Fig. 3: Conformational dynamics of Api88 in the exit tunnel.
a Trajectories of Api88 obtained from MD simulations were projected onto the two dominant conformational modes of Api88 relative to the PET. The probability of observing conformations is shown in greyscale. The initial conformations I, II, and III are indicated by blue, orange, and green circles, respectively. The conformational space explored by the combined simulations from each initial conformation is outlined by colored lines. The cyan backbone pictograms along the two axes visualize the respective conformational changes (arrows). Red circles correspond to the 5 structures that optimize the correlation with the cryo-EM map (compare panel c). b Correlation coefficients ρ between the cryo-EM map and densities calculated from different MD ensembles are shown color coded. The ensembles were generated by assigning weights, w1, w2, and w3, to the trajectories initiated from conformations I, II, and III, respectively. The weights corresponding to the maximum ρ are indicated by an ‘x’. c For different numbers of structures, the maximum ρ achieved by optimally selecting structures from the simulations is shown. The ρ values obtained from the initial structures and the full MD ensemble are shown as blue and orange dashed lines, respectively.
