Comment on "ribosome utilizes the minimum free energy changes to achieve the highest decoding rate and fidelity"

Abstract

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 RC. 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 RC, 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 RC, show they hold, explain why the alternative expression for RC is inaccurate, and discuss the underlying intuition.