Savir Y, Tlusty T. Comment on "Ribosome utilizes the minimum free energy changes to achieve the highest decoding rate and fidelity".
Phys Rev E 2016;
93:056401. [PMID:
27301009 DOI:
10.1103/physreve.93.056401]
[Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Indexed: 11/07/2022]
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 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.
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