CoChat
Sign Up
Cited by 26

The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.

Quantitative Dissection of the Binding Contributions of Ligand Lysines of the Receptor-associated Protein (RAP) to the Low Density Lipoprotein Receptor-related Protein (LRP1)

Dolmer, Klavs, Campos, Andres, Gettins, Peter G.W.·2013·Journal of Biological Chemistry
DOI 10.1074/jbc.m113.473728
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 · 10.1074/jbc.m113.473728

Cites

1 of 1 references verified0 citation errors · 0 not checkable

Statistics

Figures

FIGURE 1 Interactions in the D3-LB3-LB4 complex. The structure of the D3-LB34complex(14)( bottompanel ) shows the three-helical D3 ( red ) and the two CR domains, LB4 ( yellow ) and LB3 ( green ). The contact residues from D3 are the lysines Lys-253 and Lys-256 (to LB4) and Lys-270 and Lys-289 (to LB3). These lysines interact with three aspartates and an aromatic side chain in each of the two CR domains ( top panels ).
FIGURE 1 Interactions in the D3-LB3-LB4 complex. The structure of the D3-LB34complex(14)( bottompanel ) shows the three-helical D3 ( red ) and the two CR domains, LB4 ( yellow ) and LB3 ( green ). The contact residues from D3 are the lysines Lys-253 and Lys-256 (to LB4) and Lys-270 and Lys-289 (to LB3). These lysines interact with three aspartates and an aromatic side chain in each of the two CR domains ( top panels ).CC-BY · From the PDF
FIGURE 2 CDspectra of D3 variants show similar helical content. Spectra of 10 𝛍 MD3speciesareshown. Cyan , wild type D3; red , K4 variant; green , K3-1; purple , K2-1.
FIGURE 2 CDspectra of D3 variants show similar helical content. Spectra of 10 𝛍 MD3speciesareshown. Cyan , wild type D3; red , K4 variant; green , K3-1; purple , K2-1.CC-BY · From the PDF
FIGURE 3 Fluorescence difference spectra of D3-CR56 complexes. Difference spectra between the complex of 1 𝛍 MCR56withagiven D3 species and the summed contributions from the component CR56 and D3 species are shown. Spectra are shown for wild type D3 ( cyan ), K4 variant ( green ), K3-1 ( red ), K3-4 ( black ), and K2-1 ( gray ).
FIGURE 3 Fluorescence difference spectra of D3-CR56 complexes. Difference spectra between the complex of 1 𝛍 MCR56withagiven D3 species and the summed contributions from the component CR56 and D3 species are shown. Spectra are shown for wild type D3 ( cyan ), K4 variant ( green ), K3-1 ( red ), K3-4 ( black ), and K2-1 ( gray ).CC-BY · From the PDF
FIGURE4 RepresentativefluorescencetitrationsofselectedD3variantswithCR56. Dataarepresentedforthosefivevariantswhosedifferencespectraare given in Fig. 3. The data points represent fluorescence enhancement at 335 nm as a percentage of the maximum, after correction for contribution of D3, obtained by a separate titration of D3 into buffer. [CR56] was 100 nM for all titrations except K2-1, for which [CR56] was 200 nM. The buffer was 20 mM Tris, pH 7.4, containing 1 mM CaCl 2 and with 150 mM NaCl added for K3-1, K3-4, and K2-1, and 300 mM NaCl added for wild type D3 and K4 to weaken affinity. Note that good curvature is observed for all titrations, reflecting appropriate conditions for obtaining accurate determination of Kd values.
FIGURE4 RepresentativefluorescencetitrationsofselectedD3variantswithCR56. Dataarepresentedforthosefivevariantswhosedifferencespectraare given in Fig. 3. The data points represent fluorescence enhancement at 335 nm as a percentage of the maximum, after correction for contribution of D3, obtained by a separate titration of D3 into buffer. [CR56] was 100 nM for all titrations except K2-1, for which [CR56] was 200 nM. The buffer was 20 mM Tris, pH 7.4, containing 1 mM CaCl 2 and with 150 mM NaCl added for K3-1, K3-4, and K2-1, and 300 mM NaCl added for wild type D3 and K4 to weaken affinity. Note that good curvature is observed for all titrations, reflecting appropriate conditions for obtaining accurate determination of Kd values.CC-BY · From the PDF
FIGURE 5 Ionic strength dependence of WT and K4 and K2-1 D3 variants binding to CR56. Debye-Hückel plot shows WT ( open squares ) and D3 variants K4 ( closed squares ) and K2-1 ( closed triangles ) binding to CR56. The slope of the plot gives the number of ionic interactions involved.
FIGURE 5 Ionic strength dependence of WT and K4 and K2-1 D3 variants binding to CR56. Debye-Hückel plot shows WT ( open squares ) and D3 variants K4 ( closed squares ) and K2-1 ( closed triangles ) binding to CR56. The slope of the plot gives the number of ionic interactions involved.CC-BY · From the PDF
FIGURE 6 Relationship of key residues of D3 to one another. The figure shows a ribbon diagram of the two major helices of D3, which carry the four interacting lysines, as well as the location of other key residues. This illustrates the relationship of the lysines to one another, with Lys-253, Lys-256, and Lys-270 being fixed by virtue of being on the same helix, whereas Lys-289 is on the flanking helix, with the two 𝛜 -amino groups of Lys-270 and Lys-289 much further apart than those of Lys-253 and Lys-256. The two residues, Tyr-260 and His-247, which were separately mutated to lysine, and Arg-285 are also shown (in silhouette). Beneath is a schematic of the separations between all pairs of 𝛜 -amino groups of the four lysines (in the complex with LB34).
FIGURE 6 Relationship of key residues of D3 to one another. The figure shows a ribbon diagram of the two major helices of D3, which carry the four interacting lysines, as well as the location of other key residues. This illustrates the relationship of the lysines to one another, with Lys-253, Lys-256, and Lys-270 being fixed by virtue of being on the same helix, whereas Lys-289 is on the flanking helix, with the two 𝛜 -amino groups of Lys-270 and Lys-289 much further apart than those of Lys-253 and Lys-256. The two residues, Tyr-260 and His-247, which were separately mutated to lysine, and Arg-285 are also shown (in silhouette). Beneath is a schematic of the separations between all pairs of 𝛜 -amino groups of the four lysines (in the complex with LB34).CC-BY · From the PDF
Image 7
CC-BY · From the PDF
FIGURE 8 Schematic of free energy contributions of individual lysines of D3 in binding to CR56. A and B , top panels , apparent 𝚫 G 0 values (in kcal mol -1 ) of each of the lysines 253, 256, 270, and 289 deduced from comparison of observed affinities of each K3x species with that of K4 for binding to CR56. A , bottom panel , predicted affinity of K2-2 from summation of apparent individual lysine binding contributions, compared with observed affinity of K2-2forCR56.Closeagreementisobtained. B , bottompanel , predicted affinity of K2-3 from summation of apparent individual lysine binding contributions, comparedwithobservedaffinity of K2-3 for CR56. Note the large discrepancy between observed and predicted affinities, indicating that one or both individual contributions is greatly underestimated by the approach of comparing affinities of K3 species with K4 for these two lysines. C , good agreement between the affinity of K4 predicted from summation of the observed affinities of the lysine pairs Lys-253/Lys-256 (K2-2) and Lys-270/Lys-289 (K2-3) for CR56 and the affinity observed for K4 binding to CR56. This indicates independence of the two CR domain binding sites.
FIGURE 8 Schematic of free energy contributions of individual lysines of D3 in binding to CR56. A and B , top panels , apparent 𝚫 G 0 values (in kcal mol -1 ) of each of the lysines 253, 256, 270, and 289 deduced from comparison of observed affinities of each K3x species with that of K4 for binding to CR56. A , bottom panel , predicted affinity of K2-2 from summation of apparent individual lysine binding contributions, compared with observed affinity of K2-2forCR56.Closeagreementisobtained. B , bottompanel , predicted affinity of K2-3 from summation of apparent individual lysine binding contributions, comparedwithobservedaffinity of K2-3 for CR56. Note the large discrepancy between observed and predicted affinities, indicating that one or both individual contributions is greatly underestimated by the approach of comparing affinities of K3 species with K4 for these two lysines. C , good agreement between the affinity of K4 predicted from summation of the observed affinities of the lysine pairs Lys-253/Lys-256 (K2-2) and Lys-270/Lys-289 (K2-3) for CR56 and the affinity observed for K4 binding to CR56. This indicates independence of the two CR domain binding sites.CC-BY · From the PDF
Image 9
CC-BY · From the PDF

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

Research works printed but not linked: 25

  1. Herz, 2001, LRP. A multifunctional scavenger and signaling receptor, J. Clin. Invest, 108, 779, 10.1172/JCI200113992 · DOI · Paper page
  2. Nielsen, 1996, Identification of residues in α-macroglobulins important for binding to the α2-macroglobulin receptor/Low density lipoprotein receptor-related protein, J. Biol. Chem, 271, 12909, 10.1074/jbc.271.22.12909 · DOI
  3. Migliorini, 2003, Allosteric modulation of ligand binding to low density lipoprotein receptor-related protein by the receptor-associated protein requires critical lysine residues within its carboxyl-terminal domain, J. Biol. Chem, 278, 17986, 10.1074/jbc.M212592200 · DOI
  4. Arandjelovic, 2005, Mutation of lysine 1370 in full-length human α2-macroglobulin blocks binding to the low density lipoprotein receptor-related protein-1, Arch. Biochem. Biophys, 438, 29, 10.1016/j.abb.2005.03.019 · DOI
  5. Sarafanov, 2006, Identification of coagulation factor VIII A2 domain residues forming the binding epitope for low-density lipoprotein receptor-related protein, Biochemistry, 45, 1829, 10.1021/bi0520380 · DOI
  6. Jensen, 2006, Binding site structure of one LRP-RAP complex. Implications for a common ligand-receptor binding motif, J. Mol. Biol, 362, 700, 10.1016/j.jmb.2006.07.013 · DOI
  7. Dolmer, 2006, Three complement-like repeats compose the complete α2-macroglobulin binding site in the second ligand binding cluster of the low density lipoprotein receptor-related protein, J. Biol. Chem, 281, 34189, 10.1074/jbc.M604389200 · DOI
  8. Yasui, 2010, Structural basis for specific recognition of reelin by its receptors, Structure, 18, 320, 10.1016/j.str.2010.01.010 · DOI
  9. van den Biggelaar, 2011, A single lysine of the two-lysine recognition motif of the D3 domain of receptor-associated protein is sufficient to mediate endocytosis by low-density lipoprotein receptor-related protein, Int. J. Biochem. Cell Biol, 43, 431, 10.1016/j.biocel.2010.11.017 · DOI
  10. Guttman, 2010, Structure of the minimal interface between ApoE and LRP, J. Mol. Biol, 398, 306, 10.1016/j.jmb.2010.03.022 · DOI
  11. Gettins, 2012, A proximal pair of positive charges provides the dominant ligand-binding contribution to complement-like domains from the LRP (low-density lipoprotein receptor-related protein), Biochem. J, 443, 65, 10.1042/BJ20111867 · DOI
  12. Horn, 1998, Plasminogen activator inhibitor 1 contains a cryptic high affinity receptor binding site that is exposed upon complex formation with tissue-type plasminogen activator, Thromb. Haemost, 80, 822, 10.1055/s-0037-1615365 · DOI
  13. 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
  14. Estrada, 2008, Unfolding of the RAP-D3 helical bundle facilitates dissociation of RAP-receptor complexes, Biochemistry, 47, 1532, 10.1021/bi702076y · DOI
  15. Beglova, 2001, Backbone dynamics of a module pair from the ligand-binding domain of the LDL receptor, Biochemistry, 40, 2808, 10.1021/bi0027276 · DOI
  16. Jensen, 2009, Receptor-associated protein (RAP) has two high-affinity binding sites for the low-density lipoprotein receptor-related protein (LRP). Consequences for the chaperone functions of RAP, Biochem. J, 421, 273, 10.1042/BJ20090175 · DOI · Paper page
  17. Lee, 2006, RAP uses a histidine switch to regulate its interaction with LRP in the ER and Golgi, Mol. Cell, 22, 423, 10.1016/j.molcel.2006.04.011 · DOI
  18. Andersen, 2001, Analysis of a two-domain binding site for the urokinase-type plasminogen activator-plasminogen activator inhibitor-1 complex in low-density-lipoprotein-receptor-related protein, Biochem. J, 357, 289, 10.1042/bj3570289 · DOI
  19. Jensen, 2009, Specificity of binding of the low density lipoprotein receptor-related protein to different conformational states of the clade E serpins plasminogen activator inhibitor-1 and proteinase nexin-1, J. Biol. Chem, 284, 17989, 10.1074/jbc.M109.009530 · DOI
  20. Lazic, 2006, Dissection of RAP-LRP interactions. Binding of RAP and RAP fragments to complement-like repeats 7 and 8 from ligand binding cluster II of LRP, Arch. Biochem. Biophys, 450, 167, 10.1016/j.abb.2006.04.007 · DOI
  21. 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
  22. Fass, 1997, Molecular basis of familial hypercholesterolaemia from structure of LDL receptor module, Nature, 388, 691, 10.1038/41798 · DOI
  23. Huang, 1999, NMR solution structure of complement-like repeat CR8 from the low density lipoprotein receptor-related protein, J. Biol. Chem, 274, 14130, 10.1074/jbc.274.20.14130 · DOI
  24. Dolmer, 2000, NMR solution structure of complement-like repeat CR3 from the low density lipoprotein receptor-related protein. Evidence for specific binding to the receptor binding domain of human α2-macroglobulin, J. Biol. Chem, 275, 3264, 10.1074/jbc.275.5.3264 · DOI
  25. Simonovic, 2001, Calcium coordination and pH dependence of the calcium affinity of ligand-binding repeat CR7 from the LRP. Comparison with related domains from the LRP and the LDL receptor, Biochemistry, 40, 15127, 10.1021/bi015688m · DOI

Cited by

Sorted by citations

See all 26

Metadata

Authors
Dolmer, K., Campos, A., & Gettins, P. G. W.
Venue
Journal of Biological Chemistry
Publisher
Elsevier BV
Published
2013-08
Volume
288
Issue
33
Pages
24081-24090
ISSN
0021-9258
DOI
10.1074/jbc.m113.473728
Cited by
26
References
1
Language
en
Licence

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