Chemical Cross-Linking/Mass Spectrometry Maps the Amyloid β Peptide Binding Region on Both Apo lipoprotein E Domains

Apolipoprotein E (apoE) binds the amyloid beta peptide (A beta), one of the major culprits in Alzheimers disease development. The formation of apoE:A beta complexes is implicated in both A beta clearance and fibrillization. However, the binding interface between apoE and A beta is poorly defined despite substantial previous research efforts, and the exact role of apoE in the pathology of Alzheimers disease remains largely elusive. Here, we compared the three main isoforms of apoE (E2, E3, and E4) for their interaction with A beta 142 in an early stage of aggregation and at near physiological conditions. Using electron microscopy and Western blots, we showed that all three isoforms are able to prevent A beta fibrillization and form a noncovalent complex, with one molecule of A beta bound per apoE. Using chemical cross-linking coupled to mass spectrometry, we further examined the interface of interaction between apoE2/3/4 and A beta. Multiple high-confidence intermolecular apoE2/3/4:A beta cross-links confirmed that Lys16 is located in the region of A beta binding to apoE2/3/4. Further, we demonstrated that both N- and C-terminal domains of apoE2/3/4 are interacting with A beta. The cross-linked sites were mapped onto and evaluated in light of a recent structure of apoE. Our results support binding of the hydrophobic A beta at the apoE domaindomain interaction interface, which would explain how apoE is able to stabilize A beta and thereby prevent its subsequent aggregation.