Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
Channels (Austin). 2011 Jan-Feb;5(1):23-33. doi: 10.4161/chan.5.1.13905. Epub 2011 Jan 1.
Mechanosensitive TREK channels belong to the family of K2P channels, a family of widely distributed, well modulated channels that uniquely have two similar or identical subunits, each with two TM1-P-TM2 motifs. Our goal is to build viable structural models of TREK channels, as representatives of K2P channels family. The structures available to be used as templates belong to the 2TM channels superfamily. These have low sequence similarity and different structural features: four symmetrically arranged subunits, each having one TM1-P-TM2 motif. Our model building strategy used two subunits of the template (KcsA) to build one subunit of the target (TREK-1). Our models of the Closed channel were adjusted to differ substantially from those of the template, e.g., TM2 of the 2nd repeat is near the axis of the pore whereas TM2 of the 1st repeat is far from the axis. Segments linking the two repeats and immediately following the last TM segment were modeled ab initio as α-helices based on helical periodicities of hydrophobic and hydrophilic residues, highly conserved and poorly conserved residues, and statistically related positions from multiple sequence alignments. The models were further refined by two-fold symmetry-constrained MD simulations using a protocol we developed previously. We also built models of the Open state and suggest a possible tension-activated gating mechanism characterized by helical motion with two-fold symmetry. Our models are consistent with deletion/truncation mutagenesis and thermodynamic analysis of gating described in the accompanying paper.
机械敏感 TREK 通道属于 K2P 通道家族，该家族广泛分布，调控良好，其独特之处在于有两个相似或相同的亚基，每个亚基有两个 TM1-P-TM2 结构域。我们的目标是构建 TREK 通道的可行结构模型，作为 K2P 通道家族的代表。可用于模板的结构属于 2TM 通道超家族。这些结构具有较低的序列相似性和不同的结构特征：四个对称排列的亚基，每个亚基具有一个 TM1-P-TM2 结构域。我们的建模策略使用模板（KcsA）的两个亚基来构建靶标（TREK-1）的一个亚基。我们构建的关闭通道模型与模板模型有很大区别，例如，第二个重复的 TM2 靠近通道轴，而第一个重复的 TM2 远离通道轴。连接两个重复结构并紧跟最后一个 TM 结构域的片段根据疏水性和亲水性残基、高度保守和低度保守残基以及来自多序列比对的统计相关位置的螺旋周期性，从头开始建模为α-螺旋。使用我们之前开发的协议，通过双重对称约束 MD 模拟对模型进行进一步细化。我们还构建了开放状态的模型，并提出了一种可能的张力激活门控机制，其特征是具有双重对称的螺旋运动。我们的模型与伴随论文中描述的门控缺失/截断突变和热力学分析一致。
