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Beenken A, Cerutti G, Brasch J, Guo Y, Sheng Z, Erdjument-Bromage H, Aziz Z, Robbins-Juarez SY, Chavez EY, Ahlsen G, Katsamba PS, Neubert TA, Fitzpatrick AWP, Barasch J, Shapiro L. Structures of LRP2 reveal a molecular machine for endocytosis. Cell 2023; 186:821-836.e13. [PMID: 36750096 PMCID: PMC9993842 DOI: 10.1016/j.cell.2023.01.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/29/2022] [Accepted: 01/10/2023] [Indexed: 02/08/2023]
Abstract
The low-density lipoprotein (LDL) receptor-related protein 2 (LRP2 or megalin) is representative of the phylogenetically conserved subfamily of giant LDL receptor-related proteins, which function in endocytosis and are implicated in diseases of the kidney and brain. Here, we report high-resolution cryoelectron microscopy structures of LRP2 isolated from mouse kidney, at extracellular and endosomal pH. The structures reveal LRP2 to be a molecular machine that adopts a conformation for ligand binding at the cell surface and for ligand shedding in the endosome. LRP2 forms a homodimer, the conformational transformation of which is governed by pH-sensitive sites at both homodimer and intra-protomer interfaces. A subset of LRP2 deleterious missense variants in humans appears to impair homodimer assembly. These observations lay the foundation for further understanding the function and mechanism of LDL receptors and implicate homodimerization as a conserved feature of the LRP receptor subfamily.
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Affiliation(s)
- Andrew Beenken
- Division of Nephrology, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Gabriele Cerutti
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Julia Brasch
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Yicheng Guo
- Aaron Diamond AIDS Research Center, Columbia University, New York, NY 10032, USA
| | - Zizhang Sheng
- Aaron Diamond AIDS Research Center, Columbia University, New York, NY 10032, USA
| | - Hediye Erdjument-Bromage
- Department of Cell Biology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Zainab Aziz
- Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | | | - Estefania Y Chavez
- Department of Pediatrics, Columbia University College of Physicians and Surgeons, New York, NY 10032, USA
| | - Goran Ahlsen
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Phinikoula S Katsamba
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Thomas A Neubert
- Department of Cell Biology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Anthony W P Fitzpatrick
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA; Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032, USA.
| | - Jonathan Barasch
- Division of Nephrology, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA; Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA; Columbia University George M. O'Brien Urology Center, New York, NY 10032, USA.
| | - Lawrence Shapiro
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Aaron Diamond AIDS Research Center, Columbia University, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA.
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Abstract
Vesicular stomatitis virus (VSV) is an oncolytic rhabdovirus and its glycoprotein G is widely used to pseudotype other viruses for gene therapy. Low-density lipoprotein receptor (LDL-R) serves as a major entry receptor for VSV. Here we report two crystal structures of VSV G in complex with two distinct cysteine-rich domains (CR2 and CR3) of LDL-R, showing that their binding sites on G are identical. We identify two basic residues on G, which are essential for its interaction with CR2 and CR3. Mutating these residues abolishes VSV infectivity even though VSV can use alternative receptors, indicating that all VSV receptors are members of the LDL-R family. Collectively, our data suggest that VSV G has specifically evolved to interact with receptor CR domains. These structural insights into the interaction between VSV G and host cell receptors provide a basis for the design of recombinant viruses with an altered tropism.
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Molecular mapping of α-thrombin (αT)/β2-glycoprotein I (β2GpI) interaction reveals how β2GpI affects αT functions. Biochem J 2016; 473:4629-4650. [PMID: 27760842 DOI: 10.1042/bcj20160603] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 09/07/2016] [Accepted: 10/14/2016] [Indexed: 01/15/2023]
Abstract
β2-Glycoprotein I (β2GpI) is the major autoantigen in the antiphospholipid syndrome, a thrombotic autoimmune disease. Nonetheless, the physiological role of β2GpI is still unclear. In a recent work, we have shown that β2GpI selectively inhibits the procoagulant functions of human α-thrombin (αT; i.e. prolongs fibrin clotting time, tc, and inhibits αT-induced platelet aggregation) without affecting the unique anticoagulant activity of the protease, i.e. the proteolytic generation of the anticoagulant protein C (PC) from the PC zymogen, which interacts with αT exclusively at the protease catalytic site. Here, we used several different biochemical/biophysical techniques and molecular probes for mapping the binding sites in the αT-β2GpI complex. Our results indicate that αT exploits the highly electropositive exosite-II, which is also responsible for anchoring αT on the platelet GpIbα (platelet receptor glycoprotein Ibα) receptor, for binding to a continuous negative region on β2GpI structure, spanning domain IV and (part of) domain V, whereas the protease active site and exosite-I (i.e. the fibrinogen-binding site) remain accessible for substrate/ligand binding. Furthermore, we provided evidence that the apparent increase in tc, previously observed with β2GpI, is more likely caused by alteration in the ensuing fibrin structure rather than by the inhibition of fibrinogen hydrolysis. Finally, we produced a theoretical docking model of αT-β2GpI interaction, which was in agreement with the experimental results. Altogether, these findings help to understand how β2GpI affects αT interactions and suggest that β2GpI may function as a scavenger of αT for binding to the GpIbα receptor, thus impairing platelet aggregation while enabling normal cleavage of fibrinogen and PC.
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Structural basis of transcobalamin recognition by human CD320 receptor. Nat Commun 2016; 7:12100. [PMID: 27411955 PMCID: PMC4947154 DOI: 10.1038/ncomms12100] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 05/27/2016] [Indexed: 12/20/2022] Open
Abstract
Cellular uptake of vitamin B12 (cobalamin) requires capture of transcobalamin (TC) from the plasma by CD320, a ubiquitous cell surface receptor of the LDLR family. Here we present the crystal structure of human holo-TC in complex with the extracellular domain of CD320, visualizing the structural basis of the TC-CD320 interaction. The observed interaction chemistry can rationalize the high affinity of CD320 for TC and lack of haptocorrin binding. The in vitro affinity and complex stability of TC-CD320 were quantitated using a solid-phase binding assay and thermostability analysis. Stable complexes with TC were also observed for the disease-causing CD320ΔE88 mutant and for the isolated LDLR-A2 domain. We also determined the structure of the TC-CD320ΔE88 complex, which revealed only minor changes compared with the wild-type complex. Finally, we demonstrate significantly reduced in vitro affinity of TC for CD320 at low pH, recapitulating the proposed ligand release during the endocytic pathway. Cellular uptake of vitamin B12 (cobalamin) requires the binding of holo-transcobalamin (TC) from plasma by CD320. Here, the authors report the structure of a complex between CD320 and TC loaded with cyanocobalamin, alongside additional functional analysis.
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5
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Stefas I, Tigrett S, Dubois G, Kaiser M, Lucarz E, Gobby D, Bray D, Ellerbrok H, Zarski JP, Veas F. Interactions between Hepatitis C Virus and the Human Apolipoprotein H Acute Phase Protein: A Tool for a Sensitive Detection of the Virus. PLoS One 2015; 10:e0140900. [PMID: 26502286 PMCID: PMC4621047 DOI: 10.1371/journal.pone.0140900] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 10/01/2015] [Indexed: 12/20/2022] Open
Abstract
The Hepatitis C virus (HCV) infection exhibits a high global prevalence frequently associated with hepatocellular carcinoma, taking years to develop. Despite the standardization of highly sensitive HCV quantitative RT-PCR (qRT-PCR) detection methods, false-negative diagnoses may be generated with current methods, mainly due to the presence of PCR inhibitors and/or low viral loads in the patient’s sample. These false-negative diagnoses impact both public health systems, in developing countries, and an in lesser extent, in developed countries, including both the risk of virus transmission during organ transplantation and/or blood transfusion and the quality of the antiviral treatment monitoring. To adopt an appropriate therapeutic strategy to improve the patient’s prognosis, it is urgent to increase the HCV detection sensitivity. Based upon previous studies on HBV, we worked on the capacity of the scavenger acute phase protein, Apolipoprotein H (ApoH) to interact with HCV. Using different approaches, including immunoassays, antibody-inhibition, oxidation, ultracentrifugation, electron microscopy and RT-PCR analyses, we demonstrated specific interactions between HCV particles and ApoH. Moreover, when using a two-step HCV detection process, including capture of HCV by ApoH-coated nanomagnetic beads and a home-made real-time HCV-RT-PCR, we confirmed the presence of HCV for all samples from a clinical collection of HCV-seropositive patients exhibiting an RT-PCR COBAS® TaqMan® HCV Test, v2.0 (COBAS)-positive result. In contrast, for HCV-seropositive patients with either low HCV-load as determined with COBAS or exhibiting HCV-negative COBAS results, the addition of the two-step ApoH-HCV-capture and HCV-detection process was able to increase the sensitivity of HCV detection or more interestingly, detect in a genotype sequence-independent manner, a high-proportion (44%) of HCV/RNA-positive among the COBAS HCV-negative patients. Thus, the immune interaction between ApoH and HCV could be used as a sample preparation tool to enrich and/or cleanse HCV patient’s samples to enhance the detection sensitivity of HCV and therefore significantly reduce the numbers of false-negative HCV diagnosis results.
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Affiliation(s)
- Ilias Stefas
- ApoH-Technologies, Faculté de Pharmacie, Université de Montpellier, Montpellier, France
| | - Sylvia Tigrett
- ApoH-Technologies, Faculté de Pharmacie, Université de Montpellier, Montpellier, France; Institut de Recherche pour le Développement, UMR-Ministère de la Défense 3, Laboratoire d'Immuno-Physiopathologie Moléculaire Comparée, Faculté de Pharmacie, Montpellier, France
| | - Grégor Dubois
- Institut de Recherche pour le Développement, UMR-Ministère de la Défense 3, Laboratoire d'Immuno-Physiopathologie Moléculaire Comparée, Faculté de Pharmacie, Montpellier, France
| | | | - Estelle Lucarz
- ApoH-Technologies, Faculté de Pharmacie, Université de Montpellier, Montpellier, France
| | - Delphine Gobby
- ApoH-Technologies, Faculté de Pharmacie, Université de Montpellier, Montpellier, France
| | - Dorothy Bray
- Immunoclin Corporation, Washington, DC, United States of America
| | - Heinz Ellerbrok
- Robert Koch-Institute, Centre for Biological Threats and Special Pathogens, Highly Pathogenic Viruses, Berlin, Germany
| | - Jean Pierre Zarski
- Clinique d'Hépato-gastroentérologie, Centre Hospitalier Universitaire de Grenoble, IAB, INSERM U823, Grenoble, France
| | - Francisco Veas
- Institut de Recherche pour le Développement, UMR-Ministère de la Défense 3, Laboratoire d'Immuno-Physiopathologie Moléculaire Comparée, Faculté de Pharmacie, Montpellier, France
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Mehmedbasic A, Christensen SK, Nilsson J, Rüetschi U, Gustafsen C, Poulsen ASA, Rasmussen RW, Fjorback AN, Larson G, Andersen OM. SorLA complement-type repeat domains protect the amyloid precursor protein against processing. J Biol Chem 2014; 290:3359-76. [PMID: 25525276 DOI: 10.1074/jbc.m114.619940] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
SorLA is a neuronal sorting receptor that is genetically associated with Alzheimer disease. SorLA interacts directly with the amyloid precursor protein (APP) and affects the processing of the precursor, leading to a decreased generation of the amyloid-β peptide. The SorLA complement-type repeat (CR) domains associate in vitro with APP, but the precise molecular determinants of SorLA·APP complex formation and the mechanisms responsible for the effect of binding on APP processing have not yet been elucidated. Here, we have generated protein expression constructs for SorLA devoid of the 11 CR-domains and for two SorLA mutants harboring substitutions of the fingerprint residues in the central CR-domains. We generated SH-SY5Y cell lines that stably express these SorLA variants to study the binding and processing of APP using co-immunoprecipitation and Western blotting/ELISAs, respectively. We found that the SorLA CR-cluster is essential for interaction with APP and that deletion of the CR-cluster abolishes the protection against APP processing. Mutation of identified fingerprint residues in the SorLA CR-domains leads to changes in the O-linked glycosylation of APP when expressed in SH-SY5Y cells. Our results provide novel information on the mechanisms behind the influence of SorLA activity on APP metabolism by controlling post-translational glycosylation in the Golgi, suggesting new strategies against amyloidogenesis in Alzheimer disease.
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Affiliation(s)
- Arnela Mehmedbasic
- From the Lundbeck Foundation Research Center MIND, Danish Research Institute of Translational Neuroscience Nordic-EMBL Partnership (DANDRITE), Department of Biomedicine, Aarhus University, Ole Worms Allé 3, DK-8000 AarhusC, Denmark and
| | - Sofie K Christensen
- From the Lundbeck Foundation Research Center MIND, Danish Research Institute of Translational Neuroscience Nordic-EMBL Partnership (DANDRITE), Department of Biomedicine, Aarhus University, Ole Worms Allé 3, DK-8000 AarhusC, Denmark and
| | - Jonas Nilsson
- the Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, University of Gothenburg, SE-413 45 Gothenburg, Sweden
| | - Ulla Rüetschi
- the Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, University of Gothenburg, SE-413 45 Gothenburg, Sweden
| | - Camilla Gustafsen
- From the Lundbeck Foundation Research Center MIND, Danish Research Institute of Translational Neuroscience Nordic-EMBL Partnership (DANDRITE), Department of Biomedicine, Aarhus University, Ole Worms Allé 3, DK-8000 AarhusC, Denmark and
| | - Annemarie Svane Aavild Poulsen
- From the Lundbeck Foundation Research Center MIND, Danish Research Institute of Translational Neuroscience Nordic-EMBL Partnership (DANDRITE), Department of Biomedicine, Aarhus University, Ole Worms Allé 3, DK-8000 AarhusC, Denmark and
| | - Rikke W Rasmussen
- From the Lundbeck Foundation Research Center MIND, Danish Research Institute of Translational Neuroscience Nordic-EMBL Partnership (DANDRITE), Department of Biomedicine, Aarhus University, Ole Worms Allé 3, DK-8000 AarhusC, Denmark and
| | - Anja N Fjorback
- From the Lundbeck Foundation Research Center MIND, Danish Research Institute of Translational Neuroscience Nordic-EMBL Partnership (DANDRITE), Department of Biomedicine, Aarhus University, Ole Worms Allé 3, DK-8000 AarhusC, Denmark and
| | - Göran Larson
- the Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, University of Gothenburg, SE-413 45 Gothenburg, Sweden
| | - Olav M Andersen
- From the Lundbeck Foundation Research Center MIND, Danish Research Institute of Translational Neuroscience Nordic-EMBL Partnership (DANDRITE), Department of Biomedicine, Aarhus University, Ole Worms Allé 3, DK-8000 AarhusC, Denmark and
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Kolyada A, Lee CJ, De Biasio A, Beglova N. A novel dimeric inhibitor targeting Beta2GPI in Beta2GPI/antibody complexes implicated in antiphospholipid syndrome. PLoS One 2010; 5:e15345. [PMID: 21179511 PMCID: PMC3002267 DOI: 10.1371/journal.pone.0015345] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2010] [Accepted: 11/10/2010] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND β2GPI is a major antigen for autoantibodies associated with antiphospholipid syndrome (APS), an autoimmune disease characterized by thrombosis and recurrent pregnancy loss. Only the dimeric form of β2GPI generated by anti-β2GPI antibodies is pathologically important, in contrast to monomeric β2GPI which is abundant in plasma. PRINCIPAL FINDINGS We created a dimeric inhibitor, A1-A1, to selectively target β2GPI in β2GPI/antibody complexes. To make this inhibitor, we isolated the first ligand-binding module from ApoER2 (A1) and connected two A1 modules with a flexible linker. A1-A1 interferes with two pathologically important interactions in APS, the binding of β2GPI/antibody complexes with anionic phospholipids and ApoER2. We compared the efficiency of A1-A1 to monomeric A1 for inhibition of the binding of β2GPI/antibody complexes to anionic phospholipids. We tested the inhibition of β2GPI present in human serum, β2GPI purified from human plasma and the individual domain V of β2GPI. We demonstrated that when β2GPI/antibody complexes are formed, A1-A1 is much more effective than A1 in inhibition of the binding of β2GPI to cardiolipin, regardless of the source of β2GPI. Similarly, A1-A1 strongly inhibits the binding of dimerized domain V of β2GPI to cardiolipin compared to the monomeric A1 inhibitor. In the absence of anti-β2GPI antibodies, both A1-A1 and A1 only weakly inhibit the binding of pathologically inactive monomeric β2GPI to cardiolipin. CONCLUSIONS Our results suggest that the approach of using a dimeric inhibitor to block β2GPI in the pathological multivalent β2GPI/antibody complexes holds significant promise. The novel inhibitor A1-A1 may be a starting point in the development of an effective therapeutic for antiphospholipid syndrome.
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Affiliation(s)
- Alexey Kolyada
- Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Chang-Jin Lee
- Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Alfredo De Biasio
- Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Natalia Beglova
- Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail:
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Yuriev E, Agostino M, Ramsland PA. Challenges and advances in computational docking: 2009 in review. J Mol Recognit 2010; 24:149-64. [DOI: 10.1002/jmr.1077] [Citation(s) in RCA: 223] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2010] [Revised: 07/20/2010] [Accepted: 07/21/2010] [Indexed: 12/12/2022]
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Mode of Interaction between β2GPI and Lipoprotein Receptors Suggests Mutually Exclusive Binding of β2GPI to the Receptors and Anionic Phospholipids. Structure 2010; 18:366-76. [DOI: 10.1016/j.str.2009.12.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2009] [Revised: 11/30/2009] [Accepted: 12/29/2009] [Indexed: 12/20/2022]
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