Simulation and analysis of single-ribosome translation
Simulation and analysis of single-ribosome translation
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DOI：
10.1088/1478-3975/6/2/025006
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发表时间：
2009-06-01
期刊：
影响因子：
2
通讯作者：
Wen, Jin-Der
中科院分区：
文献类型：
--
作者：
Tinoco, Ignacio, Jr.;Wen, Jin-Der
在细胞中，蛋白质由核糖体在称为翻译的多步骤过程中合成。核糖体沿着信使RNA移位，以读取编码蛋白质氨基酸序列的密码子。伸长因子，包括EF-G和EF-Tu被用来催化这一过程。最近，我们已经证明了可以使用光学镊子在单分子水平上跟踪翻译；这项技术允许我们通过测量核糖体在每个密码子上花费的寿命来研究翻译的动力学。在这里，我们分析了单分子实验的数据，并用简单的动力学模型对数据进行了拟合。我们还从系综动力学测量中模拟了基于多步机制的平移动力学。模拟得到的平均寿命与我们的实验单分子测量结果一致。我们发现，计算的寿命分布一般可以用最多五个速率决定步骤的方程来拟合。只有在低浓度的伸长因子下才能获得两个速率决定步骤。这些分析可用于设计新的单分子实验，以更好地了解翻译的动力学和机制。
In the cell, proteins are synthesized by ribosomes in a multi-step process called translation. The ribosome translocates along the messenger RNA to read the codons that encode the amino acid sequence of a protein. Elongation factors, including EF-G and EF-Tu, are used to catalyze the process. Recently, we have shown that translation can be followed at the single-molecule level using optical tweezers; this technique allows us to study the kinetics of translation by measuring the lifetime the ribosome spends at each codon. Here, we analyze the data from single-molecule experiments and fit the data with simple kinetic models. We also simulate the translation kinetics based on a multi-step mechanism from ensemble kinetic measurements. The mean lifetimes from the simulation were consistent with our experimental single-molecule measurements. We found that the calculated lifetime distributions were fit in general by equations with up to five rate-determining steps. Two rate-determining steps were only obtained at low concentrations of elongation factors. These analyses can be used to design new single-molecule experiments to better understand the kinetics and mechanism of translation.