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. 2016 Oct 31;7:13314. doi: 10.1038/ncomms13314

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Copyright © 2016, The Author(s)

This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/

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(a) Schematic representation of the current model of proofreading¹²,¹³,¹⁵,¹⁷,¹⁸,¹⁹,³⁰,³²,³³. After initial selection is completed (PIS), accommodation, EF-Tu dissociation and rejection are described as parallel kinetic steps. (b) An extended kinetic model for accommodation suggested by simulations. After initial selection, aa-tRNA will reach one of two states: accommodated (A) or rejected (R). The top branch (EF-Tu bound) transitions to the bottom branch (EF-Tu absent) at the rate of k_−Tu. (c) The free-energy profiles describing the transition between A/T and EA conformations are shown for EF-Tu bound (left) and EF-Tu absent (right). An induced fit mechanism of accommodation would imply an increased barrier height for near-cognate tRNA (ΔΔF_NC). In terms of the extended kinetic model, this would correspond to smaller values for and for near-cognate molecules, while leaving unchanged. (d) An alternative potential effect of near-cognate codon interactions is that the EA ensemble is destabilized. In that scenario, the forward rates would be identical for all tRNA molecules, whereas the reverse rates would change. To explore the impact of EF-Tu dissociation on fidelity, the proofreading factor and efficiency were calculated for each of these energetic descriptions of near-cognate molecules.

Inline graphic — (a) Schematic representation of the current model of proofreading¹²,¹³,¹⁵,¹⁷,¹⁸,¹⁹,³⁰,³²,³³. After initial selection is completed (PIS), accommodation, EF-Tu dissociation and rejection are described as parallel kinetic steps. (b) An extended kinetic model for accommodation suggested by simulations. After initial selection, aa-tRNA will reach one of two states: accommodated (A) or rejected (R). The top branch (EF-Tu bound) transitions to the bottom branch (EF-Tu absent) at the rate of k_−Tu. (c) The free-energy profiles describing the transition between A/T and EA conformations are shown for EF-Tu bound (left) and EF-Tu absent (right). An induced fit mechanism of accommodation would imply an increased barrier height for near-cognate tRNA (ΔΔF_NC). In terms of the extended kinetic model, this would correspond to smaller values for and for near-cognate molecules, while leaving unchanged. (d) An alternative potential effect of near-cognate codon interactions is that the EA ensemble is destabilized. In that scenario, the forward rates would be identical for all tRNA molecules, whereas the reverse rates would change. To explore the impact of EF-Tu dissociation on fidelity, the proofreading factor and efficiency were calculated for each of these energetic descriptions of near-cognate molecules.