Fig. 6: Study of the architecture of MtSerB2 tetramer using SEC-UV-SAXS and protein-protein docking.

a Superimposition of I(q) versus q as log-linear plots for MtSerB2 dimer (yellow, on absolute scale), trimer (green, offset by a factor 2.25), and tetramer (dark blue, offset by a factor 1.65). The SAXS curve have been offset by the indicated factors for visualisation and comparison purposes. The inset shows the Guinier fits (coloured symbols) for qR_g < 1.3 (dimer and tetramer) and qR_g < 1.0 (trimer) with cross symbols (grey) indicating data beyond the Guinier region. Error bars represent the s.d. of averaged data (31 frames for the dimer, 15 frames for the tetramer, and 13 frames for the trimer). b Dimensionless Kratky plots for the data in (a). c P(r) functions from the data in (a) normalised to I(0) for comparison purposes. d Strategy used for the in silico modelling of MtSerB2 tetramer by symmetrical protein-protein docking. The in silico modelling steps for constructing three different types of tetrameric architectures from the space coordinates of MtSerB2 dimer homology model are described schematically. e Cartoon representation of the best-fitting tetramer model resulting from the SAXS-based screening of models generated by protein-protein docking (top panel). Each monomer is shown in a distinct colour. The bottom panel depicts a schematic representation of the arrangement of monomers within the tetramer. The three C2 axes of rotation giving rise to the overall D2 symmetry of the tetramer are shown as dotted lines capped by an oval. C2_a and C2_b axes are respectively horizontal and vertical in the plane of the sheet, and C2_c axis is perpendicular to the plane of the sheet. f Fits of the best-fitting tetramer model (e) resulting from the SAXS-based screening of models generated by protein-protein docking (dark blue) and of this same model relaxed using DADIMODO⁷⁶ (light blue) to the experimental data. The error-weighted residual difference plots for the model before and after relaxation are shown in the bottom graph. g Superimposition of the structures of the best-fitting tetramer model resulting from the SAXS-based screening of models generated by protein-protein docking (white) and of this same model relaxed using DADIMODO⁷⁶ (light blue). h Location of the residues involved in MtSerB2 tetramerization ability (shown as spheres) at the tetrameric interfaces of the best-fitting tetramer model (e). i Two different perspectives highlighting the spatial proximity of the two dynamic helices α7 (second helix of the C1 cap) from monomers B and D, and C and A. j Superimposition of the crystal structures of HsPSP monomers²⁵ in open and closed conformations (PDB: 6HYY). The focus is on residues 40–56 of the C1 cap (position of helix α7 by homology in MtSerB2). The residues are folded as an alpha helix in the closed conformation (white) and the form of a flexible loop in the open conformation (pink).