Fig. 3: Identification and characterization of sucrose binding pocket.
From: Structure and sucrose binding mechanism of the plant SUC1 sucrose transporter
a, Close-up view of the sucrose binding pocket outlined in blue, as shown in Fig. 2a. b, Results from five independent MD simulation repeats each for Asp152(H) and Asp152(−), starting from the identified stable binding pose for sucrose. The repeats show consistent results, as summarized by the fraction of time in which sucrose was bound in the stable pose. Right, repeat 2 of the simulations is shown with sucrose as a pin, with the head representing the glucosyl moiety. Below, the r.m.s.d. plot of sucrose. Background of r.m.s.d. plot denoted bound (dark blue) or unbound (light blue) pose of the sucrose. c, Contact map between sucrose atoms and SUC1 residues in MD run 2 with Asp152(H). Only interactions occurring during at least 25% of the simulation time are shown, including hydrogen-bond interactions (blue) and hydrophobic interactions (red). d, Representative snapshot of the sucrose stable pose in simulations with Asp152(H). Blue dashes indicate hydrogen bonds and red dashes indicate hydrophobic interactions. e, Schematic representation of sucrose coordination by SUC1 in the snapshot shown in panel d. f, Oocyte uptake assay for SUC1 mutants targeting the residues lining the sucrose binding pocket. Uptake activities are normalized to that of the wild type. Bars are mean ± s.d. Points represent biologically independent experiments (n = 5 for Q44A and F184A; n = 6 for F298A, F427A, N449A and Q456A; n = 7 for N155A, N156A, R163A, M188A, F423A, S431A and I452A; n = 10 for W294A; n = 12 for WT and Q159A; n = 14 for T290A; n = 18 for Q83A). P values for differences between wild type and variants were obtained from a one-way analysis of variance (ANOVA) followed by the Dunnett’s multiple comparisons test. P values are shown in the figure. NS, not significant.
