Laboratoire Charles Coulomb (L2C), CNRS, Montpellier University, Montpellier, France.
Laboratory of Parasite Host Interactions (LPHI), CNRS, Montpellier University, Montpellier, France.
Eur Phys J E Soft Matter. 2021 Mar 8;44(2):19. doi: 10.1140/epje/s10189-021-00019-8.
Translation is one of the main steps in the synthesis of proteins. It consists of ribosomes that translate sequences of nucleotides encoded on mRNA into polypeptide sequences of amino acids. Ribosomes bound to mRNA move unidirectionally, while unbound ribosomes diffuse in the cytoplasm. It has been hypothesized that finite diffusion of ribosomes plays an important role in ribosome recycling and that mRNA circularization enhances the efficiency of translation, see e.g. Lodish et al. (Molecular cell biology, 8th edn, W.H. Freeman and Company, San Francisco, 2016). In order to estimate the effect of cytoplasmic diffusion on the rate of translation, we consider a totally asymmetric simple exclusion process coupled to a finite diffusive reservoir, which we call the ribosome transport model with diffusion. In this model, we derive an analytical expression for the rate of protein synthesis as a function of the diffusion constant of ribosomes, which is corroborated with results from continuous-time Monte Carlo simulations. Using a wide range of biological relevant parameters, we conclude that diffusion is not a rate limiting factor in translation initiation because diffusion is fast enough in biological cells.
翻译是蛋白质合成的主要步骤之一。它由核糖体组成，核糖体将 mRNA 上编码的核苷酸序列翻译成氨基酸的多肽序列。与 mRNA 结合的核糖体单向移动，而未结合的核糖体在细胞质中扩散。有人假设核糖体的有限扩散在核糖体回收中起着重要作用，并且 mRNA 的环化提高了翻译的效率，例如见 Lodish 等人（Molecular cell biology, 8th edn, W.H. Freeman and Company, San Francisco, 2016）。为了估计细胞质扩散对翻译速率的影响，我们考虑与有限扩散储库耦合的完全不对称简单排斥过程，我们将其称为具有扩散的核糖体运输模型。在该模型中，我们推导出了蛋白质合成速率作为核糖体扩散常数的函数的解析表达式，并用连续时间蒙特卡罗模拟的结果进行了验证。使用广泛的生物学相关参数，我们得出结论，扩散不是翻译起始的限速因素，因为扩散在生物细胞中足够快。
