Ratchet, swivel, tilt and roll: a complete description of subunit rotation in the ribosome.
Ratchet, swivel, tilt and roll: a complete description of subunit rotation in the ribosome.
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DOI：
10.1093/nar/gkac1211
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发表时间：
2023-01-25
影响因子：
14.9
通讯作者：
Whitford, Paul C.
中科院分区：
文献类型：
--
作者：
Hassan, Asem;Byju, Sandra;Freitas, Frederico Campos;Roc, Claude;Pender, Nisaa;Nguyen, Kien;Kimbrough, Evelyn M.;Mattingly, Jacob M.;Gonzalez, Ruben L.;de Oliveira, Ronaldo Junio;Dunham, Christine M.;Whitford, Paul C.
核糖体的蛋白质合成需要“小”亚基（SSU; 101 MDa）的大规模重排，包括亚基间和亚基内的旋转运动。然而，由于现在有近2000种核糖体和核糖体亚基的结构是公开的，因此很难根据对所有已知旋转状态的分析来设计实验。为了克服这一点，我们开发了一种方法，其中每个SSU头和身体的方向是描述在三个角坐标（旋转，倾斜和倾斜方向）和一个单一的平移。通过考虑整个RCSB PDB数据库，我们描述了1208个完全组装的核糖体复合物和334个分离的小亚基，其中跨越50个物种。这揭示了亚基重排是普遍的方面，以及其他生物体/域特异性的方面。例如，我们发现SSU体的倾斜样重排（即“滚动”）在原核和真核（胞质和线粒体）核糖体中普遍存在。作为另一个例子，与细菌中的移码相关的结构域取向与真核核糖体中发现的结构域取向相似。总之，这项研究建立了一个共同的基础，结构，模拟，单分子和生物化学的努力可以更精确地询问这个原型分子机器的动力学。
Protein synthesis by the ribosome requires large-scale rearrangements of the ‘small’ subunit (SSU; ∼1 MDa), including inter- and intra-subunit rotational motions. However, with nearly 2000 structures of ribosomes and ribosomal subunits now publicly available, it is exceedingly difficult to design experiments based on analysis of all known rotation states. To overcome this, we developed an approach where the orientation of each SSU head and body is described in terms of three angular coordinates (rotation, tilt and tilt direction) and a single translation. By considering the entire RCSB PDB database, we describe 1208 fully-assembled ribosome complexes and 334 isolated small subunits, which span >50 species. This reveals aspects of subunit rearrangements that are universal, and others that are organism/domain-specific. For example, we show that tilt-like rearrangements of the SSU body (i.e. ‘rolling’) are pervasive in both prokaryotic and eukaryotic (cytosolic and mitochondrial) ribosomes. As another example, domain orientations associated with frameshifting in bacteria are similar to those found in eukaryotic ribosomes. Together, this study establishes a common foundation with which structural, simulation, single-molecule and biochemical efforts can more precisely interrogate the dynamics of this prototypical molecular machine.
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影响因子：
2.9
作者：
Kurkcuoglu, Ozge;Kurkcuoglu, Zeynep;Doruker, Pemra;Jernigan, Robert L.
通讯作者：
Jernigan, Robert L.
影响因子：
16.6
作者：
Guyomar C;D'Urso G;Chat S;Giudice E;Gillet R
通讯作者：
Gillet R
影响因子：
14.9
作者：
Bock LV;Blau C;Vaiana AC;Grubmüller H
通讯作者：
Grubmüller H
影响因子：
16.6
作者：
Carbone CE;Loveland AB;Gamper HB Jr;Hou YM;Demo G;Korostelev AA
通讯作者：
Korostelev AA
DOI：
10.1126/science.1202692
发表时间：
2011-05-20
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Dunkle JA;Wang L;Feldman MB;Pulk A;Chen VB;Kapral GJ;Noeske J;Richardson JS;Blanchard SC;Cate JH
通讯作者：
Cate JH