Global ribosome motions revealed with elastic network model
Global ribosome motions revealed with elastic network model
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DOI：
10.1016/j.jsb.2004.01.005
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发表时间：
2004-09-01
影响因子：
3
通讯作者：
Jernigan, RL
中科院分区：
文献类型：
--
作者：
Wang, YM;Rader, AJ;Jernigan, RL
像核糖体这样的大系统的运动是不能用传统的分子模拟完全接近的。诸如各向异性网络模型（ANM）之类的粗粒度、小于原子细节的模型是研究核糖体协同运动的方便信息工具。用ANM分析了小的30S亚基、大的50S亚基和两个亚基的整个70S组装的运动。ANM预测的最低频率集体模式表明50S亚基和30S亚基在70S组装运动中呈强反相关。观察到的棘轮运动与实验报道的棘轮运动很好地对应。其他慢模式也被研究，因为它们与核糖体的易位步骤有潜在的联系。我们确定了几种可能促进E-tRNA从组装中退出的模式。在这些慢速模式下，A-site t-RNA和P-site t-RNA被发现是强耦合和正相关的，这表明这两种t-RNA的易位是同时发生的，而E-site t-RNA的运动相关性较小，因此不太可能同时发生。总的来说，t- rna表现出相对较大的变形。这些慢速运动模式的动画可以在http://ribosome.bb.iastate.edu/70SnKmode上查看。(C) 2004爱思唯尔公司版权所有。
The motions of large systems such as the ribosome are not fully accessible with conventional molecular simulations. A coarse-grained, less-than-atomic-detail model such as the anisotropic network model (ANM) is a convenient informative tool to study the cooperative motions of the ribosome. The motions of the small 30S subunit, the larger 50S subunit, and the entire 70S assembly of the two subunits have been analyzed using ANM. The lowest frequency collective modes predicted by ANM show that the 50S subunit and 30S subunit are strongly anti-correlated in the motion of the 70S assembly. A ratchet-like motion is observed that corresponds well to the experimentally reported ratchet motion. Other slow modes are also examined because of their potential links to the translocation steps in the ribosome. We identify several modes that may facilitate the E-tRNA exiting from the assembly. The A-site t-RNA and P-site t-RNA are found to be strongly coupled and positively correlated in these slow modes, suggesting that the translocations of these two t-RNAs occur simultaneously, while the motions of the E-site t-RNA are less correlated, and thus less likely to occur simultaneously. Overall the t-RNAs exhibit relatively large deformations. Animations of these slow modes of motion can be viewed at http://ribosome.bb.iastate.edu/70SnKmode. (C) 2004 Elsevier Inc. All rights reserved.