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Modeling and dynamics of the inward-facing state of a Na+/Cl- dependent neurotransmitter transporter homologue.

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Figure 1. The crystal structure of LeuT. Views of the LeuT structure as would be seen along the plane of the lipid bilayer, oriented such that the upper side represents the extracellular half
Figure 2. Schematic of the modeling methodology. The combined approach adopted for generation of the inward-facing model is presented (see Methods)
Figure 4. RMSD variation in TMD-1 eq and TMD-2 eq . Root mean square deviations (RMSDs) of C a positions from the crystal structure (red, blue) and from the starting (t~0 ns) structure (orange, cyan) during the 50 ns TMD+20 ns equilibration in monomer A (r
Fig. 7 shows the variation in distance between salt bridging residues for TMD -1 eq and TMD -2 eq simulations, in the monomer undergoing TMD, as well as the second monomer undergoing free MD (control system)
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