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. 2019 Mar 27;47(9):4721–4735. doi: 10.1093/nar/gkz213

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© The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 8. — The schematic PMFs from the nucleotide pre-insertion to insertion for the cognate rATP and non-cognate dATP. The PMF of rATP is shown in black curve, the on-path and off-path PMFs of dATP are shown in blue and purple, respectively. The relative binding free energy for the on-path dATP pre-insertion (config 1) to that of rATP has been calculated alchemically. The final configuration (config 5) of dATP off-path locates in between config 4 and 5 on-path (see Supplementary Figure S8). The dissociation barriers at nucleotide pre-insertion are treated similarly as in Figure 5, except for the off-path pre-insertion being an intermediate configuration as during the translocation (see text).