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

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  • 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
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    References listed on IDEAS

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    1. 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.
    2. 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.
    3. 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.
    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.
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