Normal-mode refinement of anisotropic thermal parameters for potassium channel KcsA at 3.2 Å crystallographic resolution
Normal-mode refinement of anisotropic thermal parameters for potassium channel KcsA at 3.2 Å crystallographic resolution
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DOI：
10.1016/j.str.2007.06.012
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发表时间：
2007-08-01
期刊：
影响因子：
5.7
通讯作者：
Ma, Jianpeng
中科院分区：
文献类型：
--
作者：
Chen, Xiaorui;Poon, Billy K.;Ma, Jianpeng
我们报告了一种用于膜蛋白结构各向异性细化的正态模式方法，该方法基于晶体中膜蛋白的全局近天然状态无序遵循低频正态模式的假设。因此，一小组的模式是足够的，以代表各向异性的热运动在X射线晶体学细化。通过将该方法应用于钾通道KcsA在3.2埃，我们得到了一个结构模型与衍射数据的改进拟合。此外，改进的电子密度图允许对每个亚基中的12个残基进行大的结构调整，包括重建3个缺失的侧链。总的来说，在3.2埃处的各向异性KcsA结构系统地更接近于2.0埃KcsA结构，特别是在选择性滤波器中。此外，各向异性的热椭球从细化揭示功能相关的结构灵活性。我们希望这种方法是一个有价值的工具，许多膜蛋白的结构优化与中等分辨率的衍射数据。
We report a normal-mode method for anisotropic refinement of membrane-protein structures, based on a hypothesis that the global near-native-state disordering of membrane proteins in crystals follows low-frequency normal modes. Thus, a small set of modes is sufficient to represent the anisotropic thermal motions in X-ray crystallographic refinement. By applying the method to potassium channel KcsA at 3.2 angstrom, we obtained a structural model with an improved fit with the diffraction data. Moreover, the improved electron density maps allowed for large structural adjustments for 12 residues in each subunit, including the rebuilding of 3 missing side chains. Overall, the anisotropic KcsA structure at 3.2 angstrom was systematically closer to a 2.0 angstrom KcsA structure, especially in the selectivity filter. Furthermore, the anisotropic thermal ellipsoids from the refinement revealed functionally relevant structural flexibility. We expect this method to be a valuable tool for structural refinement of many membrane proteins with moderate-resolution diffraction data.