Models of oligomers that correspond to “beads”.
The next challenge was to generate structural models consistent with these bead sizes. The following features are common to all small non-APF oligomer (bead) models presented below.
  1. The number of monomers, M, of an oligomer is an integer multiple of six or eight. Models presented here are only for assemblies of six or more monomers. Hexamers, dodecamers, and octadecamers are based on results of cross-linking studies47. Octamers are based on solid-state NMR studies31.
  2. All models have two or three concentric β-barrels. Six or eight antiparallel S3 β-strands comprise the innermost β-barrel.
  3. All have 2-fold perpendicular symmetry and 3-fold or 4-fold radial symmetry.
  4. All adjacent β strands are antiparallel.
  5. Except for the octadecamer, all putative β-strands are components of β-barrels. S1 can be either a S1a-S1b β-hairpin or a single β-strand.
  6. S1a-S1b β-hairpins and S1 β-strands are on the surface; hydrophilic sides of the strands are exposed to water while hydrophobic side chains on the opposite side interact with S3 or S2.
  7. The vast majority of side chains buried in the interior of the assembly are hydrophobic, the few buried polar side chain atoms from the outer strands can form H-bonds with other groups.
  8. Electrostatic interactions are also favorable; almost all charged groups form salt-bridges and almost all polar backbone atoms form H-bonds. Concentric β-barrel models of oligomers presented in the text are not unique; some alternatives with differing details are described in the supplement. Resolutions of EM images and molecular modeling methods are not sufficient to identify the best of these alternatives. However, all are consistent with the hypothesis of concentric β-barrel assemblies. The smallest β-barrel oligomer modeled here is a hexamer (Fig. 3). S3 strands form a hydrophobic core as a six-stranded antiparallel β-barrel. Although six stranded β-barrels are rare, this one is made possible by the absence of side chains at the inward-pleated G33 and G37 residue backbones, and the flexibility of the M35 side chains that fit next to these glycines. The S3 core of the hexamer is surrounded by an 18-stranded antiparallel β-barrel formed by S1a, S1b, and S2 strands. The illustrated hexamer has an outer diameter of ~4.4 nm (Fig. 3a) assuming an outer diameter 1.0 nm greater than the diameter of the outer β-barrel’s wall. (An alternative model with a S/N ratio of 2/3 has a diameter of ~4.1 nm (see supplement Fig. S1)). Side chains at the axes of 2-fold symmetry intermesh; i.e., V18 of S2 and V36 of S3 (green circle) are both oriented outwardly, and F4 of S1a and M35 of S3 (purple circle) are both oriented inwardly.