Computational Screening of Filamin Mechanical Binding Proteins using AlphaFold2

Abstract

Filamins are dimeric actin binding protein that play a critical role in mechanical signaling. They contain a mechanosensory region (MSR) that naturally folds into a globular closed conformation. Under mechanical stress, the MSR unfolds into an open conformation, exposing binding sites for numerous proteins. Filamins are involved in diverse cellular functions, and their mechanical binding targets are highly context dependent. In this study, we employed AlphaFold2 modeling for screening proteins that specifically recognize the open conformation of filamins. We focused on the Drosophila melanogaster filamin, Cheerio, and conducted a biased screen to identify mechanical binding proteins. We selected the top 132 hits from the initial screening for further characterization. All identified binding proteins specifically recognize the open conformation of the MSR and not the closed conformation. Interestingly, the binding regions of these proteins lack obvious sequence similarity. While some false positives were identified, they could be effectively filtered out based on the secondary structure formed at the binding interface. This study provides a framework for identifying specifically filamin interactions in mechanosignaling.