Özer, Mahmut

Article | 2004 | NeuroReport15 ( 9 ) , pp.1451 - 1455

We previously formulated dynamics of ion channel gates by the path probability method. In this study, we apply that theoretical approach to derive the activation rate kinetics of T-type calcium channel in thalamic relay neurons. We derive explicit expressions of the forward and backward rate constants and show that the proposed rate constants accurately capture form of the empirical time constant, and that they also provide its saturation to a constant value at depolarized membrane potentials. We also compare our derivations with linear and nonlinear thermodynamic models of rate kinetics obtained from the same calcium channel, and s . . .how that it is possible to capture saturation of the time constant for the depolarized membrane potentials by the only proposed rate constants. © 2004 Lippincott Williams & Wilkins Daha fazlası Daha az

Özer, Mahmut | Erdem, Rıza

Article | 2003 | NeuroReport14 ( 7 ) , pp.1071 - 1073

A voltage-gated ion channel is fundamental in generation and propagation of electrical signals in the excitable membranes. Dynamics of (in)activation gates of the ion channel is modeled by first-order kinetics. The equilibrium value function is crucial in the kinetics of the (in)activation gates for fitting experimental data. We present a new methodology to define the equilibrium value function based on the lowest approximation of the cluster variation method and the static properties in the molecular field approximation. The methodology allows for exploration of the gating dynamics. © 2003 Lippincott Williams & Wilkins.

Özer, Mahmut

Article | 2004 | NeuroReport15 ( 12 ) , pp.1953 - 1957

Thermodynamic models of ionic currents are used to deduce exact functional form of rate constant. It is first assumed that free energy depends linearly on voltage. A major criticism of this approach is that time constant can reach arbitrarily small values resulting in an aberrant behavior. Recently, non-linear effects of electric field on the free energy were considered to solve this problem based on T-type calcium channel. In this study, we show that the current model approximately captures the voltage-dependence of the time constant only in a specific range of voltage and does not provide saturation of the time constant outside th . . .is range. Then, we propose an improved non-linear thermodynamic model and illustrate its applicability based on T-type calcium channel. © 2004 Lippincott Williams & Wilkins Daha fazlası Daha az

Özer, Mahmut

Article | 2007 | Physica A: Statistical Mechanics and its Applications379 ( 2 ) , pp.579 - 586

The linear, nonlinear and improved nonlinear thermodynamic models of the voltage-dependent ion channels were proposed to deduce the exact functional form of the rate constants. In this context, we present a comparative analysis of the linear, nonlinear and improved nonlinear thermodynamic models of voltage-dependent channel kinetics based on the sodium activation experimental data of Cav3.1 channel. We also provide some insight on the assumptions used to derive the thermodynamic models of the channels and show that the improved nonlinear thermodynamic model provides a simple and physically plausible approach to describe the behavior . . . of the voltage-dependent ion channels. © 2007 Elsevier B.V. All rights reserved Daha fazlası Daha az

Özer, Mahmut | Erdem, Rıza | Provaznik, Ivo

Article | 2004 | NeuroReport15 ( 2 ) , pp.335 - 338

Voltage-gated ion channels are of great importance in the generation and propagation of electrical signals in the excitable cell membranes. How these channels respond to changes in the potential across the membrane has been a challenging problem, and different approaches have been proposed to address the mechanism of voltage sensing and gating in these channels. In this study, we attempt a new approach by considering a simple two-state gate system and applying the path probability method to construct a nonequilibrium statistical mechanical model of the system. The model which is based on the principles of statistical physics provide . . .s a firm physical basis for ion channel gating. © 2004 Lippincott Williams & Wilkins Daha fazlası Daha az

Özer, Mahmut

Article | 2005 | Physica A: Statistical Mechanics and its Applications357 ( 03.Apr ) , pp.397 - 414

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. © 2005 Elsevier B.V. All rights reserved Daha fazlası Daha az