Inter-domain flexibility in F-Box proteins revealed by integrative modeling

Abstract

F-box proteins, the substrate-recognition modules of the SCF (Skp1-Cul1-F-box) ubiquitin ligase complex, play a central role in targeted protein degradation by enabling the selective recruitment of diverse substrates. F-box proteins share a common architecture with a conserved anchor domain linked to the substrate-binding domain. Despite extensive structural characterization of F-box proteins, their potential conformational dynamics remain poorly understood. Here, we employ an integrative modeling approach combining cryo-EM structures, cross-linking mass spectrometry (XL-MS), and deep learning-based conformational ensemble prediction to profile the accessible conformations of F-box proteins. Our analyses reveal a significant inter-domain flexibility in FBXL2 and FBXL17 that enables sampling of a broad range of conformations within assembled SCF and CSN-SCF complexes. By contrast, other F-box proteins, including FBXL1 and FBXO22, exhibit intrinsic flexibility but are restricted to a considerably narrower conformational landscape. Together, our work highlights inter-domain plasticity as a tunable architectural feature of F-box proteins, which may shape their functional versatility within SCF complexes.