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Cited by 283Protein Structure and DynamicsCholesterol and Lipid MetabolismLipoproteins and Cardiovascular Health

Topology of human apolipoprotein E3 uniquely regulates its diverse biological functions

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Chen, Jianglei, Li, Qianqian, Wang, Jianjun·2011·Proceedings of the National Academy of Sciences
DOI 10.1073/pnas.1106420108PMC PMC3169138
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Abstract

Human apolipoprotein E (apoE) is one of the major determinants in lipid transport, playing a critical role in atherosclerosis and other diseases. Binding to lipid and heparan sulfate proteoglycans (HSPG) induces apoE to adopt active conformations for binding to low-density lipoprotein receptor (LDLR) family. ApoE also interacts with beta amyloid peptide, manifests critical isoform-specific effects on Alzheimer’s disease. Despite the importance of apoE in these major human diseases, the fundamental questions of how apoE adjusts its structure upon binding to regulate its diverse functions remain unsolved. We report the NMR structure of apoE3, displaying a unique topology of three structural domains. The C-terminal domain presents a large exposed hydrophobic surface that likely initiates interactions with lipids, HSPG, and beta amyloid peptides. The unique topology precisely regulates apoE tertiary structure to permit only one possible conformational adaptation upon binding and provides a double security in preventing lipid-free and partially-lipidated apoE from premature binding to apoE receptors during receptor biogenesis. This topology further ensures the optimal receptor-binding activity by the fully lipidated apoE during lipoprotein transport in circulation and in the brain. These findings provide a structural framework for understanding the structural basis of the diverse functions of this important protein in human diseases.

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  • In the 2L7B structure, the C-terminal domain is highly helical and folded around the N-terminal domain so as to completely protect the LDL-receptor binding region 136-150 from the solvent.

    “The C-terminal domain is highly helical and folded around the N-terminal domain in such a configuration to completely protect the LDL-receptor binding region 136-150 from the solvent (Figure 9B).”

    From Biophysical Analysis of Apolipoprotein E3 Variants Linked with Development of Type III Hyperlipoproteinemia (2011) · cites this paper as [68]

    The Results (page not given) describe the C-terminal domain’s helices interacting with the N-terminal domain and shielding the major LDLR-binding region. But Table 2 reports small, nonzero accessible surface areas for several residues from 136 to 150, so the claim that the region is completely protected from solvent overstates the evidence. The paper identifies 2L7B as its deposited structure. (LLM, conf=0.88)

    Experimental — accuracy not yet measured

  • In the newly published structure of a monomeric mutant of apoE3 (2L7B), the N-terminal segment is folded in a four-helix bundle with the locations of R136, R145 and K146 in similar configurations as in structure 1LPE.

    “In this structure (pdb code: 2L7B) the N-terminal segment of the protein is also folded in a four-helix bundle (Figure 9A) with the locations of amino acids R136, R145 and K146 in similar configurations as in structure 1LPE.”

    From Biophysical Analysis of Apolipoprotein E3 Variants Linked with Development of Type III Hyperlipoproteinemia (2011) · cites this paper as [68]

    The Results describe the monomeric apoE3 mutant and its N-terminal four-helix bundle, and the data-deposition footnote identifies the structure as PDB 2L7B. The Results say the bundle is broadly similar to isolated N-terminal structures, but our copy does not establish that R136, R145, and K146 have similar configurations to those in 1LPE. (LLM, conf=0.83)

    Experimental — accuracy not yet measured

  • Lipid-free ApoE readily self-associates through hydrophobic interactions, forming oligomers and aggregates that complicate thermal stability measurements.

    “Lipid-free ApoE readily self-associates through hydrophobic interactions, forming oligomers and aggregates that complicate thermal stability measurements 40,41 .”

    From Utilizing a cell culture based novel cellular thermal shift assay to understand the isoform-dependent thermal stability of ApoE variants (2026) · cites this paper as [40]

    The Results (page unavailable) state that apoE forms a mixture of oligomers that hindered structural determination, and identify exposed hydrophobic residues in apoE3. They do not say that hydrophobic interactions cause self-association or aggregation, or that these processes complicate thermal stability measurements; the reported difficulty concerns NMR structure determination. (LLM, conf=0.85)

    Experimental — accuracy not yet measured

  • The whole structure of apoE, including the C-terminal domain, was first reported in 2011.

    “Despite extensive analysis, it took 20 years until the whole structure of apoE, including the C-terminal domain, was determined because of its very high affinity for lipids, and the higher-order structure of the full-length protein was first reported in 2011 11).”

    From Impact of Apolipoprotein E Variants: A Review of Naturally Occurring Variants and Clinical Features (2025) · cites this paper as [11]

    The Results (page unavailable) report an NMR structure of full-length apoE3 that includes the C-terminal domain, supporting the 2011 structure claim. The paper does not establish the stated 20-year interval or attribute the delay to high lipid affinity; it identifies the formation of mixed oligomers as the major challenge to structural determination. (LLM, conf=0.88)

    Experimental — accuracy not yet measured

  • Lipidation of ApoE is required to expose its LDLR-binding site.

    “Since lipidation of ApoE is required to expose its LDLR-binding site30, we lipidated HEK293 cell-derived ApoE (lipApoE) with 1-palmitoyl-2-oleoyl-glycero-3-phosphocholine (POPC).”

    From Decreased lipidated ApoE‐receptor interactions confer protection against pathogenicity of ApoE and its lipid cargoes in lysosomes (2025) · cites this paper as [30]

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Research works printed but not linked: 31

  1. [3]Mahley RW, Ji ZS. Remnant lipoprotein metabolism: key pathways involving cell-surface heparan sulfate proteoglycans and apolipoprotein E. J Lipid Res. 1999;40:1–16. [PubMed] [Google Scholar]
  2. [4]Luc G, et al. Impact of apolipoprotein E polymorphism on lipoproteins and risk of myocardial infarction. The ECTIM Study. Arterioscler Thromb. 1994;14:1412–1419. doi: 10.1161/01.atv.14.9.1412. [DOI] [PubMed] [Google Scholar] · DOI
  3. [5]Mahley RW, Rall SC Jr, editors. The Metabolic and Molecular Base of Inherited Disease. 8 Ed. New York: (McGraw-Hill); 2001. pp. 2835–2862. [Google Scholar]
  4. [6]Burt TD, et al. Apolipoprotein (apo) E4 enhances HIV-1 cell entry in vitro, and the APOE epsilon4/epsilon4 genotype accelerates HIV disease progression. Proc Natl Acad Sci USA. 2008;105:8718–8723. doi: 10.1073/pnas.0803526105. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  5. [7]Ma SW, Benzie IF, Yeung VT. Type 2 diabetes mellitus and its renal complications in relation to apolipoprotein E gene polymorphism. Transl Res. 2008;152:134–142. doi: 10.1016/j.trsl.2008.07.003. [DOI] [PubMed] [Google Scholar] · DOI
  6. [9]Wardell MR, Rall SC, Jr, Schaefer EJ, Kane JP, Weisgraber KH. Two apolipoprotein E5 variants illustrate the importance of the position of additional positive charge on receptor-binding activity. J Lipid Res. 1991;32:521–528. [PubMed] [Google Scholar]
  7. [10]Morrow JA, et al. Effect of arginine 172 on the binding of apolipoprotein E to the low density lipoprotein receptor. J Biol Chem. 2000;275:2576–2580. doi: 10.1074/jbc.275.4.2576. [DOI] [PubMed] [Google Scholar] · DOI
  8. [11]Wilson C, et al. Salt bridge relay triggers defective LDL receptor binding by a mutant apolipoprotein. Structure. 1994;2:713–718. doi: 10.1016/s0969-2126(00)00072-1. [DOI] [PubMed] [Google Scholar] · DOI · Paper page
  9. [12]Dong LM, et al. Novel mechanism for defective receptor binding of apolipoprotein E2 in type III hyperlipoproteinemia. Nat Struct Biol. 1996;3:718–722. doi: 10.1038/nsb0896-718. [DOI] [PubMed] [Google Scholar] · DOI
  10. [13]Dong LM, et al. Human apolipoprotein E. Role of arginine 61 in mediating the lipoprotein preferences of the E3 and E4 isoforms. J Biol Chem. 1994;269:22358–22365. [PubMed] [Google Scholar]
  11. [14]Dong LM, Weisgraber KH. Human apolipoprotein E4 domain interaction. Arginine 61 and glutamic acid 255 interact to direct the preference for very low density lipoproteins. J Biol Chem. 1996;271:19053–19057. doi: 10.1074/jbc.271.32.19053. [DOI] [PubMed] [Google Scholar] · DOI · Paper page
  12. [16]Zhang Y, Chen J, Wang J. A complete backbone spectral assignment of lipid-free human apolipoprotein E (apoE) Biomol NMR Assigm. 2008;2:207–210. doi: 10.1007/s12104-008-9122-8. [DOI] [PubMed] [Google Scholar] · DOI
  13. [17]Zhao W, Zhang Y, Cui C, Li Q, Wang J. An efficient on-column expressed protein ligation strategy: application to segmental triple labeling of human apolipoprotein E3. Protein Sci. 2008;17:736–747. doi: 10.1110/ps.073383708. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  14. [19]Sivashanmugam A, Wang J. A unified scheme for initiation and conformational adaptation of human apolipoprotein E N-terminal domain upon lipoprotein binding and for receptor binding activity. J Biol Chem. 2009;284:14657–14666. doi: 10.1074/jbc.M901012200. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  15. [20]Wetterau JR, Aggerbeck LP, Rall SC, Jr, Weisgraber KH. Human apolipoprotein E3 in aqueous solution. I. Evidence for two structural domains. J Biol Chem. 1988;263:6240–6248. [PubMed] [Google Scholar]
  16. [21]Willard L, et al. VADAR: a web server for quantitative evaluation of protein structure quality. Nucleic Acids Res. 2003;31:3316–3319. doi: 10.1093/nar/gkg565. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  17. [23]Chroni A, et al. Biophysical analysis of progressive C-terminal truncations of human apolipoprotein E4: insights into secondary structure and unfolding properties. Biochemistry. 2008;47:9071–9080. doi: 10.1021/bi800469r. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI · Paper page
  18. [24]Nguyen D, Dhanasekaran P, Phillips MC, Lund-Katz S. Molecular mechanism of apolipoprotein E binding to lipoprotein particles. Biochemistry. 2009;48:3025–3032. doi: 10.1021/bi9000694. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  19. [25]Li X, Kypreos K, Zanni EE, Zannis V. Domains of apoE required for binding to apoE receptor 2 and to phospholipids: implications for the functions of apoE in the brain. Biochemistry. 2003;42:10406–10417. doi: 10.1021/bi027093c. [DOI] [PubMed] [Google Scholar] · DOI
  20. [26]Narayanaswami V, et al. Helix orientation of the functional domains in apolipoprotein E in discoidal high density lipoprotein particles. J Biol Chem. 2004;279:14273–14279. doi: 10.1074/jbc.M313318200. [DOI] [PubMed] [Google Scholar] · DOI
  21. [27]Narayanaswami V, Szeto SS, Ryan RO. Lipid association-induced N- and C-terminal domain reorganization in human apolipoprotein E3. J Biol Chem. 2001;276:37853–37860. doi: 10.1074/jbc.M102953200. [DOI] [PubMed] [Google Scholar] · DOI · Paper page
  22. [28]Peters-Libeu CA, Newhouse Y, Hatters, DM, Weisgraber KH. Model of biologically active apolipoprotein E bound to dipalmitoylphosphatidylcholine. J Biol Chem. 2006;281:1073–1079. doi: 10.1074/jbc.M510851200. [DOI] [PubMed] [Google Scholar] · DOI
  23. [29]Narita M, et al. Cellular catabolism of lipid poor apolipoprotein E via cell surface LDL receptor-related protein. J Biochem. 2002;132:743–749. doi: 10.1093/oxfordjournals.jbchem.a003282. [DOI] [PubMed] [Google Scholar] · DOI
  24. [30]Futamura M, et al. Two-step mechanism of binding of apolipoprotein E to heparin: implications for the kinetics of apolipoprotein E-heparan sulfate proteoglycan complex formation on cell surfaces. J Biol Chem. 2005;280:5414–5422. doi: 10.1074/jbc.M411719200. [DOI] [PubMed] [Google Scholar] · DOI · Paper page
  25. [33]Herz J, Marschang P. Coaxing the LDL receptor family into the fold. Cell. 2003;112:289–292. doi: 10.1016/s0092-8674(03)00073-4. [DOI] [PubMed] [Google Scholar] · DOI
  26. [35]Bu G, Schwartz AL. RAP, a novel type of ER chaperone. Trends Cell Biol. 1998;8:272–276. doi: 10.1016/s0962-8924(98)01283-5. [DOI] [PubMed] [Google Scholar] · DOI
  27. [36]Ruiz J, et al. The apoE isoform binding properties of the VLDL receptor reveal marked differences from LRP and the LDL receptor. J Lipid Res. 2005;46:1721–1731. doi: 10.1194/jlr.M500114-JLR200. [DOI] [PubMed] [Google Scholar] · DOI · Paper page
  28. [37]Hobbs HH, Brown MS, Goldstein JL. Molecular genetics of the LDL receptor gene in familial hypercholesterolemia. Hum Mutat. 1992;1:445–466. doi: 10.1002/humu.1380010602. [DOI] [PubMed] [Google Scholar] · DOI
  29. [38]Bu G. Apolipoprotein E and its receptors in Alzheimer’s disease: pathways, pathogenesis and therapy. Nat Rev Neurosci. 2009;10:333–344. doi: 10.1038/nrn2620. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI · Paper page
  30. [39]Chen J, Wang J. A segmental labeling strategy for unambiguous determination of domain-domain interactions of large multi-domain proteins. J Biomol NMR. 2011;50:403–410. doi: 10.1007/s10858-011-9526-0. [DOI] [PubMed] [Google Scholar] · DOI
  31. [40]Guntert P. Automated NMR structure calculation with CYANA. Method Mol Biol. 2004;278:353–378. doi: 10.1385/1-59259-809-9:353. [DOI] [PubMed] [Google Scholar] · DOI

Cited by

Sorted by citations

Authors
Chen, J., Li, Q., & Wang, J.
Affiliations
Wayne State University (US)
Corresponding author
Wang, Jianjun
ORCID
Venue
Proceedings of the National Academy of Sciences
Publisher
National Academy of Sciences
Published
2011-08-22
Volume
108
Issue
36
Pages
14813-14818
ISSN
  • 0027-8424 (ISSN-L)
  • 1091-6490
DOI
10.1073/pnas.1106420108
PMC
PMC3169138
OpenAlex
W1990016625
Cited by
283
References
9
Citations by year
2026: 19 · 2025: 32 · 2024: 27 · 2023: 23 · 2022: 22 · 2021: 16 · 2020: 18 · 2019: 16 · 2018: 11 · 2017: 15 · 2016: 19 · 2015: 13 · 2014: 19 · 2013: 13 · 2012: 15
FWCI
6.63
Type
journal article
Language
en
Open access
Locations
  • Proceedings of the National Academy of Sciences (publishedVersion)
  • Europe PMC (PubMed Central) (publishedVersion)
  • PubMed Central (publishedVersion)
  • PubMed (publishedVersion)
Funders
  • National Institutes of Health (NIH-R01)
  • National Heart, Lung, and Blood Institute (R01HL074365)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Health Sciences › Medicine › Surgery › Cholesterol and Lipid Metabolism
  • Health Sciences › Medicine › Surgery › Lipoproteins and Cardiovascular Health
Keywords
apolipoprotein E3, protein topology, NMR structure, lipid binding, heparan sulfate proteoglycans, LDL receptor, amyloid-beta, Alzheimer's disease, atherosclerosis, lipid transport, conformational adaptation, receptor binding, C-terminal domain
MeSH terms
Amyloid, Biological Transport, Humans, Lipids, Peptides, Protein Binding, Structure-Activity Relationship, Protein Structure, Tertiary, Nuclear Magnetic Resonance, Biomolecular, Low Density Lipoprotein Receptor-Related Protein-1, Lipid Metabolism, Apolipoprotein E3, Hydrophobic and Hydrophilic Interactions

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