Extended Data Fig. 9: MD analysis identifies potential conformational changes in MraY upon lipid II binding.

(a) Structure of MraY dimer in state when lipid II is bound (not shown). Residues V208 and S226 are indicated and colored purple. (b-d) An overlay of the structure of MraY at the end of simulations with (purple) or without (gray) lipid II present. (b) The structure is shown from the top, lipid II is hidden, and helices with notable differences are indicated. (c, d) MraY with lipid II, boxes indicate where lipid II clashes with the structure from the simulation without lipid II, indicating why the periplasmic helix 221-228 is moved apart when lipid II is bound. (c) is top (periplasmic) view, while (d) is a side view. (e) A boxplot of the average distance between V208 (a residue in the lipid II binding pocket) of each MraY monomer, in simulations with or without lipid II present. The data represented by each box plot is the mean distance from all time points in each of 5 repeats (minima/maxima: 17.2/18.7, no lip2; 21.2/22.0, lip2). Box plot center line represents the median, while the box limits represent the upper and lower quartiles. The whiskers represent the 1.5x interquartile range. (f) A boxplot of the average distance between S226 (a residue in the periplasmic helix above the lipid II binding site) of each MraY monomer, in simulations with or without lipid II present. The data represented by each box plot is the mean distance from all time points in each of 5 repeats (minima/maxima: 12.0/15.8, no lip2; 18.5/21.6, lip2). Box plot center line represents the median, while the box limits represent the upper and lower quartiles. The whiskers represent the 1.5x interquartile range.