Harnessing AlphaFold3 to Elucidate BBSome Structure and Protein Partners.

This study used a powerful computer program called AlphaFold3 to create detailed 3D models of the BBSome - a group of eight proteins that work together and are involved in Bardet-Biedl Syndrome (BBS). The BBSome helps transport important proteins in and out of cilia, which are tiny hair-like structures on cells that act like antennas for receiving signals. The researchers found that two specific proteins in the BBSome (BBS1 and BBS9) act as the main "connection hubs" that hold the complex together, and they discovered that a common genetic mutation called BBS1M390R makes the whole complex less stable, which helps explain why this mutation causes BBS symptoms. The study also used the computer models to predict how the BBSome interacts with other important proteins in the body, particularly those involved in metabolism and weight control (like receptors for leptin and insulin). The researchers then tested some of these predictions in the lab and found evidence supporting their computer models. This is significant because it suggests the BBSome plays a role in how cells respond to signals about hunger, metabolism, and weight - which could explain why people with BBS often struggle with obesity and diabetes. While this is still laboratory research, it provides a new "roadmap" for understanding how the BBSome works and why it malfunctions in BBS. This detailed understanding could potentially help scientists develop better treatments in the future by showing them exactly which protein interactions to target.

The BBSome, an eight-protein complex implicated in Bardet-Biedl syndrome (BBS), plays a crucial role in ciliary function. Although important aspects of its structural organization and protein interactions have been elucidated, additional questions remain regarding how these features relate to cargo recognition and complex dynamics. Using AlphaFold3, we generated a structural model closely matching recent cryo-EM data (Cα RMSD: 1.203 Å). Interface residue analysis of the model identified BBSome proteins BBS1 and BBS9 as central interaction hubs (most interface residues between two proteins), with BBS2 and BBS7 showing the most polar contacts. The common BBS1M390R pathogenic mutation, known to cause BBS, was predicted to destabilize the complex. BBS4 was also found to interact stably with pericentriolar material 1, suggesting a role in centriolar satellite localization. AlphaFold3-mediated analysis of BBSome interactions with G protein-coupled receptors (GPCRs) led to the identification of contact hotspots on BBS1, BBS4, and BBS5. These predictions were supported by immunoprecipitation and peptide competition assays. The modeling also suggested plausible interfaces between specific BBS proteins and metabolic signaling proteins, including MRAP2 (an MC4R chaperonin), the leptin receptor, and the insulin receptor. These predicted interfaces align with previously reported biochemical associations between BBS proteins and these receptors, supporting the idea that the BBSome regulates trafficking and signaling in metabolic pathways. Together, these findings provide new insights into BBSome structure and receptor interactions, offering a predictive framework to explore its role in ciliary trafficking and human disease.