Comment on "Ribosome utilizes the minimum free energy changes to achieve the highest decoding rate and fidelity".
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.
Department of Physiology, Biophysics and Systems Biology, Faculty of Medicine, Technion, Haifa, 31096, Israel.
Yonatan
Y
Savir
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.
Tsvi
T
Tlusty