I owe a very special thanks to Shiying Huang and all members of the Baskin Lab (@jeremybaskin.bsky.social) for helping this yeasty boy learn the ins and outs of cell culture.
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More broadly, I think this work is a nice example of the power of AlphaFold in identifying both previously-unknown protein-protein interactions and protein functions.

Overall, this work identifies a new class of monomeric “DENN GAP” proteins, with Avl9 and DENND6A as its founding members. Future work is aimed at determining the substrates and biological roles of the remaining DENN GAPs.

We tested one of those candidates, DENND6A, and found that it indeed possesses strong GAP activity towards the Arf-like GTPase ARL8B:

Based on these findings, we predicted that other monomeric DENN domain proteins may be Arf-GAPs.
We predicted that other yeast (Anr2 + Afi1) and human (DENND11 + DENND6A/B) proteins are likely Arf-GAPs:

Avl9 GAP function is (likely) conserved in humans.
Mutation of the predicted catalytic arginine in human AVL9 abolishes its ability to promote cell migration, linking its enzymatic activity to cancer physiology:

Additional structural predictions hinted that Avl9 also interacts with a Rab.
We found that Avl9 localization is mediated by Rab8, which binds a distinct, non-catalytic surface of Avl9. Rab8 recruitment strongly enhances Avl9’s Arf1-GAP activity on membranes:

Biochemical assays confirmed this prediction.
Avl9 exhibits robust GAP activity toward Arf-family GTPases, with highest activity toward Arf1:

Using large-scale AlphaFold-multimer–based interaction screens, we identified a high-confidence interaction between Arf1 and Avl9. The predicted interaction resembles that of a GTPase–GAP interaction, with a conserved arginine finger of Avl9 pointed at Arf-bound GTP:

Monomeric DENN domain proteins are widely thought to function solely as Rab-GEFs, yet the molecular function of Avl9 has remained unclear despite its role in secretion and cell migration.