CoChat
Sign Up
Cited by 42

The DOI matches its Crossref record; 5 of the 5 references it cites were found in a registry or an index.

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

Henry, Nicolas, Krammer, Eva-Maria, Stengel, Florian, Adams, Quentin, Van Liefferinge, François, Hubin, Ellen, Chaves, Rui, Efremov, Rouslan, Aebersold, Ruedi, Vandenbussche, Guy, Prévost, Martine, Raussens, Vincent, Deroo, Stéphanie·2018·PLOS Computational Biology
DOI 10.1371/journal.pcbi.1006165PMC PMC6033463
Open this paper in CoChat — free account

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1371/journal.pcbi.1006165

Cites

5 of 5 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Flagged first, then by citations

Research works printed but not linked: 76

  1. TL Innerarity, 1979, apoprotein after recombination with phospholipid vesicles to the low density lipoprotein receptors of fibroblasts, J Biol Chem, 254, 4186, 10.1016/S0021-9258(18)50713-4 · DOI · Paper page
  2. L Goedeke, 2012, Regulation of cholesterol homeostasis, Cell Mol Life Sci, 69, 915, 10.1007/s00018-011-0857-5 · DOI
  3. L Anchisi, 2013, Cholesterol homeostasis: a key to prevent or slow down neurodegeneration, Front Physiol, 3, 486, 10.3389/fphys.2012.00486 · DOI
  4. RE Pitas, 1987, Lipoproteins and their receptors in the central nervous system. Characterization of the lipoproteins in cerebrospinal fluid and identification of apolipoprotein B,E(LDL) receptors in the brain, J Biol Chem, 262, 14352, 10.1016/S0021-9258(18)47945-8 · DOI · Paper page
  5. RW Mahley, 1984, Plasma lipoproteins: apolipoprotein structure and function, J Lipid Res, 25, 1277, 10.1016/S0022-2275(20)34443-6 · DOI · Paper page
  6. MS Brown, 1986, A receptor-mediated pathway for cholesterol homeostasis, Science, 232, 34, 10.1126/science.3513311 · DOI · Paper page
  7. EH Corder, 1993, Gene dose of apolipoprotein E type 4 allele and the risk of Alzheimer’s disease in late onset families, Science, 261, 921, 10.1126/science.8346443 · DOI · Paper page
  8. CC Liu, 2013, Apolipoprotein E and Alzheimer disease: risk, mechanisms and therapy, Nat Rev Neurol, 9, 106, 10.1038/nrneurol.2012.263 · DOI · Paper page
  9. Y Huang, 2014, Apolipoprotein E: Structure and function in lipid metabolism, neurobiology, and Alzheimer’s diseases, Neurobiol Dis, 72, 3, 10.1016/j.nbd.2014.08.025 · DOI · Paper page
  10. KH Weisgraber, 1981, Human E apoprotein heterogeneity. Cysteine-arginine interchanges in the amino acid sequence of the apo-E isoforms, J Biol Chem, 256, 9077, 10.1016/S0021-9258(19)52510-8 · DOI · Paper page
  11. C Frieden, 2013, Concerning the structure of apoE, Protein Sci, 22, 1820, 10.1002/pro.2379 · DOI
  12. H Saito, 2003, Effects of polymorphism on the lipid interaction of human apolipoprotein E, J Biol Chem, 278, 40723, 10.1074/jbc.M304814200 · DOI · Paper page
  13. JR Wetterau, 1988, Human apolipoprotein E3 in aqueous solution. I. Evidence for two structural domains, J Biol Chem, 263, 6240, 10.1016/S0021-9258(18)68778-2 · DOI · Paper page
  14. M Forstner, 1999, Carboxyl-terminal domain of human apolipoprotein E: expression, purification, and crystallization, Protein Expr Purif, 17, 267, 10.1006/prep.1999.1144 · DOI
  15. J Chen, 2011, Topology of human apolipoprotein E3 uniquely regulates its diverse biological functions, Proc Natl Acad Sci U S A, 108, 14813, 10.1073/pnas.1106420108 · DOI · Paper page
  16. PS Hauser, 2011, Apolipoprotein E: from lipid transport to neurobiology, Prog Lipid Res, 50, 62, 10.1016/j.plipres.2010.09.001 · DOI · Paper page
  17. KE Winkler, 1989, Characterization of nascent high density lipoprotein subfractions from perfusates of rat liver, J Lipid Res, 30, 979, 10.1016/S0022-2275(20)38300-0 · DOI
  18. V Raussens, 1998, The low density lipoprotein receptor active conformation of apolipoprotein E. Helix organization in n-terminal domain-phospholipid disc particles, J Biol Chem, 273, 25825, 10.1074/jbc.273.40.25825 · DOI
  19. V Narayanaswami, 2004, Helix orientation of the functional domains in apolipoprotein E in discoidal high density lipoprotein particles, J Biol Chem, 279, 14273, 10.1074/jbc.M313318200 · DOI
  20. V Raussens, 2005, Orientation and mode of lipid-binding interaction of human apolipoprotein E C-terminal domain, Biochem J, 387, 747, 10.1042/BJ20041536 · DOI
  21. V Gupta, 2006, Lipid-induced extension of apolipoprotein E helix 4 correlates with low density lipoprotein receptor binding ability, J Biol Chem, 281, 39294, 10.1074/jbc.M608085200 · DOI
  22. V Raussens, 2003, Lipid-bound structure of an apolipoprotein E-derived peptide, J Biol Chem, 278, 25998, 10.1074/jbc.M301753200 · DOI
  23. CA Fisher, 1999, Lipid binding-induced conformational changes in the N-terminal domain of human apolipoprotein E, J Lipid Res, 40, 93, 10.1016/S0022-2275(20)33343-5 · DOI
  24. CA Fisher, 2000, The lipid-associated conformation of the low density lipoprotein receptor binding domain of human apolipoprotein E, J Biol Chem, 275, 33601, 10.1074/jbc.M002643200 · DOI
  25. J Drury, 2005, Examination of lipid-bound conformation of apolipoprotein E4 by pyrene excimer fluorescence, J Biol Chem, 280, 14605, 10.1074/jbc.M414019200 · DOI
  26. CA Peters-Libeu, 2006, Model of biologically active apolipoprotein E bound to dipalmitoylphosphatidylcholine, J Biol Chem, 281, 1073, 10.1074/jbc.M510851200 · DOI · Paper page
  27. DM Hatters, 2009, Insight on the molecular envelope of lipid-bound apolipoprotein E from electron paramagnetic resonance spectroscopy, J Mol Biol, 386, 261, 10.1016/j.jmb.2008.12.040 · DOI · Paper page
  28. A Sinz, 2014, The advancement of chemical cross-linking and mass spectrometry for structural proteomics: from single proteins to protein interaction networks, Expert Rev Proteomics, 11, 733, 10.1586/14789450.2014.960852 · DOI
  29. A Leitner, 2016, Crosslinking and mass spectrometry: an integrated technology to understand the structure and function of molecular machines, Trends Biochem Sci, 41, 20, 10.1016/j.tibs.2015.10.008 · DOI
  30. A Politis, 2014, A mass spectrometry-based hybrid method for structural modeling of protein complexes, Nat Methods, 11, 403, 10.1038/nmeth.2841 · DOI
  31. C Yu, 2018, Cross-linking mass spectrometry: an emerging technology for interactomics and structural biology, Anal Chem, 90, 144, 10.1021/acs.analchem.7b04431 · DOI
  32. M Schneider, 2018, Protein tertiary structure by crosslinking/mass spectrometry, Trends Biochem Sci, 43, 157, 10.1016/j.tibs.2017.12.006 · DOI
  33. DB Lima, 2018, Characterization of homodimer interfaces with cross-linking mass spectrometry and isotopically labeled proteins, Nat Protoc, 13, 431, 10.1038/nprot.2017.113 · DOI
  34. BJ Greber, 2016, Insertion of the biogenesis factor Rei1 probes the ribosomal tunnel during 60S maturation, Cell, 164, 91, 10.1016/j.cell.2015.11.027 · DOI
  35. J Kosinski, 2016, Molecular architecture of the inner ring scaffold of the human nuclear pore complex, Science, 352, 363, 10.1126/science.aaf0643 · DOI
  36. A Petrovic, 2016, Structure of the MIS12 complex and molecular basis of its interaction with CENP-C at human kinetochores, Cell, 167, 1028, 10.1016/j.cell.2016.10.005 · DOI
  37. JP Erzberger, 2014, Molecular architecture of the 40S⋅eIF1⋅eIF3 translation initiation complex, Cell, 158, 1123, 10.1016/j.cell.2014.07.044 · DOI
  38. CE Matz, 1982, Micellar complexes of human apolipoprotein A-I with phosphatidylcholines and cholesterol prepared from cholate-lipid dispersions, J Biol Chem, 257, 4535, 10.1016/S0021-9258(18)34756-2 · DOI
  39. E Goormaghtigh, 1994, Determination of soluble and membrane protein structure by Fourier transform infrared spectroscopy. III. Secondary structures, Subcell Biochem, 23, 405, 10.1007/978-1-4615-1863-1_10 · DOI
  40. N Kučerka, 2011, Fluid phase lipid areas and bilayer thicknesses of commonly used phosphatidylcholines as a function of temperature, Biochim Biophys Acta, 1808, 2761, 10.1016/j.bbamem.2011.07.022 · DOI
  41. T Walzthoeni, 2012, False discovery rate estimation for cross-linked peptides identified by mass spectrometry, Nat Methods, 9, 901, 10.1038/nmeth.2103 · DOI
  42. ED Merkley, 2014, Distance restraints from crosslinking mass spectrometry: mining a molecular dynamics simulation database to evaluate lysine-lysine distances, Protein Sci, 23, 747, 10.1002/pro.2458 · DOI
  43. O Rinner, 2008, Identification of cross-linked peptides from large sequence databases, Nat Methods, 5, 315, 10.1038/nmeth.1192 · DOI
  44. S Deroo, 2015, Chemical cross-linking/mass spectrometry maps the amyloid β peptide binding region on both apolipoprotein E domains, ACS Chem Biol, 10, 1010, 10.1021/cb500994j · DOI
  45. D Frishman, 1995, Knowledge-based protein secondary structure assignment, Proteins, 23, 566, 10.1002/prot.340230412 · DOI
  46. JA Morrow, 2000, Effect of arginine 172 on the binding of apolipoprotein E to the low density lipoprotein receptor, J Biol Chem, 275, 2576, 10.1074/jbc.275.4.2576 · DOI
  47. RY Wang, 2015, De novo protein structure determination from near-atomic-resolution cryo-EM maps, Nat Methods, 12, 335, 10.1038/nmeth.3287 · DOI
  48. D Russel, 2012, Putting the pieces together: integrative modeling platform software for structure determination of macromolecular assemblies, PLoS Biol, 10, e1001244, 10.1371/journal.pbio.1001244 · DOI
  49. RG Walker, 2014, The structure of human apolipoprotein A-IV as revealed by stable isotope-assisted cross-linking, molecular dynamics, and small angle x-ray scattering, J Biol Chem, 289, 5596, 10.1074/jbc.M113.541037 · DOI
  50. P Singh, 2013, A pseudo-atomic model for the capsid shell of bacteriophage lambda using chemical cross-linking/mass spectrometry and molecular modeling, J Mol Biol, 425, 3378, 10.1016/j.jmb.2013.06.026 · DOI
  51. A Kahraman, 2013, Cross-link guided molecular modeling with ROSETTA, PLoS One, 8, e73411, 10.1371/journal.pone.0073411 · DOI
  52. R Huang, 2011, Apolipoprotein A-I structural organization in high-density lipoproteins isolated from human plasma, Nat Struct Mol Biol, 18, 416, 10.1038/nsmb.2028 · DOI
  53. X Zhang, 2015, A model of lipid-free apolipoprotein A-I revealed by iterative molecular dynamics simulation, PLoS One, 10, e0120233, 10.1371/journal.pone.0120233 · DOI
  54. M Dong L-, 1996, Human apolipoprotein E4 domain interaction: arginine 61 and glutamic acid 255 interact to direct the preference for very low density lipoproteins, J Biol Chem, 271, 19053, 10.1074/jbc.271.32.19053 · DOI · Paper page
  55. DW Russell, 1989, Different combinations of cysteine-rich repeats mediate binding of low density lipoprotein receptor to two different proteins, J Biol Chem, 264, 21682, 10.1016/S0021-9258(20)88240-4 · DOI · Paper page
  56. C Fisher, 2004, A two-module region of the low-density lipoprotein receptor sufficient for formation of complexes with apolipoprotein E ligands, Biochemistry, 43, 1037, 10.1021/bi035529y · DOI
  57. H Jeon, 2005, Structure and physiologic function of the low-density lipoprotein receptor, Annu Rev Biochem, 74, 535, 10.1146/annurev.biochem.74.082803.133354 · DOI · Paper page
  58. MQ Xu, 2001, Intein-mediated ligation and cyclization of expressed proteins, Methods, 24, 257, 10.1006/meth.2001.1187 · DOI
  59. G Rouser, 1966, Quantitative analysis of phospholipids by thin-layer chromatography and phosphorus analysis of spots, Lipids, 1, 85, 10.1007/BF02668129 · DOI
  60. H Schägger, 1991, Blue native electrophoresis for isolation of membrane protein complexes in enzymatically active form, Anal Biochem, 199, 223, 10.1016/0003-2697(91)90094-A · DOI
  61. UK Laemmli, 1970, Cleavage of structural proteins during the assembly of the head of bacteriophage T4, Nature, 227, 680, 10.1038/227680a0 · DOI · Paper page
  62. SJ Ludtke, 1999, EMAN: semiautomated software for high-resolution single-particle reconstructions, J Struct Biol, 128, 82, 10.1006/jsbi.1999.4174 · DOI
  63. A Shevchenko, 2006, In-gel digestion for mass spectrometric characterization of proteins and proteomes, Nat Protoc, 1, 2856, 10.1038/nprot.2006.468 · DOI
  64. AT Brunger, 1998, Crystallography and NMR system: A new software suite for macromolecular structure determination, Acta Crystallogr Sect D Biol Crystallogr, 54, 905, 10.1107/S0907444998003254 · DOI
  65. AT Brunger, Version 1.2 of the Crystallography and NMR system, Nat Protoc, 2, 2728, 10.1038/nprot.2007.406 · DOI
  66. JC Phillips, 2005, Scalable molecular dynamics with NAMD, J Comput Chem, 26, 1781, 10.1002/jcc.20289 · DOI · Paper page
  67. SE Feller, 2000, An improved empirical potential energy function for molecular simulations of phospholipids, J Phys Chem B, 104, 7510, 10.1021/jp0007843 · DOI
  68. AD MacKerell, 1998, All-atom empirical potential for molecular modeling and dynamics studies of proteins, J Phys Chem B, 102, 3586, 10.1021/jp973084f · DOI
  69. AD MacKerell Jr, 2004, Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations, J Comput Chem, 25, 1400, 10.1002/jcc.20065 · DOI
  70. J Hénin, 2008, United-atom acyl chains for CHARMM phospholipids, J Phys Chem B, 112, 7008, 10.1021/jp800687p · DOI
  71. M Guttman, 2011, The structure, dynamics, and binding of the LA45 module pair of the low-density lipoprotein receptor suggest an important role for LA4 in ligand release, Biochemistry, 50, 11001, 10.1021/bi2014486 · DOI
  72. SJ de Vries, 2010, The HADDOCK web server for data-driven biomolecular docking, Nat Protoc, 5, 883, 10.1038/nprot.2010.32 · DOI
  73. M Prévost, 2004, Apolipoprotein E-low density lipoprotein receptor binding: study of protein-protein interaction in rationally selected docked complexes, Proteins, 55, 874, 10.1002/prot.20080 · DOI
  74. C Fisher, 2006, Structure of an LDLR-RAP complex reveals a general mode for ligand recognition by lipoprotein receptors, Mol Cell, 22, 277, 10.1016/j.molcel.2006.02.021 · DOI · Paper page
  75. M Guttman, 2010, Structure of the minimal interface between ApoE and LRP, J Mol Biol, 398, 306, 10.1016/j.jmb.2010.03.022 · DOI
  76. G Rudenko, 2002, Structure of the LDL receptor extracellular domain at endosomal pH, Science, 298, 2353, 10.1126/science.1078124 · DOI · Paper page

Cited by

Sorted by citations

Metadata

Authors
Henry, N., Krammer, E.-M., Stengel, F., Adams, Q., Van Liefferinge, F., Hubin, E., Chaves, R., Efremov, R., Aebersold, R., Vandenbussche, G., Prévost, M., Raussens, V., & Deroo, S.
Venue
PLOS Computational Biology
Publisher
Public Library of Science (PLoS)
Published
2018-06-22
Volume
14
Issue
6
Pages
e1006165
ISSN
1553-7358
DOI
10.1371/journal.pcbi.1006165
PMC
PMC6033463
Cited by
42
References
5
Language
en
Update notices
new_version (2018-07-05)
Licence
creativecommons.org/licenses/by/4.0/ (vor)
Funders
  • F.R.S.-FNRS (PDR #70214.12)
  • SAO-FRA (S#14025)
  • Wellcome Trust (095951)
  • German Science foundation Emmy Noether (STE 2517/1-1)
  • European Research Council (233226 and 679821)

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review