## 2 Results
### Building of a C1q/LAIR-1 Interaction Model  
As mentioned above, the central LAIR-1 arginine 59 and glutamate 61 residues are essential for C1q but also generic collagen backbone binding. Nevertheless, we showed that LAIR-1 recognition of C1q does not randomly occur along the CLR but is located on a specific binding site close to the C1r\({}_{2}\)s\({}_{2}\) interaction region. Therefore, we investigated the binding specificity of C1q interaction with LAIR-1. For that purpose, we designed a model based on the structural literature and the results presented above. One crystal structure of GPVI in complex with a GPO-containing collagen peptide is available in the protein data bank (PDB code: 5 OU8). Analysis of this structure reveals that the GPVI R38 and E40 residues (homologues of LAIR-1 R59 and E61, respectively) are central in collagen interaction and recognize the OGXO motif of two consecutive GPO triplets of a single chain. LAIR-1 R59 and E61 residues should likely recognize similar motifs on C1q. We identified three similar motifs in the C1q B and C chain sequences in close proximity to the C1r\({}_{2}\)s\({}_{2}\) binding site that could be recognized by LAIR-1 (underlined in Figure 8A). We performed a structure alignment of the LAIR-1 Ig-like domain (PDB code 3 RP1) with the GPVI collagen-binding domain and aligned the GPVI-associated collagen peptide with a model of one C1q collagen stem, in the region of the putative LAIR-1 binding sites on their common hydroxyproline residues. Such alignment led to the generation of three putative models of LAIR-1 in interaction with one C1q stem (Figure 8 and Figure S3). In the different models, we identified three residues facing the LAIR-1 I102 residue: A71 on C1q A chain, P73 and I76 on C1q C chain (represented in black in Figure 8 and Figure S3). Considering the constraint that a small C1q residue must face LAIR-1 I102, together with the close proximity to the C1r\({}_{2}\)s\({}_{2}\) and the presence of two possible electrostatic interactions at side of the central R59 and E61, the model represented in Figure 8B with an alanine residue at this position on C1q A chain (A_A71) was selected as the most consistent one.  
Figure 7: Mutational analysis of LAIR-1 interaction with C1q. (**A**) Crystal structure of LAIR-1 Ig-like domain (PDB code: 3 KGR). The side chains of the mutated residues are shown and labeled. The central binding residues are colored in red and the distal residues are shown in green and orange (as in Figure 5). (**B**) SPR measurements of the interaction of LAIR-1 WT and mutants with sC1q, C1 qCLR_nc2 and C1 qstem_nc2. Results are expressed as the percentage of the LAIR-1 WT response and error bars represent the SD of three different experiments. The detection of a binding signal of LAIR-1 variants with the positive collagen peptide control measured with the nanoDSF method is reported at the bottom. The presence or absence of the characteristic binding signal is reported with + or \(-\) symbols, respectively. The cases where a weak binding signal remains are indicated with a \(\pm\) symbol. The raw data of the peptide interactions are presented in Figure 5B and Figure S5.