AD‐Associated Variants Directly Impair Surface Interactions Between the Hydrophobic Site of TREM2 and the Hinge Region of ApoE

Background Triggering Receptor Expressed on Myeloid Cells 2 (TREM2) and Apolipoprotein E (ApoE) are two of the strongest genetic risk factors for late‐onset Alzheimer’s disease (AD), but while their interplay in the microglial response to AD pathology is hotly studied, surprisingly little is known about the mechanism by which their variants impair this role. Method To define the structural mechanism by which AD‐associated variants impair the TREM2‐ApoE interaction, we used sequence‐based in silico methods to predict the binding site between TREM2 and ApoE, validated the predicted binding site with biolayer interferometry (BLI), then constructed initial models of TREM2‐ApoE complex structures using the identified binding site between TREM2 and APOE as restraints for unbiased molecular docking methods. The top four initial models were re‐ranked by comparing the effect of key residue mutations in the TREM2‐ApoE complex on binding affinities calculated from molecular dynamics‐molecular mechanics Poisson‐Boltzmann surface area (MD/MM‐PBSA) binding free energy analyses with binding affinities measured by BLI. The final validated TREM2‐ApoE complex structure model provides for further investigating the molecular and structural effects of AD‐associated TREM2 variants on interactions between hydrophobic site of TREM2 and hinge region of ApoE. Result Our iterative MD/MM‐PBSA–BLI procedure generated an all‐atom model of the TREM2‐ApoE complex that replicates the binding effects of both engineered mutations in TREM2 and AD‐associated variants in both TREM2 and ApoE. The validated model shows the interaction centered on the apical hydrophobic site of TREM2 and the hinge region of ApoE. The interaction sites in the TREM2‐ApoE complex model are consistent with regions affected by AD‐associated variants in simulations of the individual proteins, with biophysical studies using truncated constructs of the two proteins, and with a recently reported minimal active peptide of TREM2 that is sufficient to stimulate its cytoprotective and cytokine regulating roles in primary microglia. Conclusion Iterative molecular modeling and biophysical binding affinity assays show the hydrophobic site of TREM2 binding the hinge region of ApoE, an interaction which is impaired by AD‐associated variants and which can be targeted to generate novel therapeutics for AD.