Molecular chaperone RAP interacts with LRP1 in a dynamic bivalent mode and enhances folding of ligand-binding regions of other LDLR family receptors

Marakasova, Ekaterina; Olivares, Philip; Karnaukhova, Elena; Chun, Haarin; Hernandez, Nancy E.; Kurasawa, James H.; Hassink, Gabriela U.; Shestopal, Svetlana A.; Strickland, Dudley K.; Sarafanov, Andrey G.

doi:10.1016/j.jbc.2021.100842

Title: Molecular chaperone RAP interacts with LRP1 in a dynamic bivalent mode and enhances folding of ligand-binding regions of other LDLR family receptors

Journal Article · Sat May 29 00:00:00 EDT 2021 · Journal of Biological Chemistry

DOI:https://doi.org/10.1016/j.jbc.2021.100842· OSTI ID:1816953

^[1];

^[1]; Karnaukhova, Elena ^[1];

^[1];

^[1]; Kurasawa, James H. ^[1]; Hassink, Gabriela U. ^[1];

^[1]; Strickland, Dudley K. ^[2];

^[1]

U.S. Food and Drug Administration (FDA), Silver Spring, MD (United States). Center for Biologics Evalutation and Research
Univ. of Maryland Baltimore County (UMBC), Baltimore, MD (United States). Center for Vascular and Inflammatory Diseases

The low-density lipoprotein receptor (LDLR) family of receptors are cell-surface receptors that internalize numerous ligands and play crucial role in various processes, such as lipoprotein metabolism, hemostasis, fetal development, etc. Previously, receptor-associated protein (RAP) was described as a molecular chaperone for LDLR-related protein 1 (LRP1), a prominent member of the LDLR family. We aimed to verify this role of RAP for LRP1 and two other LDLR family receptors, LDLR and vLDLR, and to investigate the mechanisms of respective interactions using a cell culture model system, purified system, and in silico modelling. Upon coexpression of RAP with clusters of the ligand-binding complement repeats (CRs) of the receptors in secreted form in insect cells culture, the isolated proteins had increased yield, enhanced folding, and improved binding properties compared with proteins expressed without RAP, as determined by circular dichroism and surface plasmon resonance. Within LRP1 CR-clusters II and IV, we identified multiple sites comprised of adjacent CR doublets, which provide alternative bivalent binding combinations with specific pairs of lysines on RAP. Mutational analysis of these lysines within each of isolated RAP D1/D2 and D3 domains having high affinity to LRP1 and of conserved tryptophans on selected CR-doublets of LRP1, as well as in silico docking of a model LRP1 CR-triplet with RAP, indicated a universal role for these residues in interaction of RAP and LRP1. Consequently, we propose a new model of RAP interaction with LDLR family receptors based on switching of the bivalent contacts between molecules over time in a dynamic mode.

View Accepted Manuscript (DOE)

Cite

Export

Save

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division; USDA

Grant/Contract Number:: SC0014664

OSTI ID:: 1816953

Journal Information:: Journal of Biological Chemistry, Vol. 297, Issue 1; ISSN 0021-9258

Publisher:: American Society for Biochemistry and Molecular BiologyCopyright Statement

Country of Publication:: United States

Language:: English

References (63)

Localization of the low-density lipoprotein receptor-related protein regions involved in binding to the A2 domain of coagulation factor VIII Sarafanov, Andrey; Makogonenko, Evgeny; Andersen, Olav Thrombosis and Haemostasis, Vol. 98, Issue 12 https://doi.org/10.1160/TH07-05-0353	journal	January 2007
A novel mechanism for controlling the activity of alpha 2-macroglobulin receptor/low density lipoprotein receptor-related protein. Multiple regulatory sites for 39-kDa receptor-associated protein. Williams, S. E.; Ashcom, J. D.; Argraves, W. S. Journal of Biological Chemistry, Vol. 267, Issue 13 https://doi.org/10.1016/S0021-9258(19)50384-2	journal	May 1992
I-TASSER server: new development for protein structure and function predictions Yang, Jianyi; Zhang, Yang Nucleic Acids Research, Vol. 43, Issue W1 https://doi.org/10.1093/nar/gkv342	journal	April 2015
Cluster III of Low-Density Lipoprotein Receptor-Related Protein 1 Binds Activated Blood Coagulation Factor VIII Kurasawa, James H.; Shestopal, Svetlana A.; Woodle, Samuel A. Biochemistry, Vol. 54, Issue 2 https://doi.org/10.1021/bi5011688	journal	December 2014
Lipoprotein receptors – an evolutionarily ancient multifunctional receptor family Dieckmann, Marco; Dietrich, Martin Frederik; Herz, Joachim Biological Chemistry, Vol. 391, Issue 11 https://doi.org/10.1515/bc.2010.129	journal	November 2010
39-kDa protein modulates binding of ligands to low density lipoprotein receptor-related protein/alpha 2-macroglobulin receptor. Herz, J.; Goldstein, J. L.; Strickland, D. K. Journal of Biological Chemistry, Vol. 266, Issue 31 https://doi.org/10.1016/S0021-9258(18)54845-6	journal	November 1991
Identification of Coagulation Factor VIII A2 Domain Residues Forming the Binding Epitope for Low-Density Lipoprotein Receptor-Related Protein ^, Sarafanov, Andrey G.; Makogonenko, Evgeny M.; Pechik, Igor V. Biochemistry, Vol. 45, Issue 6 https://doi.org/10.1021/bi0520380	journal	January 2006
I-TASSER: a unified platform for automated protein structure and function prediction Roy, Ambrish; Kucukural, Alper; Zhang, Yang Nature Protocols, Vol. 5, Issue 4 https://doi.org/10.1038/nprot.2010.5	journal	March 2010
High-affinity binding of plasminogen-activator inhibitor 1 complexes to LDL receptor–related protein 1 requires lysines 80, 88, and 207 Migliorini, Mary; Li, Shih-Hon; Zhou, Anqi Journal of Biological Chemistry, Vol. 295, Issue 1 https://doi.org/10.1074/jbc.RA119.010449	journal	January 2020
X-ray structure of a minor group human rhinovirus bound to a fragment of its cellular receptor protein Verdaguer, Nuria; Fita, Ignacio; Reithmayer, Manuela Nature Structural & Molecular Biology, Vol. 11, Issue 5 https://doi.org/10.1038/nsmb753	journal	April 2004
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 Jensen, Jan K.; Dolmer, Klavs; Schar, Christine Biochemical Journal, Vol. 421, Issue 2 https://doi.org/10.1042/BJ20090175	journal	June 2009
High-throughput optimization of protein expression in the baculovirus system based on determination of relative expression efficiency of viral stocks Sarafanov, Andrey; Saenko, Evgueni Analytical Biochemistry, Vol. 328, Issue 1 https://doi.org/10.1016/j.ab.2003.11.028	journal	May 2004
39-kDa receptor-associated protein (RAP) facilitates secretion and ligand binding of extracellular region of very-low-density-lipoprotein receptor: implications for a distinct pathway from low-density-lipoprotein receptor Sato, Atsushi; Shimada, Yoshimi; Herz, Joachim Biochemical Journal, Vol. 341, Issue 2 https://doi.org/10.1042/bj3410377	journal	July 1999
The Mammalian Low-Density Lipoprotein Receptor Family Hussain, M. Mahmood; Strickland, Dudley K.; Bakillah, Ahmed Annual Review of Nutrition, Vol. 19, Issue 1 https://doi.org/10.1146/annurev.nutr.19.1.141	journal	July 1999
Calcium Ion Coordination: A Comparison with That of Beryllium, Magnesium, and Zinc Katz, Amy Kaufman; Glusker, Jenny P.; Beebe, Scott A. Journal of the American Chemical Society, Vol. 118, Issue 24 https://doi.org/10.1021/ja953943i	journal	January 1996
The closed conformation of the LDL receptor is destabilized by the low Ca ⁺⁺ concentration but favored by the high Mg ⁺⁺ concentration in the endosome Martínez-Oliván, Juan; Arias-Moreno, Xabier; Hurtado-Guerrero, Ramón FEBS Letters, Vol. 589, Issue 23 https://doi.org/10.1016/j.febslet.2015.10.014	journal	October 2015
Improved side-chain modeling for protein-protein docking Wang, Chu; Schueler-Furman, Ora; Baker, David Protein Science, Vol. 14, Issue 5 https://doi.org/10.1110/ps.041222905	journal	May 2005
Functional duplication of ligand-binding domains within low-density lipoprotein receptor-related protein for interaction with receptor associated protein, α2-macroglobulin, factor IXa and factor VIII Meijer, Alexander B.; Rohlena, Jakub; van der Zwaan, Carmen Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Vol. 1774, Issue 6 https://doi.org/10.1016/j.bbapap.2007.04.003	journal	June 2007
A united residue force-field for calcium-protein interactions Khalili, Mey; Saunders, Jeffrey A.; Liwo, Adam Protein Science, Vol. 13, Issue 10 https://doi.org/10.1110/ps.04878904	journal	October 2004
The Use of Circular Dichroism in the Investigation of Protein Structure and Function Kelly, Sharon; Price, Nicholas Current Protein & Peptide Science, Vol. 1, Issue 4, p. 349-384 https://doi.org/10.2174/1389203003381315	journal	December 2000
The GeneOptimizer Algorithm: using a sliding window approach to cope with the vast sequence space in multiparameter DNA sequence optimization Raab, David; Graf, Marcus; Notka, Frank Systems and Synthetic Biology, Vol. 4, Issue 3 https://doi.org/10.1007/s11693-010-9062-3	journal	September 2010
Differential Functions of Triplicated Repeats Suggest Two Independent Roles for the Receptor-associated Protein as a Molecular Chaperone Obermoeller, Lynn M.; Warshawsky, Ilka; Wardell, Mark R. Journal of Biological Chemistry, Vol. 272, Issue 16 https://doi.org/10.1074/jbc.272.16.10761	journal	April 1997
Modeling oblong proteins and water-mediated interfaces with RosettaDock in CAPRI rounds 28-35: Oblong & Water-Mediated CAPRI Complexes Marze, Nicholas A.; Jeliazkov, Jeliazko R.; Roy Burman, Shourya S. Proteins: Structure, Function, and Bioinformatics, Vol. 85, Issue 3 https://doi.org/10.1002/prot.25168	journal	October 2016
The I-TASSER Suite: protein structure and function prediction Yang, Jianyi; Yan, Renxiang; Roy, Ambrish Nature Methods, Vol. 12, Issue 1 https://doi.org/10.1038/nmeth.3213	journal	December 2014
More than Cholesterol Transporters: Lipoprotein Receptors in CNS Function and Neurodegeneration Lane-Donovan, Courtney; Philips, Gary T.; Herz, Joachim Neuron, Vol. 83, Issue 4 https://doi.org/10.1016/j.neuron.2014.08.005	journal	August 2014
The Second and Fourth Cluster of Class A Cysteine-rich Repeats of the Low Density Lipoprotein Receptor-related Protein Share Ligand-binding Properties Neels, Jaap G.; van den Berg, Birgit M. M.; Lookene, Aivar Journal of Biological Chemistry, Vol. 274, Issue 44 https://doi.org/10.1074/jbc.274.44.31305	journal	October 1999
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 Migliorini, Mary M.; Behre, Evan H.; Brew, Shelesa Journal of Biological Chemistry, Vol. 278, Issue 20 https://doi.org/10.1074/jbc.M212592200	journal	May 2003
Receptor-associated Protein Is a Folding Chaperone for Low Density Lipoprotein Receptor-related Protein Bu, Guojun; Rennke, Stephanie Journal of Biological Chemistry, Vol. 271, Issue 36 https://doi.org/10.1074/jbc.271.36.22218	journal	September 1996
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) Gettins, Peter G. W.; Dolmer, Klavs Biochemical Journal, Vol. 443, Issue 1 https://doi.org/10.1042/BJ20111867	journal	March 2012
Interaction of Fibrin with the Very Low-Density Lipoprotein (VLDL) Receptor: Further Characterization and Localization of the VLDL Receptor-Binding Site in Fibrin βN-Domains Yakovlev, Sergiy; Medved, Leonid Biochemistry, Vol. 56, Issue 19 https://doi.org/10.1021/acs.biochem.7b00087	journal	May 2017
Structure of an LDLR-RAP Complex Reveals a General Mode for Ligand Recognition by Lipoprotein Receptors Fisher, Carl; Beglova, Natalia; Blacklow, Stephen C. Molecular Cell, Vol. 22, Issue 2 https://doi.org/10.1016/j.molcel.2006.02.021	journal	April 2006
The 39-kDa Receptor-associated Protein Modulates Lipoprotein Catabolism by Binding to LDL Receptors Medh, Jheem D.; Fry, Glenna L.; Bowen, Susan L. Journal of Biological Chemistry, Vol. 270, Issue 2 https://doi.org/10.1074/jbc.270.2.536	journal	January 1995
Binding Site Structure of One LRP–RAP Complex:Implications for a Common Ligand–Receptor Binding Motif Jensen, Gitte A.; Andersen, Olav M.; Bonvin, Alexandre M. J. J. Journal of Molecular Biology, Vol. 362, Issue 4 https://doi.org/10.1016/j.jmb.2006.07.013	journal	September 2006
The Role of a Conserved Acidic Residue in Calcium-dependent Protein Folding for a Low Density Lipoprotein (LDL)-A Module Guo, Ying; Yu, Xuemei; Rihani, Kayla Journal of Biological Chemistry, Vol. 279, Issue 16 https://doi.org/10.1074/jbc.M400157200	journal	April 2004
RAP, a specialized chaperone, prevents ligand-induced ER retention and degradation of LDL receptor-related endocytic receptors. Willnow, T. E.; Rohlmann, A.; Horton, J. The EMBO Journal, Vol. 15, Issue 11 https://doi.org/10.1002/j.1460-2075.1996.tb00623.x	journal	June 1996
Regulation of tau internalization, degradation, and seeding by LRP1 reveals multiple pathways for tau catabolism Cooper, Joanna M.; Lathuiliere, Aurelien; Migliorini, Mary Journal of Biological Chemistry, Vol. 296 https://doi.org/10.1016/j.jbc.2021.100715	journal	January 2021
Recognition of α2-Macroglobulin by the Low Density Lipoprotein Receptor-related Protein Requires the Cooperation of Two Ligand Binding Cluster Regions Mikhailenko, Irina; Battey, Frances D.; Migliorini, Mary Journal of Biological Chemistry, Vol. 276, Issue 42 https://doi.org/10.1074/jbc.M104382200	journal	October 2001
Functional expression of low density lipoprotein receptor-related protein is controlled by receptor-associated protein in vivo. Willnow, T. E.; Armstrong, S. A.; Hammer, R. E. Proceedings of the National Academy of Sciences, Vol. 92, Issue 10 https://doi.org/10.1073/pnas.92.10.4537	journal	May 1995
Identification of the Minimal Functional Unit in the Low Density Lipoprotein Receptor-related Protein for Binding the Receptor-associated Protein (RAP) Andersen, Olav Michael; Christensen, Lisa Lystbæk; Christensen, Peter Astrup Journal of Biological Chemistry, Vol. 275, Issue 28 https://doi.org/10.1074/jbc.M000507200	journal	July 2000
Evidence That Factor VIII Forms a Bivalent Complex with the Low Density Lipoprotein (LDL) Receptor-related Protein 1 (LRP1) Young, Patricia A.; Migliorini, Mary; Strickland, Dudley K. Journal of Biological Chemistry, Vol. 291, Issue 50 https://doi.org/10.1074/jbc.M116.754622	journal	December 2016
Protein–Protein Docking with Backbone Flexibility Wang, Chu; Bradley, Philip; Baker, David Journal of Molecular Biology, Vol. 373, Issue 2 https://doi.org/10.1016/j.jmb.2007.07.050	journal	October 2007
Recombinant Expression of the Full-length Ectodomain of LDL Receptor-related Protein 1 (LRP1) Unravels pH-dependent Conformational Changes and the Stoichiometry of Binding with Receptor-associated Protein (RAP) De Nardis, Camilla; Lössl, Philip; van den Biggelaar, Maartje Journal of Biological Chemistry, Vol. 292, Issue 3 https://doi.org/10.1074/jbc.M116.758862	journal	January 2017
Protein–Protein Docking with Simultaneous Optimization of Rigid-body Displacement and Side-chain Conformations Gray, Jeffrey J.; Moughon, Stewart; Wang, Chu Journal of Molecular Biology, Vol. 331, Issue 1 https://doi.org/10.1016/S0022-2836(03)00670-3	journal	August 2003
The apoE isoform binding properties of the VLDL receptor reveal marked differences from LRP and the LDL receptor Ruiz, Jose; Kouiavskaia, Diana; Migliorini, Molly Journal of Lipid Research, Vol. 46, Issue 8 https://doi.org/10.1194/jlr.M500114-JLR200	journal	August 2005
Low-density lipoprotein receptor structure and folding Gent, J.; Braakman, I. Cellular and Molecular Life Sciences, Vol. 61, Issue 19-20 https://doi.org/10.1007/s00018-004-4090-3	journal	October 2004
High Affinity Binding of the Receptor-associated Protein D1D2 Domains with the Low Density Lipoprotein Receptor-related Protein (LRP1) Involves Bivalent Complex Formation Prasad, Joni M.; Young, Patricia A.; Strickland, Dudley K. Journal of Biological Chemistry, Vol. 291, Issue 35 https://doi.org/10.1074/jbc.M116.744904	journal	August 2016
Calcium Binding to Amino Acids and Small Glycine Peptides in Aqueous Solution: Toward Peptide Design for Better Calcium Bioavailability Tang, Ning; Skibsted, Leif H. Journal of Agricultural and Food Chemistry, Vol. 64, Issue 21 https://doi.org/10.1021/acs.jafc.6b01534	journal	May 2016
Dominant Thermodynamic Role of the Third Independent Receptor Binding Site in the Receptor-Associated Protein RAP Andersen, Olav M.; Schwarz, Frederick P.; Eisenstein, Edward Biochemistry, Vol. 40, Issue 50 https://doi.org/10.1021/bi0110692	journal	November 2001
Contributions of tryptophan side chains to the far-ultraviolet circular dichroism of proteins Woody, RobertW. European Biophysics Journal, Vol. 23, Issue 4 https://doi.org/10.1007/BF00213575	journal	October 1994
Benchmarking and Analysis of Protein Docking Performance in Rosetta v3.2 Chaudhury, Sidhartha; Berrondo, Monica; Weitzner, Brian D. PLoS ONE, Vol. 6, Issue 8 https://doi.org/10.1371/journal.pone.0022477	journal	August 2011
Origin of the positive 225–230 nm circular dichroism band in proteins Hider, R. C.; Kupryszewski, G.; Rekowski, P. Biophysical Chemistry, Vol. 31, Issue 1-2 https://doi.org/10.1016/0301-4622(88)80007-3	journal	August 1988
The Role of Low-Density Lipoprotein Receptor-Related Protein 1 in Lipid Metabolism, Glucose Homeostasis and Inflammation Actis Dato, Virginia; Chiabrando, Gustavo International Journal of Molecular Sciences, Vol. 19, Issue 6 https://doi.org/10.3390/ijms19061780	journal	June 2018
An analysis of the 225-230-nm CD band of elapid toxins Hider, R. C.; Drake, A. F.; Tamiya, N. Biopolymers, Vol. 27, Issue 1 https://doi.org/10.1002/bip.360270109	journal	January 1988
A Minimal Binding Domain of the Low Density Lipoprotein Receptor Family Bajari, Tarek M.; Lindstedt, Ken A.; Riepl, Michael Biological Chemistry, Vol. 379, Issue 8-9 https://doi.org/10.1515/bchm.1998.379.8-9.1053	journal	January 1998
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 van den Biggelaar, Maartje; Sellink, Erica; Klein Gebbinck, Jacqueline W. T. M. The International Journal of Biochemistry & Cell Biology, Vol. 43, Issue 3 https://doi.org/10.1016/j.biocel.2010.11.017	journal	March 2011
Molecular basis of familial hypercholesterolaemia from structure of LDL receptor module Fass, Deborah; Blacklow, Stephen; Kim, Peter S. Nature, Vol. 388, Issue 6643 https://doi.org/10.1038/41798	journal	August 1997
The Reelin Receptors Apolipoprotein E receptor 2 (ApoER2) and VLDL Receptor Dlugosz, Paula; Nimpf, Johannes International Journal of Molecular Sciences, Vol. 19, Issue 10 https://doi.org/10.3390/ijms19103090	journal	October 2018
Sulfur dioxide induced aggregation of wine thaumatin-like proteins: Role of disulfide bonds Chagas, Ricardo; Laia, César A. T.; Ferreira, Ricardo B. Food Chemistry, Vol. 259 https://doi.org/10.1016/j.foodchem.2018.03.115	journal	September 2018
Structural Basis for Specific Recognition of Reelin by Its Receptors Yasui, Norihisa; Nogi, Terukazu; Takagi, Junichi Structure, Vol. 18, Issue 3 https://doi.org/10.1016/j.str.2010.01.010	journal	March 2010
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. Journal of Biological Chemistry, Vol. 288, Issue 33 https://doi.org/10.1074/jbc.M113.473728	journal	August 2013
Apolipoprotein E isoform-specific binding to the low-density lipoprotein receptor Yamamoto, Taichi; Choi, Hyung Won; Ryan, Robert O. Analytical Biochemistry, Vol. 372, Issue 2 https://doi.org/10.1016/j.ab.2007.09.005	journal	January 2008
Mapping the Binding Region on the Low Density Lipoprotein Receptor for Blood Coagulation Factor VIII Kurasawa, James H.; Shestopal, Svetlana A.; Karnaukhova, Elena Journal of Biological Chemistry, Vol. 288, Issue 30 https://doi.org/10.1074/jbc.M113.468108	journal	July 2013
Using circular dichroism spectra to estimate protein secondary structure Greenfield, Norma J Nature Protocols, Vol. 1, Issue 6, p. 2876-2890 https://doi.org/10.1038/nprot.2006.202	journal	January 2007

Similar Records

Structure of an LDLR-RAP Complex Reveals a General Mode for Ligand Recognition by Lipoprotein Receptors

Journal Article · Sun Jan 01 00:00:00 EST 2006 · Mol. Cell · OSTI ID:1816953

Fisher, C; Beglova, N; Blacklow, s

Chromosomal localization of human genes for the LDL receptor family member glycoprotein 330 (LRP2) and its associated protein RAP (LRPAP1)

Journal Article · Fri Jul 01 00:00:00 EDT 1994 · Genomics · OSTI ID:1816953

Korenberg, J R; Chen, X N; Argraves, K M

Characterization of lipid metabolism in insulin-sensitive adipocytes differentiated from immortalized human mesenchymal stem cells

Journal Article · Fri Feb 15 00:00:00 EST 2008 · Experimental Cell Research · OSTI ID:1816953

Prawitt, Janne; Niemeier, Andreas; Kassem, Moustapha; +2 more

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
low-density lipoprotein (LDL)
factor VIII (FVIII)
molecular chaperone
protein expression
protein folding
LDL-receptor related protein-associated protein (RAP)

Title: Molecular chaperone RAP interacts with LRP1 in a dynamic bivalent mode and enhances folding of ligand-binding regions of other LDLR family receptors

Citation Formats

References (63)

Similar Records

Related Subjects