IDEAS home Printed from https://ideas.repec.org/a/eee/phsmap/v357y2005i3p397-414.html
   My bibliography  Save this article

Determination of rate kinetics in ion channels by the path probability method and Onsager reciprocity theorem

Author

Listed:
  • Ozer, Mahmut

Abstract

In this study, we propose a theoretical framework for the determination of rate kinetics in the ion channels. In this framework, we firstly formulate the kinetic equation for the time-dependent open-state probability of the gate and forward and backward rate kinetics based on the path probability method with three parameters, explicitly. Then, we construct a tool to determine if fitted rate kinetics satisfy the experimental data by deriving kinetic coefficients of activation and inactivation gates based on the Onsager reciprocity theorem. The proposed framework is based on the principles of statistical physics and conceptually quite different from those of conventional models. We also illustrate its applicability based on the empirical inactivation kinetics of T-type calcium channel from thalamic relay neurons, and then compare it with the linear and nonlinear thermodynamic models for the same calcium channel. The results of the present study indicate that our methodology suggests a general framework for the determination of rate kinetics in ion channels.

Suggested Citation

  • Ozer, Mahmut, 2005. "Determination of rate kinetics in ion channels by the path probability method and Onsager reciprocity theorem," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 357(3), pages 397-414.
    • Handle: RePEc:eee:phsmap:v:357:y:2005:i:3:p:397-414
    DOI: 10.1016/j.physa.2005.04.008
    as

    Download full text from publisher

    File URL: http://www.sciencedirect.com/science/article/pii/S0378437105003468
    Download Restriction: Full text for ScienceDirect subscribers only. Journal offers the option of making the article available online on Science direct for a fee of $3,000
    File URL: https://libkey.io/10.1016/j.physa.2005.04.008?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    References listed on IDEAS

    as
    1. Youxing Jiang & Alice Lee & Jiayun Chen & Vanessa Ruta & Martine Cadene & Brian T. Chait & Roderick MacKinnon, 2003. "X-ray structure of a voltage-dependent K+ channel," Nature, Nature, vol. 423(6935), pages 33-41, May.
    2. Özer, Mahmut & Erdem, Rıza, 2004. "Dynamics of voltage-gated ion channels in cell membranes by the path probability method," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 331(1), pages 51-60.
    3. Yang, Y.S. & Thompson, C.J. & Anderson, V. & Wood, A.W., 1999. "A statistical mechanical model of cell membrane ion channels in electric fields: The mean-field approximation," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 268(3), pages 424-432.
    4. Youxing Jiang & Vanessa Ruta & Jiayun Chen & Alice Lee & Roderick MacKinnon, 2003. "The principle of gating charge movement in a voltage-dependent K+ channel," Nature, Nature, vol. 423(6935), pages 42-48, May.
    5. Ekiz, Cesur & Keskin, Mustafa & Yalçın, Orhan, 2001. "Metastable and unstable states of the Blume–Capel model obtained by the cluster variation method and the path probability method," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 293(1), pages 215-232.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Rocha-Neto, Mário J.G. & Camelo-Neto, G. & Nogueira Jr., E. & Coutinho, S., 2018. "The Blume–Capel model on hierarchical lattices: Exact local properties," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 494(C), pages 559-573.
    2. Turkan Haliloglu & Nir Ben-Tal, 2008. "Cooperative Transition between Open and Closed Conformations in Potassium Channels," PLOS Computational Biology, Public Library of Science, vol. 4(8), pages 1-11, August.
    3. Tobias Linder & Bert L de Groot & Anna Stary-Weinzinger, 2013. "Probing the Energy Landscape of Activation Gating of the Bacterial Potassium Channel KcsA," PLOS Computational Biology, Public Library of Science, vol. 9(5), pages 1-9, May.
    4. Spencer C. Guo & Rong Shen & Benoît Roux & Aaron R. Dinner, 2024. "Dynamics of activation in the voltage-sensing domain of Ciona intestinalis phosphatase Ci-VSP," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    5. Shrivastava, Rajan & Malik, Chetan & Ghosh, Subhendu, 2016. "Open channel current noise analysis of S6 peptides from KvAP channel on bilayer lipid membrane shows bimodal power law scaling," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 451(C), pages 533-540.
    6. Mendes, R.G.B. & Sá Barreto, F.C. & Santos, J.P., 2018. "Thermodynamic states of the mixed spin 1/2 and spin 1 hexagonal nanotube system obtained from a eighteen-site cluster within an improved mean field approximation," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 505(C), pages 1186-1195.
    7. Bryan Cernuda & Christopher Thomas Fernandes & Salma Mohamed Allam & Matthew Orzillo & Gabrielle Suppa & Zuleen Chia Chang & Demosthenes Athanasopoulos & Zafir Buraei, 2019. "The molecular determinants of R-roscovitine block of hERG channels," PLOS ONE, Public Library of Science, vol. 14(9), pages 1-26, September.
    8. Alan J Situ & Tobias S Ulmer, 2019. "Universal principles of membrane protein assembly, composition and evolution," PLOS ONE, Public Library of Science, vol. 14(8), pages 1-20, August.
    9. Jin Wang & Zeyuan Song & Miaolu He & Yongchao Qian & Di Wang & Zheng Cui & Yuan Feng & Shangzhen Li & Bo Huang & Xiangyu Kong & Jinming Han & Lei Wang, 2024. "Light-responsive and ultrapermeable two-dimensional metal-organic framework membrane for efficient ionic energy harvesting," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    10. Marcos Matamoros & Xue Wen Ng & Joshua B. Brettmann & David W. Piston & Colin G. Nichols, 2023. "Conformational plasticity of NaK2K and TREK2 potassium channel selectivity filters," Nature Communications, Nature, vol. 14(1), pages 1-12, December.

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:eee:phsmap:v:357:y:2005:i:3:p:397-414. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Catherine Liu (email available below). General contact details of provider: http://www.journals.elsevier.com/physica-a-statistical-mechpplications/ .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.