Fig. 3: XylE IC50 values and protein–sugar interactions probed by MD simulations.
a, IC50 values for XylE–WT uptake of 3H-D-xylose in the presence of either cold D-xylose or D-glucose. Error bars: mean ± s.e.m. of n = 6 independent experiments. b, IC50 values for XylE double mutant XylE-Q175I/L297F uptake of 14C-D-glucose in the presence of cold D-glucose. Error bars: mean ± s.e.m. of n = 6 independent experiments c, D-Xylose (teal, sticks) and coordinating residues (sticks) in the frequently populated clusters (for example, with more than two members) for five independent 1-µs-long simulations using the D-xylose complex structure (helices shown as cartoon with TM1, TM2 and TM4 omitted for clarity colored as in Fig. 1b). The O1 atom of D-xylose is shown accentuated by red spheres for reference. d, D-Glucose (blue, sticks) and coordinating residues (sticks) in the frequently populated clusters in five 1-µs-long simulations of the D-glucose-bound structure shown as in c. e,f, Extracellular gate distances over time and the resulting probability density for each of the five repeats for D-xylose (e) and D-glucose (f). g, Comparison between the probability density of extracellular gate distances with D-xylose for frames in which the sugar occupies the pose resolved in the published structure (blue) and any other pose (yellow). h, As in g but for D-glucose.
