Analysis of structural dynamics in the ribosome by TLS crystallographic refinement
Analysis of structural dynamics in the ribosome by TLS crystallographic refinement
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DOI：
10.1016/j.jmb.2007.08.054
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发表时间：
2007-11-02
影响因子：
5.6
通讯作者：
Noller, Harry F.
中科院分区：
文献类型：
--
作者：
Korostelev, Andrei;Noller, Harry F.
核糖体结构和功能研究的一个主要目标是获得核糖体在蛋白质合成的许多步骤中的构象动力学的完整描述。在这里，我们报告了一种新的方法来研究核糖体动力学的平移振动螺丝(TLS)精化与实验X射线衍射数据。对70个S核糖体复合体的热释光分析表明，其许多结构特征具有内在的各向异性运动趋势。对30个S核糖体亚基和50个S核糖体亚基的位移分析表明，存在“棘齿状”亚基间旋转的内在偏向。这两个亚基的振动轴都穿过肽基转移酶中心(PTC)，表明结构旋转的趋势发生在肽键形成的位置周围。核糖体核糖体成分，包括30个S亚基的头部、L1和L11茎以及tRNAs的两个主要臂的各向异性运动模式被发现与它们各自的运动模式有关，这些模式是通过比较不同功能状态下的核糖体而得出的。在小亚基中，与Shine-Dalgarno螺旋相互作用的特征的迁移率在Shine-Dalgarno螺旋的存在下降低，支持这样的假设，即在起始过程中Shine-Dalgarno螺旋的形成可能有助于小亚基的稳定，以实现与启动子tRNA(FMet)的最佳相互作用。相似核糖体复合体的两个独立结构的TLS参数的相似性表明，TLS分析可以提供关于非常大的大分子对象的动力学的有用信息，并且分辨率低于通常应用的TLS精化。(C)2007爱思唯尔有限公司。保留所有权利。
A major goal in the study of ribosome structure and function is to obtain a complete description of the conformational dynamics of the ribosome during the many steps of protein synthesis. Here, we report a new approach to the study of ribosome dynamics using translation-libration-screw (TLS) refinement against experimental X-ray diffraction data. TLS analysis of complexes of the 70 S ribosome suggests that many of its structural features have an inherent tendency for anisotropic movement. Analysis of displacements of the 30 S and 50 S ribosomal subunits reveals an intrinsic bias for "ratchet-like" intersubunit rotation. The libration axes for both subunits pass through the peptidyl transferase center (PTC), indicating a tendency for structural rotations to occur around the site of peptide bond formation. The modes of anisotropic movement of ribosomal RNA components, including the head of the 30 S subunit, the L1 and L11 stalks and the two main arms of the tRNAs were found to correlate with their respective modes of movement previously inferred from comparisons of ribosomes trapped in different functional states. In the small subunit, the mobilities of features interacting with the Shine-Dalgarno helix are decreased in the presence of the Shine-Dalgarno helix, supporting the proposal that that formation of the Shine-Dalgarno helix during initiation may contribute to stabilization of the small subunit for optimal interaction with initiator tRNA(fMet). The similarity of TLS parameters for two independently solved structures of similar ribosome complexes suggests that TLS analysis can provide useful information about the dynamics of very large macromolecular objects and at resolutions lower than those at which TLS refinement has commonly been applied. (C) 2007 Elsevier Ltd. All rights reserved.