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Lytje K, Pedersen JS. Validation of electron-microscopy maps using solution small-angle X-ray scattering. Acta Crystallogr D Struct Biol 2024; 80:493-505. [PMID: 38935344 PMCID: PMC11220840 DOI: 10.1107/s2059798324005497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 06/09/2024] [Indexed: 06/28/2024] Open
Abstract
The determination of the atomic resolution structure of biomacromolecules is essential for understanding details of their function. Traditionally, such a structure determination has been performed with crystallographic or nuclear resonance methods, but during the last decade, cryogenic transmission electron microscopy (cryo-TEM) has become an equally important tool. As the blotting and flash-freezing of the samples can induce conformational changes, external validation tools are required to ensure that the vitrified samples are representative of the solution. Although many validation tools have already been developed, most of them rely on fully resolved atomic models, which prevents early screening of the cryo-TEM maps. Here, a novel and automated method for performing such a validation utilizing small-angle X-ray scattering measurements, publicly available through the new software package AUSAXS, is introduced and implemented. The method has been tested on both simulated and experimental data, where it was shown to work remarkably well as a validation tool. The method provides a dummy atomic model derived from the EM map which best represents the solution structure.
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Affiliation(s)
- Kristian Lytje
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO)Aarhus UniversityGustav Wieds Vej 148000AarhusDenmark
| | - Jan Skov Pedersen
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO)Aarhus UniversityGustav Wieds Vej 148000AarhusDenmark
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2
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Jourdi G, Boukhatem I, Barcelona PF, Fleury S, Welman M, Saragovi HU, Pasquali S, Lordkipanidzé M. Alpha-2-macroglobulin prevents platelet aggregation induced by brain-derived neurotrophic factor. Biochem Pharmacol 2023; 215:115701. [PMID: 37487878 DOI: 10.1016/j.bcp.2023.115701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 07/07/2023] [Accepted: 07/21/2023] [Indexed: 07/26/2023]
Abstract
The brain-derived neurotrophic factor (BDNF) has been recently shown to have activating effects in isolated platelets. However, BDNF circulates in plasma and a mechanism to preclude constant activation of platelets appears necessary. Hence, we investigated the mechanism regulating BDNF bioavailability in blood. Protein-protein interactions were predicted by molecular docking and validated through immunoprecipitation. Platelet aggregation was assessed using light transmission aggregometry with washed platelets in response to classical agonists or BDNF, in the absence or presence of alpha-2-macroglobulin (α2M), and in platelet-rich plasma. BDNF signaling was assessed with phospho-blots. As little as 25% autologous plasma was sufficient to completely abolish platelet aggregation in response to BDNF. Docking predicted two forms of BDNF binding to native or activated α2M, in parallel and perpendicular arrangements, and the model suggested that the BDNF-α2M complex cannot bind to the high-affinity BDNF receptor, tropomyosin receptor kinase B (TrkB). Experimentally, native and activated α2M formed stable complexes with BDNF preventing BDNF-induced TrkB activation and signal transduction. Both native and activated α2M inhibited BDNF induced-platelet aggregation in a concentration-dependent manner with comparable half-maximal inhibitory concentrations (IC50≈ 125-150 nM). Our study implicates α2M as a physiological regulator of BDNF bioavailability, and as an inhibitor of BDNF-induced platelet activation in blood.
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Affiliation(s)
- Georges Jourdi
- Research Center, Montreal Heart Institute, Montreal, QC H1T 1C8, Canada; Faculty of Pharmacy, Université de Montréal, Montreal, QC H3T 1J4, Canada; Université Paris Cité, INSERM, Innovative Therapies in Haemostasis, F-75006 Paris, France; Service d'Hématologie Biologique, AP-HP, Hôpital Lariboisière, F-75010 Paris, France
| | - Imane Boukhatem
- Research Center, Montreal Heart Institute, Montreal, QC H1T 1C8, Canada; Faculty of Pharmacy, Université de Montréal, Montreal, QC H3T 1J4, Canada
| | - Pablo F Barcelona
- Departamento de Bioquímica Clínica, Centro de Investigaciones en Bioquímica Clínica e, Inmunología (CIBICI-CONICET), Universidad Nacional de Córdoba, Córdoba 5016, Argentina
| | - Samuel Fleury
- Research Center, Montreal Heart Institute, Montreal, QC H1T 1C8, Canada; Faculty of Pharmacy, Université de Montréal, Montreal, QC H3T 1J4, Canada
| | - Melanie Welman
- Research Center, Montreal Heart Institute, Montreal, QC H1T 1C8, Canada
| | - H Uri Saragovi
- Lady Davis Institute-Jewish General Hospital, Montreal, QC H3T 1E2, Canada; Department of Pharmacology and Therapeutics, McGill University, Montreal, QC H3A 0G4, Canada
| | - Samuela Pasquali
- Université Paris Cité, CNRS UMR 8038, Laboratoire Cibles Thérapeutiques et Conception de Médicaments, F-75006 Paris, France; Université Paris Cité, CNRS UMR 8251, Laboratoire Biologie Fonctionnelle et Adaptative, F-75006 Paris, France
| | - Marie Lordkipanidzé
- Research Center, Montreal Heart Institute, Montreal, QC H1T 1C8, Canada; Faculty of Pharmacy, Université de Montréal, Montreal, QC H3T 1J4, Canada.
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Tomihari A, Kiyota M, Matsuura A, Itakura E. Alpha 2-macroglobulin acts as a clearance factor in the lysosomal degradation of extracellular misfolded proteins. Sci Rep 2023; 13:4680. [PMID: 36977730 PMCID: PMC10050189 DOI: 10.1038/s41598-023-31104-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 03/06/2023] [Indexed: 03/30/2023] Open
Abstract
Proteostasis regulates protein folding and degradation; its maintenance is essential for resistance to stress and aging. The loss of proteostasis is associated with many age-related diseases. Within the cell, molecular chaperones facilitate the refolding of misfolded proteins into their bioactive forms, thus preventing undesirable interactions and aggregation. Although the mechanisms of intracellular protein degradation pathways for intracellular misfolded proteins have been extensively studied, the protein degradation pathway for extracellular proteins remain poorly understood. In this study, we identified several misfolded proteins that are substrates for alpha 2-macroglobulin (α2M), an extracellular chaperone. We also established a lysosomal internalization assay for α2M, which revealed that α2M mediates the lysosomal degradation of extracellular misfolded proteins. Comparative analyses of α2M and clusterin, another extracellular chaperone, indicated that α2M preferentially targets aggregation-prone proteins. Thus, we present the degradation pathway of α2M, which interacts with aggregation-prone proteins for lysosomal degradation via selective internalization.
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Affiliation(s)
- Ayaka Tomihari
- Department of Biology, Graduate School of Science and Engineering, Chiba University, Inage-Ku, Chiba, 263-8522, Japan
| | - Mako Kiyota
- Department of Biology, Graduate School of Science and Engineering, Chiba University, Inage-Ku, Chiba, 263-8522, Japan
| | - Akira Matsuura
- Department of Biology, Graduate School of Science, Chiba University, Inage-Ku, Chiba, 263-8522, Japan
| | - Eisuke Itakura
- Department of Biology, Graduate School of Science, Chiba University, Inage-Ku, Chiba, 263-8522, Japan.
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Mendes SR, Gomis-Rüth FX, Goulas T. Frozen fresh blood plasma preserves the functionality of native human α 2-macroglobulin. Sci Rep 2023; 13:4579. [PMID: 36941303 PMCID: PMC10027685 DOI: 10.1038/s41598-023-31800-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 03/17/2023] [Indexed: 03/23/2023] Open
Abstract
Human α2-macroglobulin (hα2M) is a large homotetrameric protein involved in the broad inhibition of endopeptidases. Following cleavage within a bait region, hα2M undergoes stepwise transitions from its native, expanded, highly flexible, active conformation to an induced, compact, triggered conformation. As a consequence, the peptidase is entrapped by an irreversible Venus flytrap mechanism. Given the importance of hα2M, biochemical studies galore over more than seven decades have attempted to ascertain its role, typically using authentic hα2M purified from frozen and non-frozen fresh blood plasma, and even outdated plasma. However, hα2M is sensitive once isolated and purified, and becomes heterogeneous during storage and/or freezing, raising concerns about the functional competence of frozen plasma-derived hα2M. We therefore used a combination of native and sodium dodecylsulfate polyacrylamide gel electrophoresis, affinity and ion-exchange chromatography, multi-angle laser light scattering after size-exclusion chromatography, free cysteine quantification, and peptidase inhibition assays with endopeptidases of two catalytic classes and three protein substrates, to characterize the biochemical and biophysical properties of hα2M purified ad hoc either from fresh plasma or frozen fresh plasma after thawing. We found no differences in the molecular or functional properties of the preparations, indicating that protective components in plasma maintain native hα2M in a functionally competent state despite freezing.
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Affiliation(s)
- Soraia R Mendes
- Proteolysis Lab, Molecular Biology Institute of Barcelona (CSIC), Barcelona Science Park, c/Baldiri Reixac 15-21, 08028, Barcelona, Catalonia, Spain
| | - F Xavier Gomis-Rüth
- Proteolysis Lab, Molecular Biology Institute of Barcelona (CSIC), Barcelona Science Park, c/Baldiri Reixac 15-21, 08028, Barcelona, Catalonia, Spain.
| | - Theodoros Goulas
- Department of Food Science and Nutrition, School of Agricultural Sciences, University of Thessaly, 43100, Karditsa, Greece.
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Gomis-Rüth FX, Stöcker W. Structural and evolutionary insights into astacin metallopeptidases. Front Mol Biosci 2023; 9:1080836. [PMID: 36685277 PMCID: PMC9848320 DOI: 10.3389/fmolb.2022.1080836] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 11/30/2022] [Indexed: 01/05/2023] Open
Abstract
The astacins are a family of metallopeptidases (MPs) that has been extensively described from animals. They are multidomain extracellular proteins, which have a conserved core architecture encompassing a signal peptide for secretion, a prodomain or prosegment and a zinc-dependent catalytic domain (CD). This constellation is found in the archetypal name-giving digestive enzyme astacin from the European crayfish Astacus astacus. Astacin catalytic domains span ∼200 residues and consist of two subdomains that flank an extended active-site cleft. They share several structural elements including a long zinc-binding consensus sequence (HEXXHXXGXXH) immediately followed by an EXXRXDRD motif, which features a family-specific glutamate. In addition, a downstream SIMHY-motif encompasses a "Met-turn" methionine and a zinc-binding tyrosine. The overall architecture and some structural features of astacin catalytic domains match those of other more distantly related MPs, which together constitute the metzincin clan of metallopeptidases. We further analysed the structures of PRO-, MAM, TRAF, CUB and EGF-like domains, and described their essential molecular determinants. In addition, we investigated the distribution of astacins across kingdoms and their phylogenetic origin. Through extensive sequence searches we found astacin CDs in > 25,000 sequences down the tree of life from humans beyond Metazoa, including Choanoflagellata, Filasterea and Ichtyosporea. We also found < 400 sequences scattered across non-holozoan eukaryotes including some fungi and one virus, as well as in selected taxa of archaea and bacteria that are pathogens or colonizers of animal hosts, but not in plants. Overall, we propose that astacins originate in the root of Holozoa consistent with Darwinian descent and that the latter genes might be the result of horizontal gene transfer from holozoan donors.
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Affiliation(s)
- F. Xavier Gomis-Rüth
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona (IBMB), Higher Scientific Research Council (CSIC), Barcelona, Catalonia, Spain,*Correspondence: F. Xavier Gomis-Rüth, ; Walter Stöcker,
| | - Walter Stöcker
- Institute of Molecular Physiology (IMP), Johannes Gutenberg-University Mainz (JGU), Mainz, Germany,*Correspondence: F. Xavier Gomis-Rüth, ; Walter Stöcker,
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Recent cryogenic electron microscopy structures of human A2M may not be representative of the native protein. Proc Natl Acad Sci U S A 2022; 119:e2210218119. [PMID: 35972981 PMCID: PMC9477409 DOI: 10.1073/pnas.2210218119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Reply to Harwood et al.: Alternative functional conformations of native human α 2-macroglobulin. Proc Natl Acad Sci U S A 2022; 119:e2211048119. [PMID: 35972982 PMCID: PMC9477416 DOI: 10.1073/pnas.2211048119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Huang X, Wang Y, Yu C, Zhang H, Ru Q, Li X, Song K, Zhou M, Zhu P. Cryo-EM structures reveal the dynamic transformation of human alpha-2-macroglobulin working as a protease inhibitor. SCIENCE CHINA. LIFE SCIENCES 2022; 65:2491-2504. [PMID: 35781771 DOI: 10.1007/s11427-022-2139-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 06/06/2022] [Indexed: 10/17/2022]
Abstract
Human alpha-2-macroglobulin is a well-known inhibitor of a broad spectrum of proteases and plays important roles in immunity, inflammation, and infections. Here, we report the cryo-EM structures of human alpha-2-macroglobulin in its native state, induced state transformed by its authentic substrate, human trypsin, and serial intermediate states between the native and fully induced states. These structures exhibit distinct conformations, which reveal the dynamic transformation of alpha-2-macro-globulin that acts as a protease inhibitor. The results shed light on the molecular mechanism of alpha-2-macroglobulin in entrapping substrates.
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Affiliation(s)
- Xiaoxing Huang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Youwang Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Cong Yu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hui Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiang Ru
- The Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College (PUMC), Beijing, 100193, China
| | - Xinxin Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kai Song
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Min Zhou
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ping Zhu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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