Atomistic MD simulations of the free dimer in solution.

Colors black, red and blue represent different independent simulations. (A) Time series of RMSD of core regions (see Materials and Methods) -carbons in the capsomers (dotted) and the dimer (solid). (B) Histogram of RMSDs sampled by the capsomers (unshaded) and dimer (shaded) for the 400 ns simulation. (C) Time series of relative “twist angle” of capsomers in the dimer (see also Figure S3 in File S1). (D) The corresponding “twist angle” distribution for the three simulation trajectories. (E) Relative orientation maps (ROMs) of the dimers (averaged over all atomistic simulations, i.e. a total of 600 ns). For details regarding the projections shown see main text. Coloring according to the normalized probability of finding these relative orientations. The blue circles are drawn with a radius of the longest internal axis of the capsomer.