Garai Ashok, Chowdhury Debashish, Ramakrishnan T V
Department of Physics, Indian Institute of Technology, Kanpur 208016, India.
Phys Rev E Stat Nonlin Soft Matter Phys. 2009 Jan;79(1 Pt 1):011916. doi: 10.1103/PhysRevE.79.011916. Epub 2009 Jan 21.
Proteins are polymerized by cyclic machines called ribosomes, which use their messenger RNA (mRNA) track also as the corresponding template, and the process is called translation. We explore, in depth and detail, the stochastic nature of the translation. We compute various distributions associated with the translation process; one of them--namely, the dwell time distribution--has been measured in recent single-ribosome experiments. The form of the distribution, which fits best with our simulation data, is consistent with that extracted from the experimental data. For our computations, we use a model that captures both the mechanochemistry of each individual ribosome and their steric interactions. We also demonstrate the effects of the sequence inhomogeneities of real genes on the fluctuations and noise in translation. Finally, inspired by recent advances in the experimental techniques of manipulating single ribosomes, we make theoretical predictions on the force-velocity relation for individual ribosomes. In principle, all our predictions can be tested by carrying out in vitro experiments.
蛋白质由称为核糖体的循环机器聚合而成，核糖体将其信使核糖核酸（mRNA）轨道也用作相应模板，这一过程称为翻译。我们深入且详细地探讨了翻译的随机性质。我们计算了与翻译过程相关的各种分布；其中之一——即驻留时间分布——已在近期的单核糖体实验中被测量。与我们的模拟数据最拟合的分布形式，与从实验数据中提取的分布形式一致。为了进行计算，我们使用了一个既捕捉每个核糖体的机械化学过程又捕捉其空间相互作用的模型。我们还展示了真实基因的序列不均匀性对翻译中的涨落和噪声的影响。最后，受近期操纵单核糖体实验技术进展的启发，我们对单个核糖体的力 - 速度关系做出了理论预测。原则上，我们所有的预测都可以通过进行体外实验来检验。
