XL-MS and De Novo Protein Design Identified a Common Motif for TREM2 Binding

Despite its clinical importance, a high-resolution molecular understanding of the complex remains elusive. Here, we carried out chemical cross-linking mass spectrometry (XL-MS) analysis of the ApoE3/TREM2_ECD complex to identify intra- and interprotein cross-links, which were used as restraints to guide integrative protein–protein docking. Our data support a binding model in which a helix–loop–helix motif within the ApoE3 hinge and C-terminal region forms a transient binding pocket that wraps around the hydrophobic tip of the TREM2 ectodomain.

This model is further supported by <i>de novo</i>-designed miniprotein binders, which show the same binding mode as identified by our XL-MS experiment. These results establish a robust framework for developing miniprotein-based TREM2 agonists.