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Principles of stop-codon reading on the ribosome

机译：核糖体终止密码子阅读原理

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摘要

In termination of protein synthesis, the bacterial release factors RF1 and RF2 bind to the ribosome through specific recognition of messenger RNA stop codons and trigger hydrolysis of the bond between the nascent polypeptide and the transfer RNA at the peptidyl-tRNA site, thereby releasing the newly synthesized protein. The release factors are highly specific for a U in the first stop-codon position and recognize different combinations of purines in the second and third positions, with RF1 reading UAA and UAG and RF2 reading UAA and UGA. With recently determined crystal structures of termination complexes, it has become possible to decipher the energetics of stop-codon reading by computational analysis and to clarify the origin of the high release-factor binding accuracy. Here we report molecular dynamics free-energy calculations on different cognate and non-cognate termination complexes. The simulations quantitatively explain the basic principles of decoding in all three codon positions and reveal the key elements responsible for specificity of the release factors. The overall reading mechanism involves hitherto unidentified interactions and recognition switches that cannot be described in terms of a tripeptide anticodon model. Further simulations of complexes with tRNA~(Trp), the tRNA recognizing the triplet codon for Trp, explain the observation of a 'leaky' stop codon and highlight the fundamentally different third position reading by RF2, which leads to a high stop-codon specificity with strong discrimination against the Trp codon. The simulations clearly illustrate the versatility of codon reading by protein, which goes far beyond tRNA mimicry.
机译：在蛋白质合成的终止过程中，细菌释放因子RF1和RF2通过特异性识别信使RNA终止密码子与核糖体结合，并触发新生多肽和肽基-tRNA位点的转移RNA之间的键的水解，从而释放新的合成蛋白。释放因子对于第一个终止密码子位置的U具有高度特异性，并在第二个和第三个位置识别嘌呤的不同组合，其中RF1读取UAA和UAG，RF2读取UAA和UGA。利用最近确定的终止复合物的晶体结构，通过计算分析来破译终止密码子的能量学成为可能，并阐明高释放因子结合准确性的起源。在这里，我们报告了不同同源和非同源终止复合物的分子动力学自由能计算。模拟定量解释了所有三个密码子位置的解码基本原理，并揭示了负责释放因子特异性的关键要素。整体阅读机制涉及迄今为止无法识别的相互作用和识别开关，无法用三肽反密码子模型来描述。与tRNA〜（Trp）的复合物的进一步模拟（tRNA识别Trp的三重密码子）解释了“泄漏”终止密码子的观察结果，并突出显示了RF2读取的根本不同的第三位置，这导致了较高的终止密码子特异性对Trp密码子有强烈的歧视。该模拟清楚地说明了通过蛋白质进行密码子阅读的多功能性，这远远超出了tRNA的模仿范围。

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  • 来源
    《Nature》 |2010年第7300期|P.v947-950|共5页
  • 作者

    Johan Sund; Martin Ander; Johan Aqvist;

  • 作者单位

    Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, 5E-751 24 Uppsala, Sweden;

    Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, 5E-751 24 Uppsala, Sweden;

    Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, 5E-751 24 Uppsala, Sweden;

  • 收录信息 美国《科学引文索引》(SCI);美国《工程索引》(EI);美国《生物学医学文摘》(MEDLINE);美国《化学文摘》(CA);
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