Lipidated apolipoprotein E4 structure and its receptor binding mechanism determined by a combined cross-linking coupled to mass spectrometry and molecular dynamics approach

Abstract

Apolipoprotein E (apoE) is a forefront actor in the transport of lipids and the maintenance of cholesterol homeostasis, and is also strongly implicated in Alzheimer’s disease. Upon lipid-binding apoE adopts a conformational state that mediates the receptor-induced internalization of lipoproteins. Due to its inherent structural dynamics and the presence of lipids, the structure of the biologically active apoE remains so far poorly described. To address this issue, we developed an innovative hybrid method combining experimental data with molecular modeling and dynamics to generate comprehensive models of the lipidated apoE4 isoform. Chemical cross-linking combined with mass spectrometry provided distance restraints, characterizing the three-dimensional organization of apoE4 molecules at the surface of lipidic nanoparticles. The ensemble of spatial restraints was then rationalized in an original molecular modeling approach to generate monomeric models of apoE4 that advocated the existence of two alternative conformations. These two models point towards an activation mechanism of apoE4 relying on a regulation of the accessibility of its receptor binding region. Further, molecular dynamics simulations of the dimerized and lipidated apoE4 monomeric conformations revealed an elongation of the apoE N-terminal domain, whereby helix 4 is rearranged, together with Arg172, into a proper orientation essential for lipoprotein receptor association. Overall, our results show how apoE4 adapts its conformation for the recognition of the low density lipoprotein receptor and we propose a novel mechanism of activation for apoE4 that is based on accessibility and remodeling of the receptor binding region.

Revealing a Novel Landscape of the Association Between Blood Lipid Levels and Alzheimer's Disease: A Meta-Analysis of a Case-Control Study

“…Notably, as a key factor in cholesterol homeostasis, ApoE4 could decrease LDL receptor and LDL clearance, and increase cholesterol level by binding with TG-rich very-low-density lipoprotein. In addition, ApoE4 has been verified to contribute to the susceptibility for AD by disordering the lipids and cholesterol levels (Henry et al, 2018). Furthermore, LDL-C had been found positively associated with the densities of neuron plaques, which hints at the onset of the neurodegenerative disease (Lesser et al, 2011).…”

Selective cross-linking of coinciding protein assemblies by in-gel cross-linking mass-spectrometry

“…In-solution XL-MS has become a useful tool to study protein structures and protein-protein interactions (Henry et al, 2018;Koukos and Bonvin, 2020;Liu et al, 2014). Even though the technology of XL-MS advanced substantially over the last decade, there are still quite a few challenges left.…”

“…Currently, technological developments in XL-MS aim to further improve the cross-linking reaction efficiency and detection. The research is mainly focused on sample preparation techniques, MS fragmentation and enrichment strategies, data acquisition and analysis of cross-linked peptides, as well as the design of novel cross-linkers Dau et al, 2019;Iacobucci et al, 2018;Leitner et al, 2012;Liu et al, 2017;Mendes et al, 2019;Steigenberger et al, 2019).…”

Sex-dependent effect of APOE on Alzheimer's disease and other age-related neurodegenerative disorders

“…1 A). To resolve the three-dimensional structure of monomeric APOE, a recent study combined cross-linking and mass spectrometry at high resolution to show that APOE is highly dynamic, adapting its conformation to dimerize and bind receptors and lipids ( Henry et al, 2018 ). APOE is a lipid-transport protein expressed most highly in the liver and kidney, but also at relatively high levels in most areas of the brain ( Fagerberg et al, 2014 ).…”