Ion fluxes through nanopores and transmembrane channels

被引：32

作者：

Bordin, J. R. ^{[1
]}

Diehl, A. ^{[2
]}

Barbosa, M. C.

Levin, Y.

机构：

[1] Univ Fed Rio Grande do Sul, Inst Fis, Programa Posgrad Fis, BR-91501970 Porto Alegre, RS, Brazil

[2] Univ Fed Pelotas, Inst Fis & Matemat, Dept Fis, BR-96010900 Pelotas, RS, Brazil

来源：

PHYSICAL REVIEW E | 2012年 / 85卷 / 03期

关键词：

CANONICAL MOLECULAR-DYNAMICS; GRADIENT-DRIVEN DIFFUSION; LENNARD-JONES FLUIDS; NERNST-PLANCK THEORY; GRAMICIDIN CHANNEL; BROWNIAN DYNAMICS; CARBON NANOTUBES; COMPUTATIONAL MODELS; CONTINUUM-THEORIES; PERMEATION;

D O I：

10.1103/PhysRevE.85.031914

中图分类号：

O35 [流体力学]; O53 [等离子体物理学];

学科分类号：

070204 ; 080103 ; 080704 ;

摘要：

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.

引用

页数：7

共 52 条

[1] Imaging α-hemolysin with molecular dynamics:: Ionic conductance, osmotic permeability, and the electrostatic potential map [J].

Aksimentiev, A ;

Schulten, K .

BIOPHYSICAL JOURNAL, 2005, 88 (06) :3745-3761

[2]

Allen M. P., 1987, COMPUTER SIMULATION

[3] Molecular dynamics - potential of mean force calculations as a tool for understanding ion permeation and selectivity in narrow channels [J].

Allen, Toby W. ;

Andersen, Olaf S. ;

Roux, Benoit .

BIOPHYSICAL CHEMISTRY, 2006, 124 (03) :251-267

[4] Ion permeation through a narrow channel: Using gramicidin to ascertain all-atom molecular dynamics potential of mean force methodology and biomolecular force fields [J].

Allen, TW ;

Andersen, OS ;

Roux, B .

BIOPHYSICAL JOURNAL, 2006, 90 (10) :3447-3468

[5] On the importance of atomic fluctuations, protein flexibility, and solvent in ion permeation [J].

Allen, TW ;

Andersen, OS ;

Roux, B .

JOURNAL OF GENERAL PHYSIOLOGY, 2004, 124 (06) :679-690

[6] Gramicidin channels [J].

Andersen, OS ;

Koeppe, RE ;

Roux, B .

IEEE TRANSACTIONS ON NANOBIOSCIENCE, 2005, 4 (01) :10-20

[7] Toward an Understanding of the Specific Ion Effect Using Density Functional Theory [J].

Baer, Marcel D. ;

Mundy, Christopher J. .

JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 2011, 2 (09) :1088-1093

[8] Energetics of ion conduction through the K+ channel [J].

Bernèche, S ;

Roux, B .

NATURE, 2001, 414 (6859) :73-77

[9] Molecular dynamics simulations of ion transport through carbon nanotubes. I. Influence of geometry, ion specificity, and many-body interactions [J].

Beu, Titus A. .

JOURNAL OF CHEMICAL PHYSICS, 2010, 132 (16)

[10] Atoms-to-microns model for small solute transport through sticky nanochannels [J].

Carr, Rogan ;

Comer, Jeffrey ;

Ginsberg, Mark D. ;

Aksimentiev, Aleksei .

LAB ON A CHIP, 2011, 11 (22) :3766-3773

← 1 2 3 4 5 6 →