Figure 8. Model of the 32mer WCsAPF. (a-c) Flattened representation of β-strands for four subunits. The green and purple circles behind the strands indicate the axes of 2-fold perpendicular symmetry and the horizontal dashed line indicates the plane containing those axes. Parameters of the β-barrels are indicated beside or below the schematics. (a) The 3-stranded S1a-S1b-S2 β-sheets that comprise the outer β-barrel. (b) The S3 β-strands of the middle β-barrel. Cout S3 strands are darker blue. (c) The S1b-S2 α-helices and S1b β-strands of two TIM barrel-like structures of Cin subunits. (d) Interactions indicated by NMR studies of Gao et al.32 between residues of S1b-S2 and S3. Red lines and residue list on the left side indicate possible interactions between S1b-S2 residues and outwardly-oriented S3 side chains; green lines and residue list on the right indicate possible interactions between the Cin S1b-S2 α-helix residues and inwardly-oriented S3 side chains. (e) A helical net representation of the S1b-S2 α-helix showing observed interactions among residues that are sequentially separated by three or four positions. (f) Schematic cross-section of the upper portion of the 32-mer model.
An atomic-scale model of a 32mer sAPF is shown in Fig. 9. Side chains of the S1b-S2 helix make direct contact with side chains of S3 β-strands indicated in green in Fig. 8. Some side chains of the S1b and S2 β-strands predicted by NRM to interact did not make direct contact, but distances between the closest side chain atoms were relatively small. One interaction proposed by the NMR study, between K15 and M35, was not satisfied. The EM images of the putative 32mer in Fig. 7 closely corresponds to the size and shape of the cross-section pictures of Fig. 9e and f (also see Supplement Fig. S4). The atomic-scale model is also consistent with our modeling criteria: almost all conserved hydrophobic side chains are buried and pack tightly in at least one of the two conformations, almost all charged groups form salt-bridges, and almost all backbone polar atoms form H-bonds due to the high content of β and α-secondary structure.