Example of a simulated time course of conformational transitions of AdiC, a segment of a video illustrating a transporter model in 4D, and simulated time courses of net ligand transport. (A) Time course of AdiC transitioning among four types of conformations, simulated with the model shown in Fig. S6 as described in Results for the initial presence of 1 mM extracellular Arg⁺ and 1 mM intracellular Agm²⁺. For distinction, AdiC’s presence in the apo, Arg⁺-bound, and Agm²⁺-bound forms are indicated by individual filled circles in the lower, middle, and upper sections of the panel, respectively; its adoptions of C₁ (S₁ + S₅) are colored yellow, C₂ (S₂ and S₆) colored blue, C₃ (S₃ and S₇) colored orange, and C₄ (S₄ and S₈) colored cyan. Shown underneath this simulated time course is a segment from Video 2, exhibiting a 4D model of the transporter proper transitioning among four types of conformations while transporting ligands. The video was generated using the simulated time course shown in the panel A as the temporal template to connect the structures of different states, as described in Results. The shown video frames correspond to the segment of simulated time course from 2,211 to 2,250 ms. (B) The time course of uptake of Arg⁺ extracted from the simulation shown in panel A. The black trace illustrates the time course yielded from a simulation of a single subunit of AdiC, where the inset exhibits its first 100 s in an enlarged view. The red trace corresponds to the average of the outcomes from 100 such simulations. (C) The observed time course of the fractional net uptake of radioactive Arg⁺ for the initial conditions of 50 μM external radioactive Arg⁺ and 5 mM internal Agm²⁺ (closed blue circles) (Tsai et al., 2012), overlaid with a single simulated time course (black trace) and the mean of 50 such simulations (red trace). The gray colored zone in panels B or C represents what is defined by mean ± σ, corresponding to the 68% confidence interval.