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. 2023 Dec 20;14:8482. doi: 10.1038/s41467-023-44174-2

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© The Author(s) 2023

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 4 — a Active site in the pre-reaction state after equilibration with QM/MM MD. b Helmholtz free energy (F) as a function of the reaction coordinate (RC) in the presence of Li⁺ ion (in green) in comparison to the free energy profile obtained when K⁺ ion was bound in the active site instead (in violet). As in the case of the K⁺ ion, the reaction exhibits an intermediate state (I), two transition states (TS1 and TS2), and two proton transfer steps (PT1 and PT2). The arrows denote the activation barrier and the free energy difference between the reactant (R) and product state (P). The free energy profiles were obtained by integrating the mean constraint force over the RC. At each RC value, the mean constraint force was calculated from the last 6000 frames. The corresponding errors were obtained from SD using error propagation. c Distances between atom pairs depicted in panel a as a function of the reaction coordinate. Data are presented as mean values ± SD (n = 1000 frames). For clarity, only distances exhibiting a marked change during the reaction are shown. Source data are provided as a Source Data file.