Yufeng Liu, Meng Ke, Haipeng Gong Biophysical Journal

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Protonation of Glu135 Facilitates the Outward-to-Inward Structural Transition of Fucose Transporter Yufeng Liu, Meng Ke, Haipeng Gong Biophysical Journal Volume 109, Issue 3, Pages 542-551 (August 2015) DOI: 10.1016/j.bpj.2015.06.037 Copyright © 2015 Biophysical Society Terms and Conditions

Figure 1 Structural fluctuation in the equilibrium simulations. (A) Time series of CαRMSD for the 135Psub (black) and 135NPsub (red) systems. (B) Time series of dEC for the 135Psub (black) and 135NPsub (red) systems. (C) Time series of dIC for the 135Psub (black) and 135NPsub (red) systems. (D) Schematic plot showing the definitions of dIC and dEC. Cα atoms belonging to the NTD (blue spheres) and CTD (yellow spheres) are used in the definition. To see this figure in color, go online. Biophysical Journal 2015 109, 542-551DOI: (10.1016/j.bpj.2015.06.037) Copyright © 2015 Biophysical Society Terms and Conditions

Figure 2 Structural transition in the AT simulations. (A) Time series of CαRMSD for the 135Psub (black) and 135NPsub (red) systems. (B) Time series of dIC (black) and dEC (red) for the 135Psub system. (C) Time series of dIC (black) and dEC (red) for the 135NPsub system. To see this figure in color, go online. Biophysical Journal 2015 109, 542-551DOI: (10.1016/j.bpj.2015.06.037) Copyright © 2015 Biophysical Society Terms and Conditions

Figure 3 Distributions of structural snapshots on the dIC-dEC map for the AT trajectories of the 135Psub (left panel) and 135NPsub (right panel) systems. Biophysical Journal 2015 109, 542-551DOI: (10.1016/j.bpj.2015.06.037) Copyright © 2015 Biophysical Society Terms and Conditions

Figure 4 Free energy landscape and the structural transition pathway. (A) The two-dimensional PMF profiles for the 135Psub system, with reaction pathway (red line). (B) The two-dimensional PMF profiles for the 135NPsub system, with reaction pathway (red line). (C) Overlay of the pathways of the 135Psub (black) and 135NPsub (red) systems on the same plot. (D) The one-dimensional along-the-pathway PMF profiles for the 135Psub (black) and 135NPsub (red) systems. (Triangle, circle, diamond, and square) Free energy minima according to States 1–4, respectively. The scales of free energy values for the two-dimensional PMF profiles are shown in the color bar, in the units of kcal/mol. To see this figure in color, go online. Biophysical Journal 2015 109, 542-551DOI: (10.1016/j.bpj.2015.06.037) Copyright © 2015 Biophysical Society Terms and Conditions