An investigation of models of the IP3R channel in Xenopus oocyte

Abstract

We consider different models of inositol 1,4,5-trisphosphate (IP(3)) receptor (IP(3)R) channels in order to fit nuclear membrane patch clamp data of the stationary open probability, mean open time, and mean close time of channels in the Xenopus oocyte. Our results indicate that rather than to treat the tetrameric IP(3)R as four independent and identical subunits, one should assume sequential binding-unbinding processes of Ca(2+) ions and IP(3) messengers. Our simulations also favor the assumption that a channel opens through a conformational transition from a close state to an active state.

Figure 1

Model 1: (a) The structure of the De Young–Keizer IP₃R subunit model. The graph shows the dependence of (b) the open probability P_O, (c) the mean open time τ_O, and (d) the mean close time τ_C as a function of Ca²⁺ concentration for different concentrations of IP₃. The lines show the results calculated with the deterministic transition matrix theory and the symbols show the results obtained from single-channel patch clamp from IP₃R on native nuclear membranes (Refs. 11, 12, 13). Here, thick lines and stars are for [IP₃]=10 μM, thin lines and circles are for 0.033 μM, dashed lines and squares are for 0.02 μM, and dotted lines and triangles are for 0.01 μM. Same notations are used in the following figures. The parameters used in the model are K₁=0.0072 μM, K₂=78 μM, K₃=0.22 μM, K₄=K₁K₂∕K₃, K₅=0.21 μM, a₁=500 μM⁻¹ s⁻¹, a₂=0.01 μM⁻¹ s⁻¹, and a₅=400 μM⁻¹ s⁻¹.

Figure 2

Model 2: (a) The subunit structure of the channel model, (b) the open probability P_O, (c) the mean open time τ_O, and (d) the mean close time τ_C. In the model K₁=0.008 μM, K₂=78 μM, K₃=0.22 μM, K₄=K₁K₂∕K₃, K₅=0.21 μM, a₁=400 μM⁻¹ s⁻¹, a₂=0.01 μM⁻¹ s⁻¹, and a₅=400 μM⁻¹ s⁻¹.

Figure 3

Model 3: (a) The subunit structure of the channel model. A conformational transition to an active state (state-A) occurs before the subunit can contribute to channel opening. (b) The open probability P_O, (c) the mean open time τ_O, and (d) the mean close time τ_C. In the model K₁=0.0054 μM, K₂=17.6 μM, K₃=0.64 μM, K₄=K₁K₂∕K₃, and K₅=1.04 μM. For the conformational change, K₀=0.135 μM and a₀=535 μM⁻¹ s⁻¹.

Figure 4

Model 4: (a) The subunit structure of the channel model, (b) the open probability P_O, (c) the mean open time τ_O, and (d) the mean close time τ_C. In the model K₁=0.018 μM, K₂=24 μM, K₃=0.4 μM, K₄=K₁K₂∕K₃, K₅=0.56 μM, and K₀=0.194 μM with a₀=360 μM⁻¹ s⁻¹.

Figure 5

Model 5: (a) The subunit structure of the channel model, (b) the open probability P_O, (c) the mean open time τ_O, and (d) the mean close time τ_C. In the model K₁=0.005 μM, K₂=15.6 μM, K₃=2.25 μM, K₄=K₁K₂∕K₃, K₅=1.01 μM, and K₀=0.135 μM with a₀=535 μM⁻¹ s⁻¹.

Figure 6

Model 6: (a) The state structure of the sequential binding IP₃R model, (b) the open probability P_O, (c) the mean open time τ_O, and (d) the mean close time τ_C. In (c), the mean open time is independent of IP₃ concentration. In the model K₁=0.009 μM, K₂=48 μM, K₃=0.3 μM, K₄=K₁K₂∕K₃, K₅=0.18 μM, a₁=240 μM⁻¹ s⁻¹, a₂=0.3 μM⁻¹ s⁻¹, and a₅=720 μM⁻¹ s⁻¹.

Figure 7

Model 7: (a) The state structure of the sequential binding IP₃R model, (b) the open probability P_O, (c) the mean open time τ_O, and (d) the mean close time τ_C. In the model K₁=0.016 μM, K₂=8 μM, K₃=0.3 μM, K₄=K₁K₂∕K₃, K₅=0.44 μM, and K₀=0.151 μM with a₀=960 μM⁻¹ s⁻¹.

Figure 8

Model 8: (a) The state structure of the sequential binding IP₃R model, (b) the open probability P_O, and (c) the mean close time τ_C. The inset figure in (c) is the plot of the mean open time τ_O. In the model K₁=0.02 μM, K₂=53 μM, K₃=0.2 μM, K₄=K₁K₂∕K₃, K₅=0.21 μM, and K₀=0.233 μM with a₀=155 μM⁻¹ s⁻¹.