Skip to main content
Fig. 3 | BMC Biology

Fig. 3

From: How structural elements evolving from bacterial to human SLC6 transporters enabled new functional properties

Fig. 3

hDAT tICA space in presence and absence of PIP2 lipids. a and b Population-weighted tICA landscape for hDAT trajectories in PIP2-containing membranes (a) and for the no-PIP2 system (b). For each system, all conformations in all 50 trajectories are projected on the space of the tICA first and second eigenvectors. Regions differing with respect to the location of Na+/Na2 are highlighted on the tICA landscape with transparent boxes of different colors. c All the conformations are projected on the reaction coordinate based on Na+/Na2 distance from the sodium at site Na1, and the free energy (∆G) is population-based and is calculated as [∆G = −RT ln(population)]. The intermediate state is highlighted by the magenta box; note the absence of a distinct minimum in the absence of PIP2 (red line). Error bars (shown as transparent shades) are calculated using the bootstrap method on 100 blocks of frames with 160-ns time range that are randomly extracted from all 50 trajectories. d Comparing percentage of broken interactions of intracellular gates in the control simulation (PIP2-containing membrane) (red bars) and in the no-PIP2 system (blue bars) averaged over all 50 trajectories of each construct. Error bars are calculated using the bootstrap method by randomly selecting 50 trajectories (with replacement) and repeating the process for 1000 iterations

Back to article page