A mechanism for lipid binding to apoE and the role of intrinsically disordered regions coupled to domain–domain interactions

Abstract

Relative to the apolipoprotein E (apoE) E3 allele of the APOE gene, apoE4 strongly increases the risk for the development of late-onset Alzheimer's disease. However, apoE4 differs from apoE3 by only a single amino acid at position 112, which is arginine in apoE4 and cysteine in apoE3. It remains unclear why apoE3 and apoE4 are functionally different. Described here is a proposal for understanding the functional differences between these two isoforms with respect to lipid binding. A mechanism is proposed that is based on the full-length monomeric structure of the protein, on hydrogen-deuterium exchange mass spectrometry data, and on the role of intrinsically disordered regions to control protein motions. It is proposed that lipid binds between the N-terminal and C-terminal domains and that separation of the two domains, along with the presence of intrinsically disordered regions, controls this process. The mechanism explains why apoE3 differs from apoE4 with respect to different lipid-binding specificities, why lipid increases the binding of apoE to its receptor, and why specific residues are conserved.hydrogen-deuterium exchange | domain-domain interaction | conserved residues | protein structure | apolipoprotein E A poE is a 34-kDa protein whose normal function in the brain is to transport lipids and cholesterol to neuronal cells. In humans, there are three common isoforms-apoE2, apoE3, and apoE4-that appear to differ in important functional properties such as the distinct differences between apoE isoforms with respect to lipid transport (1). ApoE4 is the most studied since, relative to apoE3, it is known to be the major risk factor for the development of late-onset Alzheimer's disease (2, 3), whereas apoE2, the less common form, is associated with type III hyperlipoproteinemia (4, 5). A great many papers have discussed possible mechanisms for lipid binding (i.e., refs. 6-11), but there is no proposal for the mechanism of lipid binding that would explain the differences between the isoforms. From studies using FRET, small-angle X-ray diffraction, and electron paramagnetic resonance spectroscopy, it has been shown that apoE undergoes a conformational change on lipid binding, with the protein adopting a hairpin-like structure (7,(11)(12)(13). Here again, however, specific details are lacking.In this paper, we assemble a number of experimental and computational observations to provide a model for the mechanism of lipid binding. This model includes a consideration of the fulllength apoE structure, results from hydrogen-deuterium exchange (HDX) experiments, information on conserved and nonconserved residues, an appreciation of the role of intrinsically disordered regions (IDRs), and molecular dynamics calculations.The proposed model explains why there are differences between apoE isoforms with respect to lipid binding and why lipid enhances apoE binding to receptors such as the low-density lipoprotein receptor (LDLR). As such, it opens the way to develop small molecular weight compounds that could preferentially inf...

High‐affinity multivalent interactions between apolipoprotein E and the oligomers of amyloid‐β

“…Since the N-and the C-terminal domains are connected by a long intrinsically disordered region (IDR), it is possible that Ab intercalates at the interface of the domains disrupting the native salt bridges and hydrophobic interactions. Furthermore, the disordered hinge domain may allow rotation of the C-terminal domain generating more than one interfaces as proposed by Frieden et al [50]. A recent computational study using docking and molecular dynamics simulations has shown that Ab can replace the native salt bridges and disrupt the structure of the N-terminal domain of apoE [33].…”

“…Furthermore, the disordered hinge domain may allow rotation of the C‐terminal domain generating more than one interfaces as proposed by Frieden et al . . A recent computational study using docking and molecular dynamics simulations has shown that Aβ can replace the native salt bridges and disrupt the structure of the N‐terminal domain of apoE .…”

Lack of hepatic apoE does not influence early Aβ deposition: observations from a new APOE knock-in model

“…Some studies report apoE4 is more susceptible to proteolysis compared to the other major isoforms of APOE [73,74], and other studies have demonstrated the presence of apoE4 fragments (14-20 kDa) in AD brains [75,76]. Structural differences between apoE3 and apoE4, particularly at the hinge region between the N-and C-terminal domains, may explain their different susceptibility to proteolytic degradation as well as lipid binding affinity [77]. In spite of these numerous observations, the exact nature of the protease responsible for apoE4 cleavage is unknown, although several candidates have been reported including cathepsin D [78], aspartic proteases [79], and a chymotrypsin-like protease [73].…”

Thermodynamic destabilization and aggregation propensity as the mechanism behind the association of apoE3 mutants and lipoprotein glomerulopathy

“…Additionally, it has been shown that apoE contains intrinsically disordered regions and smaller flexible regions that surround structured helices, affecting the conformation and functional properties of apoE (14)(15)(16). Several biophysical studies have shown that apoE displays low thermodynamic stability and significant conformational plasticity, and allelic differences as well as single point mutations have been shown to affect protein conformation and to hinder physiological function (13,15,16,(18)(19)(20). Furthermore, apoE has been shown to be prone to aggregation and to form oligomeric structures in solution (21,22).…”