Figure 7. Natural variants of BIN1 can cause affinity perturbation at an interactomic scale.

(A) A summary of our affinity interactomic tests performed with 9 natural variants of the BIN1 SH3 domain. The cumulative Euclidean affinity distances to the WT BIN1, calculated based on the explored 448 dimensional affinity space, are indicated for each variant. For affinities where no detectable binding was observed the detection threshold was used for calculation, hence only the lower limit of the Euclidean distance could be estimated. Variants colored green have minor effect on affinity interactomes, while variants colored in purple displaying either perturbed affinity profiles (PAP) or general loss of functions (LOF). (B) Location of the assayed variants on the structure of WT BIN1. D537 and Y531 are positioned near the PRM binding interface, F584 is buried in the hydrophobic core of the SH3 domain. The structure of the BIN1 SH3 domain bound to a high affinity peptide taken from SMCHD1 was generated using AlphaFold2 (Tunyasuvunakool et al., 2021)⁠. (C) Affinity interactome profiles of the BIN1 variants (colored in green or purple) compared with the affinity profile of WT BIN1 (colored in black). Motifs in the affinity profiles were ranked according to their affinities measured with WT BIN1. Only the motifs displaying detectable binding out of the 449 assayed PRMs are shown. See Supplementary file 2 for further details.

Figure 7—figure supplement 1. Predicting the structural consequences of the likely pathogenic variants of BIN1 with Alphafold2.

The structure of the BIN1_513–593 – SMCHD1_1977–1991 complex was predicted using ColabFold v1.5.2 – a user friendly implementation of AlphaFold2. The complexes of 4 BIN1 variants were predicted: WT, F584S, Y531S, D537V. No major perturbations in the bound PRM conformation could be observed and only minor local changes could be observed in the proximity of the Y531S, or D537V sequence variants. Only the side chains of the core optimal BIN1-binding PxPPxRR motif is shown on the SMCHD1 PRM and only the side chains of residues 531, 537, and 584 are shown on the BIN1_SH3. For each BIN1 variant, below the structures focusing on the binding sites, structures are shown colored by the pLDDT scores of AlphaFold2. No major change has been observed upon mutation in these scores.