Fig. 8: Molecular dynamics simulations of GS− binding to glutathionylated ScGrx7. | Nature Communications

Fig. 8: Molecular dynamics simulations of GS− binding to glutathionylated ScGrx7.

From: Quantitative assessment of the determinant structural differences between redox-active and inactive glutaredoxins

Fig. 8: Molecular dynamics simulations of GS− binding to glutathionylated ScGrx7.The alternative text for this image may have been generated using AI.

a Fraction of bound states with the value for wild-type ScGrx7 (WT) normalized to 100%. Error bars show the standard error of the mean over four replications for each system. Datasets were tested with a two-tailed t test assuming unequal variances; *: null-hypothesis of equal means can be rejected with P < 0.05. For WT and K105R P = 0.13; for WT and E147K P = 0.15 (see also Supplementary Table 13). b For each of the systems of the WT and the variants K105R, K105E, and E147K, bound states were clustered with respect to the structural deviation of the active site and the closest GS− from the solution. The structure representing the most populated cluster is shown in the middle and important areas of the structure representing the second most populated cluster (cluster 2) are shown in the boxes next to it. The covalently bound glutathione moiety at Cys108 is depicted in salmon, the freely diffusing GS− in pink. Residues marked in orange show the mutated residues in the variants. All residues with labels were also studied experimentally. c The occupation density of the diffusing GS− is shown as a red grid on the structure of each ScGrx7 variant. Bound states were combined across replications for this analysis, and the threshold of the density grids is the same for all variants. d Arrows show the binding pathways of GS−. For each binding event, an arrow shows the linearized trajectory of the GS− molecule right before the binding event going from black (start of the pathway) to gray (bound). The active site is shown as a red surface and the sulfur atoms of the mixed disulfide bond are shown in yellow. e Histograms show the distance between the sulfur atom of GS− and the center of mass of the sulfur atoms of Cys108-SSG (“S–S-distance”) and the angle created by the three sulfur atoms (“S–S–S angle”) over all four replications each. The color of the bins ranges from dark blue (lowest populated bin) over green to yellow (highest populated bin). See Supplementary Table 14 for results of the correlation analysis.

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