Extended Data Fig. 10: MD simulations.
From: Structure and sucrose binding mechanism of the plant SUC1 sucrose transporter
a, Flowchart of MD analysis. b, r.m.s.d. Cα backbone trace over the course of all MD simulations. All runs compared to the crystal structure. c, Comparison of time course of r.m.s.d. of sucrose from initial simulations performed with sucrose in the "MelB-inspired" starting pose, with Asp152 either protonated (Asp152(H)) or deprotonated (Asp152(−)). Stable binding of sucrose to SUC1 is denoted by dark blue background. d, Contact maps between sucrose atoms and SUC1 residues in all five repeats run with sucrose starting in the identified stable pose. Calculated contacts between atoms are defined by the interaction criteria provided by the ProLIF software91. Only interactions occurring in at least 25% of the frames are considered and includes hydrogen bond interactions (blue) and hydrophobic interactions (red). e, Comparison of time course of r.m.s.d. of sucrose from simulations performed with sucrose in the identified stable starting pose, also shown as a needle/pin with head representing the glucosyl moiety, with two different protonation states of Asp152: Asp152(H) and Asp152(−) in five independent repeats, respectively. Background of the r.m.s.d. plot denoted bound (dark blue) or unbound (light blue) position of the sucrose.
