  Light harvesting complexes 2 (LH2) from Rhodospirillum (Rs.) molischianum and
Rhodopseudomonas (Rps.) acidophila form ring complexes out of eight or nine
identical subunits, respectively. Here, we investigate computationally what
factors govern the different ring sizes. Starting from the crystal structure
geometries, we embed two subunits of each species into their native
lipid-bilayer/water environment. Using molecular dynamics simulations with
umbrella sampling and steered molecular dynamics, we probe the free energy
profiles along two reaction coordinates, the angle and the distance between two
subunits. We find that two subunits prefer to arrange at distinctly different
angles, depending on the species, at about 42.5 deg for Rs. molischianum and at
about 38.5 deg for Rps. acidophila, which is likely to be an important factor
contributing to the assembly into different ring sizes. Our calculations
suggest a key role of surface contacts within the transmembrane domain in
constraining these angles, whereas the strongest interactions stabilizing the
subunit dimers are found in the C-, and to a lesser extent, N-terminal domains.
The presented computational approach provides a promising starting point to
investigate the factors contributing to the assembly of protein complexes, in
particular if combined with modeling of genetic variants.
