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The Free Energy Landscape of Dimerization of a Membrane Protein, NanC

Figure 1

Atomistic and coarse-grained representations of NanC along with illustrations of the orientational combinations used in the PMF calculations.

(A) The atomistic structure of NanC is shown in the plane of the bilayer, which is perpendicular to the pore axis. (BC) The coarse-grained NanC is shown in both the wide (B) and narrow (C) orientations, which are related by a rotation about the pore axis and with B being the equivalent orientation to A. The atoms/particles are represented by spheres with radii equal to their van der Waals radii. The atoms/particles from acidic residues shown in red, from basic residues in blue, from aromatic residues in yellow and from neutral residues in grey. (DG) Four combinations of protein orientations as viewed from the extracellular side of the membrane. The traces of the NanC proteins illustrate their elliptical cross-sections. For each protein, the angle of orientation is measured between the line, which goes from the centre of mass of the blue protein through the centre of mass of the red protein, and the arrow, which goes from the protein's centre of mass through the of its isoleucine at residue 209. The orientational angle for each protein trace coloured blue is labelled and for each protein coloured red is labelled . The separation between the proteins' centres of mass is given by .

Figure 1

doi: https://doi.org/10.1371/journal.pcbi.1003417.g001