help button home button Biophys. J.
HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrow reprints & permissions
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Chung, S.-H.
Right arrow Articles by Kuyucak, S.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Chung, S.-H.
Right arrow Articles by Kuyucak, S.

Biophys J, July 2002, p. 263-277, Vol. 83, No. 1

Modeling Diverse Range of Potassium Channels with Brownian Dynamics

Shin-Ho Chung,* Toby W. Allen,* and Serdar Kuyucakdagger

 *Department of Physics, The Faculty of Sciences and  dagger Department of Theoretical Physics, Research School of Physical Sciences, Australian National University, Canberra, ACT 0200, Australia

Using the experimentally determined KcsA structure as a template, we propose a plausible explanation for the diversity of potassium channels seen in nature. A simplified model of KcsA is constructed from its atomic resolution structure by smoothing out the protein-water boundary and representing the atoms forming the channel protein as a homogeneous, low dielectric medium. The properties of the simplified and atomic-detail models, deduced from electrostatic calculations and Brownian dynamics simulations, are shown to be qualitatively similar. We then study how the current flowing across the simplified model channel changes as the shape of the intrapore region is modified. This is achieved by increasing the radius of the intracellular pore systematically from 1.5 to 5 Å while leaving the dimensions of the selectivity filter and inner chamber unaltered. The strengths of the dipoles located near the entrances of the channel, the carbonyl groups lining the selectivity filter, and the helix macrodipoles are kept constant. The channel conductance increases steadily as the radius of the intracellular pore is increased. The rate-limiting step for both the outward and inward current is the time it takes for an ion to cross the residual energy barrier located in the intrapore region. The current-voltage relationship obtained with symmetrical solutions is linear when the applied potential is less than ~100 mV but deviates slightly from Ohm's law at higher applied potentials. The nonlinearity in the current-voltage curve becomes less pronounced as the radius of the intracellular pore is increased. When the strengths of the dipoles near the intracellular entrance are reduced, the channel shows a pronounced inward rectification. Finally, the conductance exhibits the saturation property observed experimentally. We discuss the implications of these findings on the transport of ions across the potassium channels and membrane channels in general.

Biophys J, July 2002, p. 263-277, Vol. 83, No. 1
© 2002 by the Biophysical Society   0006-3495/02/07/263/15  $2.00


This article has been cited by other articles:


Home page
 Biophys. JHome page
T. Vora, D. Bisset, and S.-H. Chung
Conduction of Na+ and K+ through the NaK Channel: Molecular and Brownian Dynamics Studies
Biophys. J., August 15, 2008; 95(4): 1600 - 1611.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
M. Hoyles, V. Krishnamurthy, M. Siksik, and S.-H. Chung
Brownian Dynamics Theory for Predicting Internal and External Blockages of Tetraethylammonium in the KcsA Potassium Channel
Biophys. J., January 15, 2008; 94(2): 366 - 378.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
S. Furini, F. Zerbetto, and S. Cavalcanti
Application of the Poisson-Nernst-Planck Theory with Space-Dependent Diffusion Coefficients to KcsA
Biophys. J., November 1, 2006; 91(9): 3162 - 3169.
[Abstract] [Full Text] [PDF]

Home page
 J. Gen. Physiol.Home page
J. G. Trapani, P. Andalib, J. F. Consiglio, and S. J. Korn
Control of Single Channel Conductance in the Outer Vestibule of the Kv2.1 Potassium Channel
J. Gen. Physiol., July 31, 2006; 128(2): 231 - 246.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
T. Bastug, A. Gray-Weale, S. M. Patra, and S. Kuyucak
Role of Protein Flexibility in Ion Permeation: A Case Study in Gramicidin A
Biophys. J., April 1, 2006; 90(7): 2285 - 2296.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
G. Seebohm, N. Strutz-Seebohm, O. N. Ureche, R. Baltaev, A. Lampert, G. Kornichuk, K. Kamiya, T. V. Wuttke, H. Lerche, M. C. Sanguinetti, et al.
Differential Roles of S6 Domain Hinges in the Gating of KCNQ Potassium Channels
Biophys. J., March 15, 2006; 90(6): 2235 - 2244.
[Abstract] [Full Text] [PDF]

Home page
 J. Gen. Physiol.Home page
S.-H. Yeh, H.-K. Chang, and R.-C. Shieh
Electrostatics in the Cytoplasmic Pore Produce Intrinsic Inward Rectification in Kir2.1 Channels
J. Gen. Physiol., November 28, 2005; 126(6): 551 - 562.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
C. Peter and G. Hummer
Ion Transport through Membrane-Spanning Nanopores Studied by Molecular Dynamics Simulations and Continuum Electrostatics Calculations
Biophys. J., October 1, 2005; 89(4): 2222 - 2234.
[Abstract] [Full Text] [PDF]

Home page
 J. Gen. Physiol.Home page
T. I. Brelidze and K. L. Magleby
Probing the Geometry of the Inner Vestibule of BK Channels with Sugars
J. Gen. Physiol., July 25, 2005; 126(2): 105 - 121.
[Abstract] [Full Text] [PDF]

Home page
 J. Physiol.Home page
L.-H. Xie, S. A John, B. Ribalet, and J. N Weiss
Regulation of gating by negative charges in the cytoplasmic pore in the Kir2.1 channel
J. Physiol., November 15, 2004; 561(1): 159 - 168.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
V. L. Dorman and P. C. Jordan
Ionic Permeation Free Energy in Gramicidin: A Semimicroscopic Perspective
Biophys. J., June 1, 2004; 86(6): 3529 - 3541.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
Y. Song, Y. Zhang, T. Shen, C. L. Bajaj, J. A. McCammon, and N. A. Baker
Finite Element Solution of the Steady-State Smoluchowski Equation for Rate Constant Calculations
Biophys. J., April 1, 2004; 86(4): 2017 - 2029.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
G. V. Miloshevsky and P. C. Jordan
Anion Pathway and Potential Energy Profiles along Curvilinear Bacterial ClC Cl- Pores: Electrostatic Effects of Charged Residues
Biophys. J., February 1, 2004; 86(2): 825 - 835.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
S. Garofoli and P. C. Jordan
Modeling Permeation Energetics in the KcsA Potassium Channel
Biophys. J., May 1, 2003; 84(5): 2814 - 2830.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
T. Takahashi and S. Kuyucak
Functional Properties of Threefold and Fourfold Channels in Ferritin Deduced from Electrostatic Calculations
Biophys. J., April 1, 2003; 84(4): 2256 - 2263.
[Abstract] [Full Text] [PDF]

Home page
 J. Gen. Physiol.Home page
J. F. Consiglio, P. Andalib, and S. J. Korn
Influence of Pore Residues on Permeation Properties in the Kv2.1 Potassium Channel. Evidence for a Selective Functional Interaction of K+ with the Outer Vestibule
J. Gen. Physiol., February 3, 2003; 121(2): 111 - 124.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
P. C. Jordan
Trial by Ordeal: Ionic Free Energies in Gramicidin
Biophys. J., September 1, 2002; 83(3): 1235 - 1236.
[Full Text] [PDF]

Home page
 Biophys. JHome page
P. C. Jordan
Unclogging a Pipe: Potassium Channel Pinball
Biophys. J., July 1, 2002; 83(1): 2 - 4.
[Full Text] [PDF]


HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
Copyright © 2002 by the Biophysical Society.