Savir Yonatan, Tlusty Tsvi
Department of Physiology, Biophysics and Systems Biology, Faculty of Medicine, Technion, Haifa, 31096, Israel.
Center for Soft and Living Matter, Institute for Basic Research, UNIST, Ulsan, Korea; Department of Physics, Ulsan National Institute for Science and Technology, Ulsan, Korea; Simons Center for Systems Biology, Institute for Advanced Study, Einstein Drive, Princeton NJ 08540, USA; and Simons Center for Systems Biology, Institute for Advanced Study, Princeton, New Jersey 08540, USA.
Phys Rev E. 2016 May;93(5):056401. doi: 10.1103/PhysRevE.93.056401. Epub 2016 May 13.
We examined [Y. Savir and T. Tlusty, Cell 153, 471 (2013)10.1016/j.cell.2013.03.032] the decoding performance of tRNA by the ribosome. For this purpose, we specified the kinetics of tRNA decoding and the corresponding energy landscape, from which we calculated the steady-state decoding rate R_{C}. Following our work, Xie reexamined [P. Xie, Phys. Rev. E 92, 022716 (2015)10.1103/PhysRevE.92.022716] the energy landscape of tRNA decoding. His analysis relies on an alternative expression for R_{C}, while claiming that the expression we use is missing some terms. In this Comment we rederive in detail our expression for the steady-state decoding rate R_{C}, show they hold, explain why the alternative expression for R_{C} is inaccurate, and discuss the underlying intuition.
我们研究了[Y. Savir和T. Tlusty，《细胞》153卷，471页（2013年）10.1016/j.cell.2013.03.032]核糖体对tRNA的解码性能。为此，我们确定了tRNA解码的动力学以及相应的能量景观，由此计算出稳态解码速率(R_{C})。继我们的工作之后，谢重新审视了[P. 谢，《物理评论E》92卷，022716页（2015年）10.1103/PhysRevE.92.022716]tRNA解码的能量景观。他的分析依赖于(R_{C})的另一种表达式，同时声称我们使用的表达式缺少一些项。在本评论中，我们详细重新推导了稳态解码速率(R_{C})的表达式，证明它们是成立的，解释了(R_{C})的另一种表达式为何不准确，并讨论了其背后的直觉。
