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.
- 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.
- All models have two or three concentric β-barrels. Six or eight
antiparallel S3 β-strands comprise the innermost β-barrel.
- All have 2-fold perpendicular symmetry and 3-fold or 4-fold radial
symmetry.
- All adjacent β strands are antiparallel.
- 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.
- 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.
- 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.
- 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.