Mechanistic Disruption of the TREM2–DAP12 Transmembrane Complex by Alzheimer’s Disease Mutations: A Multiscale Simulation Study

Triggering receptor expressed on myeloid cell 2 (TREM2) is an immunomodulatory receptor that plays a critical role in microglial activation through its association with the adaptor protein DNAX-activation protein 12 (DAP12). Variants in TREM2 have been implicated as genetic risk factors for Alzheimer's disease (AD), most notably the extracellular domain variant R47H. However, recent studies highlight that transmembrane domain (TMD) mutations, including W191X in isoform-219 of TREM2, may also increase AD risk. Nonetheless, the molecular mechanisms underlying the TREM2-DAP12 complex formation and the role of specific TMD mutations in disease pathology remain unclear. Here, we employ multiscale molecular dynamics (MD) simulations to investigate the structural and dynamic effects of key TREM2 TMD mutations on the complex formed with DAP12 within a lipid bilayer composed of a POPC:cholesterol (80:20) mixture. Specifically, we analyzed four mutations in isoform-230 (K186A, K186X, W194A, W194X) and three constructs in isoform-219 (wild type, W191A, W191X). Our previous studies identified that K186 forms a critical salt bridge with DAP12 residue D50 in isoform-230. In this study, we extend this understanding by combining atomistic simulations with unsupervised machine learning approaches to analyze conformational changes across mutant complexes. Across variants, we observe isoform- and mutation-specific effects on helix orientation, hydrogen bonding, and electrostatic interactions that destabilize complex formation. This study provides atomistic-level insight into how disease mutations perturb membrane protein signaling interfaces and introduces a robust simulation and data-driven framework for studying transmembrane complexes involved in neurodegeneration and immunoreceptor function.