Structural Biology and Bioinformatics Division, CSIR - Indian Institute of Chemical Biology, Kolkata -700 032, India.
J Chem Inf Model. 2012 Nov 26;52(11):2958-69. doi: 10.1021/ci300189a. Epub 2012 Nov 12.
Recent disclosure of high resolution crystal structures of Gloeobacter violaceus (GLIC) in open state and Erwinia chrysanthemii (ELIC) in closed state provides newer avenues to advance our knowledge and understanding of the physiologically and pharmacologically important ionotropic GABA(A) ion channel. The present modeling study envisions understanding the complex molecular transitions involved in ionic conductance, which were not evident in earlier disclosed homology models. In particular, emphasis was put on understanding the structural basis of gating, gating transition from the closed to the open state on an atomic scale. Homology modeling of two different physiological states of GABA(A) was carried out using their respective templates. The ability of induced fit docking in breaking the critical inter residue salt bridge (Glu155β(2) and Arg207β(2)) upon endogenous GABA docking reflects the perceived side chain rearrangements that occur at the orthosteric site and consolidate the quality of the model. Biophysical calculations like electrostatic mapping, pore radius calculation, ion solvation profile, and normal-mode analysis (NMA) were undertaken to address pertinent questions like the following: How the change in state of the ion channel alters the electrostatic environment across the lumen; How accessible is the Cl(-) ion in the open state and closed state; What structural changes regulate channel gating. A "Twist to Turn" global motion evinced at the quaternary level accompanied by tilting and rotation of the M2 helices along the membrane normal rationalizes the structural transition involved in gating. This perceived global motion hints toward a conserved gating mechanism among pLGIC. To paraphrase, this modeling study proves to be a reliable framework for understanding the structure function relationship of the hitherto unresolved GABA(A) ion channel. The modeled structures presented herein not only reveal the structurally distinct conformational states of the GABA(A) ion channel but also explain the biophysical difference between the respective states.
最近公布的紫细菌（GLIC）开放态和菊欧文氏菌（ELIC）关闭态的高分辨率晶体结构，为我们深入了解生理和药理学上重要的配体门控 GABA(A) 离子通道提供了新的途径。本建模研究旨在理解离子传导涉及的复杂分子转变，这在以前公布的同源建模中并不明显。特别是，重点放在理解门控的结构基础上，从关闭态到开放态的门控转变在原子尺度上进行。使用各自的模板对 GABA(A) 的两种不同生理状态进行同源建模。诱导契合对接的能力在将内源性 GABA 对接时打破关键的残基间盐桥（Glu155β(2)和 Arg207β(2)），反映了在正位点发生的感知侧链重排，并巩固了模型的质量。进行生物物理计算，如静电映射、孔径计算、离子溶剂化轮廓和正常模式分析（NMA），以解决以下相关问题：离子通道状态的变化如何改变腔道内的静电环境；在开放态和关闭态中 Cl(-)离子的可及性如何；哪些结构变化调节通道门控。在四级水平上表现出的“扭曲到转动”整体运动，伴随着 M2 螺旋沿膜法线的倾斜和旋转，使门控涉及的结构转变合理化。这种感知到的整体运动暗示了 pLGIC 之间存在保守的门控机制。换句话说，本建模研究为理解迄今为止未解决的 GABA(A) 离子通道的结构功能关系提供了一个可靠的框架。本文提出的模型结构不仅揭示了 GABA(A) 离子通道结构上明显不同的构象状态，还解释了各自状态之间的生物物理差异。
