Figure 1.
Scheme of the idiotypic network and specificity of the AIM2 response.
a) The idiotypic network. An antigen, Ag, is recognized by its antibody Ab1. The Ab1 becomes itself an antigen eliciting the production of anti-antibodies Ab2. This response can be divided into: i) an antigen-non inhibitable group (Ab2α), ii) an antigen-inhibitable group bringing an “internal image” of the antigen (Ab2β), and iii) an antigen-inhibitable group due to steric hindrance with the antigen binding-site (Ab2γ). b) Specificity of AIM2 response. Immunoreactivity of phage expressed AIM2 scFv was tested by ELISA against MB2.8 (used for selection) and 3 others scFv-Fc. MB3.7 is a celiac-derived anti-TG2 antibody while MB6.2 and MBV5B2 are control antibodies using the VH5 gene for VH Chain.
Table 1.
Length and canonical structure (CS) of the CDRs in the modelled antibodies and in the corresponding templates.
Figure 2.
Comparison between the top ‘CDR-directed’ and ‘blind’ docking solutions.
(a) and (c): the CONS-COCOMAPS consensus maps calculated for the 22 models from the CDR-directed docking simulations (a) and for the 30 models from the ‘blind’ ones (c). Labels have been added for the MB2.8 CDR loops L1-L3 and H1-H3. (b) and (d): Pymol [70] visualization of the representative models of the top ten clusters in both CDR-directed (c) and ‘blind’ docking simulations (d), after superimposition of Ab1-MB2.8. The MB2.8's light chain is colored in pink, its heavy chain is colored in hotpink. All the models using the MB2.8 CDR region for the binding have AIM2 colored in blue, while AIM2 is colored in silver in the 7th solution of the blind simulation.
Table 2.
Top 10 ClusPro models for the CDR-directed and “blind” simulations, with corresponding ClusPro population and ranking position by CONSRANK.
Table 3.
RMSD values calculated on the backbone of Ab1-MB2.8 upon best Ab2-AIM2 superposition.
Table 4.
Comparison of some interface features of the three selected MB2.8-AIM2 models and of the 1DVF structure, by the COCOMAPS server [30].
Figure 3.
A surface representation of the MB2.8-AIM2 interface in M1-CDR. The MB2.8 light and heavy chains are colored in pink and hotpink, respectively, while the AIM2 light and heavy chains are colored in lightblue and blue. All residues at the interface that are more than half buried upon complex formation and all residues involved in inter-molecular salt bridges are shown as sticks and labelled.
Table 5.
M1-CDR residues that are more than 50% buried upon complex formation.
Figure 4.
Comparison between M1-CDR and the X-ray structure of the D1.3-E5.2 Ab1-Ab2 complex (1DVF).
(a) and (b): the distance range contact maps by COCOMAPS [30], calculated for the MB2.8-AIM2 model (a) and the experimental structure of E5.2/D1.3 complex (PDB code: 1DVF) (b). The dots at the crossover of two residues are colored in red, yellow, green and blue if any pair of atom is closer than 7, 10, 13 and 16 Å, respectively. (c) and (d): Pymol [70] visualization of MB2.8-AIM2 model (c) and the experimental structure E5.2-D1.3 (d). The color code is the same in both figures: the Ab1 light and heavy chains are colored in light and dark blues, respectively; the Ab1 light and heavy chains are colored in light and dark pink, respectively. Labels have been added for the Ab1's and Ab2's light and heavy chains.
Figure 5.
RMSD fluctuation and gyration radius.
Top: RMSD fluctuation of the Cα atoms of M1-CDR and 1DVF from the starting geometry along the 100-ns long MD trajectory. Bottom: Gyration radius, Rγ, of M1-CDR and 1DVF along the 100-ns long MD trajectory.