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. 2025 Aug 4;11(8):1670–1680. doi: 10.1038/s41477-025-02056-z

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© The Author(s) 2025

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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/.

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Extended Data Fig. 9 — a. Cα RMSD values describing the movement of the LAX3 protein in different protonation scenarios over 1 µs of simulations and with six repeats for each scenario. The stacked density plots indicate the distribution of RMSD values for each simulation trajectory. b. The spherical angles of IAA within the binding site shown in a circular plot, with a wrapped azimuthal (φ) angle [-180°,180°] mapped on the edge of the circle, and a linear polar (θ) angle [0,180°] mapped on the radial line. The density plot of the azimuthal (φ) angle values shows the least populated angle value (30°), which was used as a plot border in the unwrapped dataset plot (Fig. 3a). c. Water count around IAA grouped by the assigned cluster as shown in B and Fig. 3. Box plot elements represent the following: centre line: median (50th percentile), box minimum: 25th percentile (Q1), box maximum: 75th percentile (Q3), box height: interquartile range (IQR) (between 25 and 75%), whisker lower edge: Q1 - 1.5 x IQR, whisker upper edge: Q2 + 1.5 x IQR. d. ProLIF fingerprint analysis showing residues in LAX3 that interact with IAA in simulations, divided by cluster. Colors indicate the interaction type (blue for H-bond, yellow for hydrophobic, red for salt-bridges and green for pi-stacking). The color intensity corresponds to the normalized frequency of the interactions in each cluster (where the 100% intensity was assigned to the most frequent protein-IAA interaction in each cluster).