels by Eisenberg and coworkers [7,19,20] and were numerically solved and compared with real experimental I-V curves in many papers; see [21,22, and references therein]. PNP has long been used outside the channel world as the simplest combination of constitutive and conservation laws that are useful in describing electrodiffusion.…”

Section: Introductionmentioning

confidence: 99%

A Poisson–Nernst–Planck Model for Biological Ion Channels—An Asymptotic Analysis in a Three-Dimensional Narrow Funnel

Singer¹,

Norbury²

2009

SIAM J. Appl. Math.

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Abstract. We wish to predict ionic currents that flow through narrow protein channels of biological membranes in response to applied potential and concentration differences across the channel when some features of channel structure are known. We propose to apply singular perturbation analysis to the coupled Poisson-Nernst-Planck equations, which are the basic continuum model of ionic permeation and semiconductor physics. In semiconductor physics the problem is a singular perturbation, because the ratio of the Debye length to the width of the channel is a very small parameter that multiplies the Laplacian term in the Poisson equation. In contrast to semiconductors, the atomic scale geometry of narrow ion channels sometimes makes this ratio a large parameter, which, surprisingly, renders the problem a singular perturbation in a different sense. We construct boundary layers and match them asymptotically across the different regions of the channel to derive good approximations for Fick's and Ohm's laws. Our aim is to extend the asymptotic analysis to a class of nonlinear problems hitherto intractable. Analytical and numerical results for the mass flux and the electric current serve as a tool for molecular biophysicists and physiologists to understand, study, and control protein channels, thereby aiding clinical and technological applications.

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Ionic channels in biological membranes- electrostatic analysis of a natural nanotube

Cited by 98 publications

References 125 publications

From Structure to Function in Open Ionic Channels

From Structure to Function in Open Ionic Channels

Biophysical changes induced by cholesterol on phosphatidylcholine artificial biomembranes containing alamethicin oligomers

A Poisson–Nernst–Planck Model for Biological Ion Channels—An Asymptotic Analysis in a Three-Dimensional Narrow Funnel

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