Fig. 5

Conformational flexibility of the Cars’ end rings in wild-type LHCII. a The dihedral distributions for the two end rings of lutein bound to site L1 and L2 of LHCII were computed over six independent MD simulations, discarding the first 400 ns of simulation per each run. The different simulations are labeled as in our previous work⁷. The values for the dihedrals measured on three different crystals of LHCII are also reported and are indicated in the plots as Crystal-S, P or C according to the organism from which LHCII was purified (spinach²⁷, pea⁴⁵ or cucumber¹⁶). The dihedrals of the ring located at the stromal side are reported on the top panels, and those of the ring at the lumenal side are presented in the middle panels. The color scheme for all the plots follows the legend inserted in the plot associated to the L2 site, stromal side (upper right panel of a). The lower panels show the atoms used to define this dihedral angle (green for the stromal and blue for the lumenal side of the membrane). Cars are shown as orange sticks. The nearby elements of LHCII apoprotein are shown in transparent white. The left panels are for site L1 and the right for site L2. b A representation of LHCII apoprotein and of the lutein in the L2 site (depicted as in a) and, in the inset, an example of the rotations of the end-ring of lutein observed at the L2 site in one of the simulations. Different lutein conformations are depicted in different colors and aligned on top of each other