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

Citation data:

Physical review. E, ISSN: 2470-0053, Vol: 93, Issue: 5, Page: 056401

Publication Year:
2016
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Repository URL:
http://scholarworks.unist.ac.kr/handle/201301/19548
PMID:
27301009
DOI:
10.1103/physreve.93.056401
Author(s):
Savir, Yonatan; Tlusty, Tsvi
Publisher(s):
American Physical Society (APS); AMER PHYSICAL SOC
Tags:
Mathematics; Physics and Astronomy; TRANSFER-RNA SELECTION; TRANSLATION; RECOGNITION; DISCRIMINATION; MECHANISMS; LEVEL
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article description
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.