Extended Data Fig. 4: MD simulation of the non-resolved EL2 sequence. | Nature

Extended Data Fig. 4: MD simulation of the non-resolved EL2 sequence.

From: Structure of the human dopamine transporter in complex with cocaine

Extended Data Fig. 4

a, Root Mean Square Fluncuation (RMSF) of EL2’s Cα atoms (amino acid residues 170-213) as a function of EL2 residues, in the last 30 ns of seven unbiased independent repeats (Supplementary Table 1). RMSF was calculated using the gmx rmsf tool using Gromacs 2021.4. b, Visual representations as ribbons, of the side view of hDAT in the last snapshots of the seven unbiased MD simulations in a zoomed-out (left) and zoomed-in view (right panel). EL2 is colored according to the MD repeat and the rest structure is colored grey in all repeats. Structures were superimposed according to the Cα atoms of their TM helices. c, Structures in panel B visualized from a top view. On the left, hDAT is depicted with both the EL2 and the rest of the structure, while on the right hDAT EL2 is depicted only for visual clarification. d, Root Mean Square Deviation (RMSD) of EL2’s Cα-atoms (amino acid residues 170-213) as a function of time, in the duration of the seven independent repeats (repeats colored mauve, blue and green). RMSD was calculated using the gmx rms tool using Gromacs 2021.4.

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