1
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Osman R, Bossu M, Dauvillée D, Spriet C, Liu C, Zeeman SC, D'Hulst C, Bompard C. LIKE EARLY STARVATION 1 interacts with amylopectin during starch biosynthesis. PLANT PHYSIOLOGY 2024; 195:1851-1865. [PMID: 38573555 DOI: 10.1093/plphys/kiae193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 03/08/2024] [Accepted: 03/13/2024] [Indexed: 04/05/2024]
Abstract
Starch is the major energy storage compound in plants. Both transient starch and long-lasting storage starch accumulate in the form of insoluble, partly crystalline granules. The structure of these granules is related to the structure of the branched polymer amylopectin: linear chains of glucose units organized in double helices that align to form semicrystalline lamellae, with branching points located in amorphous regions between them. EARLY STARVATION 1 (ESV1) and LIKE EARLY STARVATION 1 (LESV) proteins are involved in the maintenance of starch granule structure and in the phase transition of amylopectin, respectively, in Arabidopsis (Arabidopsis thaliana). These proteins contain a conserved tryptophan-rich C-terminal domain folded into an antiparallel β-sheet, likely responsible for binding of the proteins to starch, and different N-terminal domains whose structure and function are unknown. In this work, we combined biochemical and biophysical approaches to analyze the structures of LESV and ESV1 and their interactions with the different starch polyglucans. We determined that both proteins interact with amylopectin but not with amylose and that only LESV is capable of interacting with amylopectin during starch biosynthesis. While the C-terminal domain interacts with amylopectin in its semicrystalline form, the N-terminal domain of LESV undergoes induced conformational changes that are probably involved in its specific function of mediating glucan phase transition. These results clarify the specific mechanism of action of these 2 proteins in the biosynthesis of starch granules.
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Affiliation(s)
- Rayan Osman
- Université de Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Mélanie Bossu
- Université de Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - David Dauvillée
- Université de Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Corentin Spriet
- Université de Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
- University Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41-UAR 2014-PLBS, Lille F-59000, France
| | - Chun Liu
- Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092 Zurich
| | - Samuel C Zeeman
- Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092 Zurich
| | - Christophe D'Hulst
- Université de Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Coralie Bompard
- Université de Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
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2
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Hadži S, Živič Z, Kovačič M, Zavrtanik U, Haesaerts S, Charlier D, Plavec J, Volkov AN, Lah J, Loris R. Fuzzy recognition by the prokaryotic transcription factor HigA2 from Vibrio cholerae. Nat Commun 2024; 15:3105. [PMID: 38600130 PMCID: PMC11006873 DOI: 10.1038/s41467-024-47296-3] [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: 05/21/2023] [Accepted: 03/22/2024] [Indexed: 04/12/2024] Open
Abstract
Disordered protein sequences can exhibit different binding modes, ranging from well-ordered folding-upon-binding to highly dynamic fuzzy binding. The primary function of the intrinsically disordered region of the antitoxin HigA2 from Vibrio cholerae is to neutralize HigB2 toxin through ultra-high-affinity folding-upon-binding interaction. Here, we show that the same intrinsically disordered region can also mediate fuzzy interactions with its operator DNA and, through interplay with the folded helix-turn-helix domain, regulates transcription from the higBA2 operon. NMR, SAXS, ITC and in vivo experiments converge towards a consistent picture where a specific set of residues in the intrinsically disordered region mediate electrostatic and hydrophobic interactions while "hovering" over the DNA operator. Sensitivity of the intrinsically disordered region to scrambling the sequence, position-specific contacts and absence of redundant, multivalent interactions, point towards a more specific type of fuzzy binding. Our work demonstrates how a bacterial regulator achieves dual functionality by utilizing two distinct interaction modes within the same disordered sequence.
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Affiliation(s)
- San Hadži
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
- Centre for Structural Biology, VIB, Pleinlaan 2, 1050, Brussels, Belgium
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Zala Živič
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Matic Kovačič
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova, 19, 1000, Ljubljana, Slovenia
| | - Uroš Zavrtanik
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Sarah Haesaerts
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
- Centre for Structural Biology, VIB, Pleinlaan 2, 1050, Brussels, Belgium
| | - Daniel Charlier
- Research group of Microbiology, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Janez Plavec
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova, 19, 1000, Ljubljana, Slovenia
| | - Alexander N Volkov
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
- Centre for Structural Biology, VIB, Pleinlaan 2, 1050, Brussels, Belgium
- Jean Jeener NMR Centre, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Jurij Lah
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000, Ljubljana, Slovenia.
| | - Remy Loris
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium.
- Centre for Structural Biology, VIB, Pleinlaan 2, 1050, Brussels, Belgium.
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3
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Augis L, Nerbø Reiten I, Førde JL, Casas-Solvas JM, Sizun C, Bizien T, Rajkovic I, Larquet E, Michelet A, Collot M, Lesieur S, Herfindal L, Legrand FX. Development of nanoparticles based on amphiphilic cyclodextrins for the delivery of active substances. Int J Pharm 2024; 651:123723. [PMID: 38110013 DOI: 10.1016/j.ijpharm.2023.123723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 12/15/2023] [Accepted: 12/16/2023] [Indexed: 12/20/2023]
Abstract
Although amphiphilic cyclodextrin derivatives (ACDs) serve as valuable building blocks for nanomedicine formulations, their widespread production still encounters various challenges, limiting large-scale manufacturing. This work focuses on a robust alternative pathway using mineral base catalysis to transesterify β-cyclodextrin with long-chain vinyl esters, yielding ACD with modular and controlled hydrocarbon chain grafting. ACDs with a wide range of degrees of substitution (DS) were reliably synthesized, as indicated by extensive physicochemical characterization, including MALDI-TOF mass spectrometry. The influence of various factors, including the type of catalyst and the length of the hydrocarbon moiety of the vinyl ester, was studied in detail. ACDs were assessed for their ability to form colloidal suspensions by nanoprecipitation, with or without PEGylated phospholipid. Small-angle X-ray scattering and cryo-electron microscopy revealed the formation of nanoparticles with distinct ultrastructures depending on the DS: an onion-like structure for low and very high DS, and reversed hexagonal organization for DS between 4.5 and 6.1. We confirmed the furtivity of the PEGylated versions of the nanoparticles through complement activation experiments and that they were well tolerated in-vivo on a zebrafish larvae model after intravenous injection. Furthermore, a biodistribution experiment showed that the nanoparticles left the bloodstream within 10 h after injection and were phagocytosed by macrophages.
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Affiliation(s)
- Luc Augis
- Université Paris-Saclay, CNRS, Institut Galien Paris-Saclay, 91400 Orsay, France
| | - Ingeborg Nerbø Reiten
- Centre for Pharmacy, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Jan-Lukas Førde
- Centre for Pharmacy, Department of Clinical Science, University of Bergen, Bergen, Norway; Department of Internal Medicine, Haukeland University Hospital, 5021 Bergen, Norway
| | - Juan M Casas-Solvas
- Department of Chemistry and Physics, University of Almería, Ctra de Sacramento s/n, E-04120 Almería, Spain
| | - Christina Sizun
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 91198 Gif-sur-Yvette, France
| | - Thomas Bizien
- Université Paris-Saclay, Synchrotron Soleil, 91190 Saint-Aubin, France
| | - Ivan Rajkovic
- SSRL, SLAC National Accelerator Lab, Menlo Park, CA, USA
| | - Eric Larquet
- Laboratoire de Physique de la Matière Condensée (PMC), CNRS, Ecole Polytechnique, Institut Polytechnique de Paris, 91120 Palaiseau, France
| | - Alexandre Michelet
- Applications Development Lab France, PerkinElmer, Villebon-sur-Yvette, France
| | - Mayeul Collot
- Faculté de Pharmacie, Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Illkirch, France
| | - Sylviane Lesieur
- Université Paris-Saclay, CNRS, Institut Galien Paris-Saclay, 91400 Orsay, France
| | - Lars Herfindal
- Centre for Pharmacy, Department of Clinical Science, University of Bergen, Bergen, Norway
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4
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Hutin S, Tully MD, Brennich M. Small-Angle X-Ray Scattering for Macromolecular Complexes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 3234:163-172. [PMID: 38507206 DOI: 10.1007/978-3-031-52193-5_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
Small angle X-ray scattering (SAXS) is a versatile technique that can provide unique insights in the solution structure of macromolecules and their complexes, covering the size range from small peptides to complete viral assemblies. Technological and conceptual advances in the last two decades have tremendously improved the accessibility of the technique and transformed it into an indispensable tool for structural biology. In this chapter we introduce and discuss several approaches to collecting SAXS data on macromolecular complexes, including several approaches to online chromatography. We include practical advice on experimental design and point out common pitfalls of the technique.
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Affiliation(s)
- Stephanie Hutin
- Structural Biology Group, European Synchrotron Radiation Facility, Grenoble, Grenoble, France
| | - Mark D Tully
- Structural Biology Group, European Synchrotron Radiation Facility, Grenoble, Grenoble, France
| | - Martha Brennich
- European Molecular Biology Laboratory, Grenoble, Grenoble, France.
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5
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Raviv U, Asor R, Shemesh A, Ginsburg A, Ben-Nun T, Schilt Y, Levartovsky Y, Ringel I. Insight into structural biophysics from solution X-ray scattering. J Struct Biol 2023; 215:108029. [PMID: 37741561 DOI: 10.1016/j.jsb.2023.108029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 08/09/2023] [Accepted: 09/18/2023] [Indexed: 09/25/2023]
Abstract
The current challenges of structural biophysics include determining the structure of large self-assembled complexes, resolving the structure of ensembles of complex structures and their mass fraction, and unraveling the dynamic pathways and mechanisms leading to the formation of complex structures from their subunits. Modern synchrotron solution X-ray scattering data enable simultaneous high-spatial and high-temporal structural data required to address the current challenges of structural biophysics. These data are complementary to crystallography, NMR, and cryo-TEM data. However, the analysis of solution scattering data is challenging; hence many different analysis tools, listed in the SAS Portal (http://smallangle.org/), were developed. In this review, we start by briefly summarizing classical X-ray scattering analyses providing insight into fundamental structural and interaction parameters. We then describe recent developments, integrating simulations, theory, and advanced X-ray scattering modeling, providing unique insights into the structure, energetics, and dynamics of self-assembled complexes. The structural information is essential for understanding the underlying physical chemistry principles leading to self-assembled supramolecular architectures and computational structural refinement.
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Affiliation(s)
- Uri Raviv
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel; The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel.
| | - Roi Asor
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Asaf Shemesh
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Avi Ginsburg
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Tal Ben-Nun
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Yaelle Schilt
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Yehonatan Levartovsky
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Israel Ringel
- Institute for Drug Research, School of Pharmacy, The Hebrew University of Jerusalem, 9112102 Jerusalem, Israel
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6
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Blanchet CE, Round A, Mertens HDT, Ayyer K, Graewert M, Awel S, Franke D, Dörner K, Bajt S, Bean R, Custódio TF, de Wijn R, Juncheng E, Henkel A, Gruzinov A, Jeffries CM, Kim Y, Kirkwood H, Kloos M, Knoška J, Koliyadu J, Letrun R, Löw C, Makroczyova J, Mall A, Meijers R, Pena Murillo GE, Oberthür D, Round E, Seuring C, Sikorski M, Vagovic P, Valerio J, Wollweber T, Zhuang Y, Schulz J, Haas H, Chapman HN, Mancuso AP, Svergun D. Form factor determination of biological molecules with X-ray free electron laser small-angle scattering (XFEL-SAS). Commun Biol 2023; 6:1057. [PMID: 37853181 PMCID: PMC10585004 DOI: 10.1038/s42003-023-05416-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 10/04/2023] [Indexed: 10/20/2023] Open
Abstract
Free-electron lasers (FEL) are revolutionizing X-ray-based structural biology methods. While protein crystallography is already routinely performed at FELs, Small Angle X-ray Scattering (SAXS) studies of biological macromolecules are not as prevalent. SAXS allows the study of the shape and overall structure of proteins and nucleic acids in solution, in a quasi-native environment. In solution, chemical and biophysical parameters that have an influence on the structure and dynamics of molecules can be varied and their effect on conformational changes can be monitored in time-resolved XFEL and SAXS experiments. We report here the collection of scattering form factors of proteins in solution using FEL X-rays. The form factors correspond to the scattering signal of the protein ensemble alone; the scattering contributions from the solvent and the instrument are separately measured and accurately subtracted. The experiment was done using a liquid jet for sample delivery. These results pave the way for time-resolved studies and measurements from dilute samples, capitalizing on the intense and short FEL X-ray pulses.
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Affiliation(s)
- Clement E Blanchet
- European Molecular Biology Laboratory EMBL, Hamburg Site, c/o DESY Notkestrasse 85, 22603, Hamburg, Germany.
| | - Adam Round
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany.
| | - Haydyn D T Mertens
- European Molecular Biology Laboratory EMBL, Hamburg Site, c/o DESY Notkestrasse 85, 22603, Hamburg, Germany
| | - Kartik Ayyer
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Melissa Graewert
- European Molecular Biology Laboratory EMBL, Hamburg Site, c/o DESY Notkestrasse 85, 22603, Hamburg, Germany
| | - Salah Awel
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Daniel Franke
- European Molecular Biology Laboratory EMBL, Hamburg Site, c/o DESY Notkestrasse 85, 22603, Hamburg, Germany
- BIOSAXS GmbH, Notkestr. 85, 22607, Hamburg, Germany
| | - Katerina Dörner
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Saša Bajt
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Richard Bean
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Tânia F Custódio
- European Molecular Biology Laboratory EMBL, Hamburg Site, c/o DESY Notkestrasse 85, 22603, Hamburg, Germany
- Centre for Structural Systems Biology (CSSB), Notkestrasse 85, D-22607, Hamburg, Germany
| | - Raphael de Wijn
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - E Juncheng
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Alessandra Henkel
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Andrey Gruzinov
- European Molecular Biology Laboratory EMBL, Hamburg Site, c/o DESY Notkestrasse 85, 22603, Hamburg, Germany
| | - Cy M Jeffries
- European Molecular Biology Laboratory EMBL, Hamburg Site, c/o DESY Notkestrasse 85, 22603, Hamburg, Germany
| | - Yoonhee Kim
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Henry Kirkwood
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Marco Kloos
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Juraj Knoška
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | | | - Romain Letrun
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Christian Löw
- European Molecular Biology Laboratory EMBL, Hamburg Site, c/o DESY Notkestrasse 85, 22603, Hamburg, Germany
- Centre for Structural Systems Biology (CSSB), Notkestrasse 85, D-22607, Hamburg, Germany
| | | | - Abhishek Mall
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Rob Meijers
- Institute for Protein Innovation (IPI), 4 Blackfan Circle, Boston, MA, 02115, USA
| | - Gisel Esperanza Pena Murillo
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Dominik Oberthür
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Ekaterina Round
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Carolin Seuring
- Centre for Structural Systems Biology (CSSB), Notkestrasse 85, D-22607, Hamburg, Germany
- Department of Chemistry, University of Hamburg, Hamburg, Germany
- Leibniz Institute of Virology, Hamburg, Germany
| | - Marcin Sikorski
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Patrik Vagovic
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Joana Valerio
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Tamme Wollweber
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Yulong Zhuang
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Joachim Schulz
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | | | - Henry N Chapman
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Adrian P Mancuso
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, 3086, Australia
| | - Dmitri Svergun
- European Molecular Biology Laboratory EMBL, Hamburg Site, c/o DESY Notkestrasse 85, 22603, Hamburg, Germany.
- BIOSAXS GmbH, Notkestr. 85, 22607, Hamburg, Germany.
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7
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Bolinsson H, Söderberg C, Herranz-Trillo F, Wahlgren M, Nilsson L. Realizing the AF4-UV-SAXS on-line coupling on protein and antibodies using high flux synchrotron radiation at the CoSAXS beamline, MAX IV. Anal Bioanal Chem 2023; 415:6237-6246. [PMID: 37572213 PMCID: PMC10558385 DOI: 10.1007/s00216-023-04900-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/31/2023] [Accepted: 08/02/2023] [Indexed: 08/14/2023]
Abstract
In this paper, we demonstrate the coupling of synchrotron small angle X-ray scattering (SAXS) to asymmetrical flow-field flow fractionation (AF4) for protein characterization. To the best of our knowledge, this is the first time AF4 is successfully coupled to a synchrotron for on-line measurements on proteins. This coupling has potentially high impact, as it opens the possibility to characterize individual constituents of sensitive and/or complex samples, not suited for separation using other techniques, and for low electron density samples where high X-ray flux is required, e.g., biomolecules and biologics. AF4 fractionates complex samples in native or close to native environment, with low shear forces and system surface area. Many orders of magnitude in size can be fractionated in one measurement, without having to reconfigure the experimental setup. We report AF4 fractionations with correlated UV and statistically adequate SAXS data of bovine serum albumin and a monoclonal antibody and evaluate SAXS data recorded for the two protein systems.
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Affiliation(s)
- Hans Bolinsson
- Department of Food Technology, Engineering and Nutrition, Lund University, Lund, Sweden.
| | - Christopher Söderberg
- RISE Research Institutes of Sweden, Division Bioeconomy and Health, Chemical Process and Pharmaceutical Development, Lund, Sweden
| | | | - Marie Wahlgren
- Department of Food Technology, Engineering and Nutrition, Lund University, Lund, Sweden
| | - Lars Nilsson
- Department of Food Technology, Engineering and Nutrition, Lund University, Lund, Sweden
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8
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Makraki E, Miliara S, Pagkalos M, Kokkinidis M, Mylonas E, Fadouloglou VE. Probing the conformational changes of in vivo overexpressed cell cycle regulator 6S ncRNA. Front Mol Biosci 2023; 10:1219668. [PMID: 37555016 PMCID: PMC10406553 DOI: 10.3389/fmolb.2023.1219668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 07/05/2023] [Indexed: 08/10/2023] Open
Abstract
The non-coding 6S RNA is a master regulator of the cell cycle in bacteria which binds to the RNA polymerase-σ70 holoenzyme during the stationary phase to inhibit transcription from the primary σ factor. Inhibition is reversed upon outgrowth from the stationary phase by synthesis of small product RNA transcripts (pRNAs). 6S and its complex with a pRNA were structurally characterized using Small Angle X-ray Scattering. The 3D models of 6S and 6S:pRNA complex presented here, demonstrate that the fairly linear and extended structure of 6S undergoes a major conformational change upon binding to pRNA. In particular, 6S:pRNA complex formation is associated with a compaction of the overall 6S size and an expansion of its central domain. Our structural models are consistent with the hypothesis that the resultant particle has a shape and size incompatible with binding to RNA polymerase-σ70. Overall, by use of an optimized in vivo methodological approach, especially useful for structural studies, our study considerably improves our understanding of the structural basis of 6S regulation by offering a mechanistic glimpse of the 6S transcriptional control.
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Affiliation(s)
- Eleni Makraki
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology—Hellas (IMBB-FORTH), Heraklion, Greece
| | - Sophia Miliara
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology—Hellas (IMBB-FORTH), Heraklion, Greece
| | - Michalis Pagkalos
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology—Hellas (IMBB-FORTH), Heraklion, Greece
- Department of Biology, University of Crete, Heraklion, Greece
| | - Michael Kokkinidis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology—Hellas (IMBB-FORTH), Heraklion, Greece
- Department of Biology, University of Crete, Heraklion, Greece
| | - Efstratios Mylonas
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology—Hellas (IMBB-FORTH), Heraklion, Greece
| | - Vasiliki E. Fadouloglou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology—Hellas (IMBB-FORTH), Heraklion, Greece
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Komotini, Greece
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9
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Morishima K, Inoue R, Sugiyama M. Derivation of the small-angle scattering profile of a target biomacromolecule from a profile deteriorated by aggregates. AUC-SAS. J Appl Crystallogr 2023; 56:624-632. [PMID: 37284265 PMCID: PMC10241049 DOI: 10.1107/s1600576723002406] [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: 10/07/2022] [Accepted: 03/12/2023] [Indexed: 06/08/2023] Open
Abstract
Aggregates cause a fatal problem in the structural analysis of a biomacro-mol-ecule in solution using small-angle X-ray or neutron scattering (SAS): they deteriorate the scattering profile of the target molecule and lead to an incorrect structure. Recently, an integrated method of analytical ultracentrifugation (AUC) and SAS, abbreviated AUC-SAS, was developed as a new approach to overcome this problem. However, the original version of AUC-SAS does not offer a correct scattering profile of the target molecule when the weight fraction of aggregates is higher than ca 10%. In this study, the obstacle point in the original AUC-SAS approach is identified. The improved AUC-SAS method is then applicable to a solution with a relatively larger weight fraction of aggregates (≤20%).
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Affiliation(s)
- Ken Morishima
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2-1010 Asashironishi, Kumatori, Sennan-gun, Osaka 590-0494, Japan
| | - Rintaro Inoue
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2-1010 Asashironishi, Kumatori, Sennan-gun, Osaka 590-0494, Japan
| | - Masaaki Sugiyama
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2-1010 Asashironishi, Kumatori, Sennan-gun, Osaka 590-0494, Japan
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10
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Liu C, Pfister B, Osman R, Ritter M, Heutinck A, Sharma M, Eicke S, Fischer-Stettler M, Seung D, Bompard C, Abt MR, Zeeman SC. LIKE EARLY STARVATION 1 and EARLY STARVATION 1 promote and stabilize amylopectin phase transition in starch biosynthesis. SCIENCE ADVANCES 2023; 9:eadg7448. [PMID: 37235646 DOI: 10.1126/sciadv.adg7448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 04/19/2023] [Indexed: 05/28/2023]
Abstract
Starch, the most abundant carbohydrate reserve in plants, primarily consists of the branched glucan amylopectin, which forms semi-crystalline granules. Phase transition from a soluble to an insoluble form depends on amylopectin architecture, requiring a compatible distribution of glucan chain lengths and a branch-point distribution. Here, we show that two starch-bound proteins, LIKE EARLY STARVATION 1 (LESV) and EARLY STARVATION 1 (ESV1), which have unusual carbohydrate-binding surfaces, promote the phase transition of amylopectin-like glucans, both in a heterologous yeast system expressing the starch biosynthetic machinery and in Arabidopsis plants. We propose a model wherein LESV serves as a nucleating role, with its carbohydrate-binding surfaces helping align glucan double helices to promote their phase transition into semi-crystalline lamellae, which are then stabilized by ESV1. Because both proteins are widely conserved, we suggest that protein-facilitated glucan crystallization may be a general and previously unrecognized feature of starch biosynthesis.
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Affiliation(s)
- Chun Liu
- Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092 Zurich, Switzerland
| | - Barbara Pfister
- Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092 Zurich, Switzerland
| | - Rayan Osman
- Université de Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Maximilian Ritter
- Institute for Building Materials, ETH Zurich, Stefano-Franscini-Platz 3, 8093 Zurich, Switzerland
| | - Arvid Heutinck
- Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092 Zurich, Switzerland
| | - Mayank Sharma
- Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092 Zurich, Switzerland
| | - Simona Eicke
- Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092 Zurich, Switzerland
| | | | - David Seung
- Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092 Zurich, Switzerland
| | - Coralie Bompard
- Université de Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Melanie R Abt
- Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092 Zurich, Switzerland
| | - Samuel C Zeeman
- Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092 Zurich, Switzerland
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11
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Malard F, Sizun C, Thureau A, Carlier L, Lescop E. Structural transitions in TCTP tumor protein upon binding to the anti-apoptotic protein family member Mcl-1. J Biol Chem 2023:104830. [PMID: 37201583 PMCID: PMC10333598 DOI: 10.1016/j.jbc.2023.104830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 05/09/2023] [Accepted: 05/11/2023] [Indexed: 05/20/2023] Open
Abstract
Translationally Controlled Tumor Protein (TCTP) serves as a pro-survival factor in tumor cells, inhibiting the mitochondrial apoptosis pathway by enhancing the function of anti-apoptotic Bcl-2 family members Mcl-1 and Bcl-xL. TCTP specifically binds to Bcl-xL, preventing Bax-dependent Bcl-xL-induced cytochrome c release, and it reduces Mcl-1 turnover by inhibiting its ubiquitination, thereby decreasing Mcl-1-mediated apoptosis. TCTP harbors a BH3-like motif that forms a β-strand buried in the globular domain of the protein. In contrast, the crystal structure of the TCTP BH3-like peptide in complex with the Bcl-2 family member Bcl-xL reveals an α-helical conformation for the BH3-like motif, suggesting significant structural changes upon complex formation. Employing biochemical and biophysical methods, including limited proteolysis, circular dichroism NMR, and SAXS, we describe the TCTP complex with the Bcl-2 homolog Mcl-1. Our findings demonstrate that full-length TCTP binds to the BH3 binding groove of Mcl-1 via its BH3-like motif, experiencing conformational exchange at the interface on a micro- to milli-second timescale. Concurrently, the TCTP globular domain becomes destabilized, transitioning into a molten-globule state. Furthermore, we establish that the non-canonical residue D16 within TCTP BH3-like motif reduces stability while enhancing the dynamics of the intermolecular interface. In conclusion, we detail the structural plasticity of TCTP and discuss its implications for partner interactions and future anticancer drug design strategies aimed at targeting TCTP complexes.
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Affiliation(s)
- Florian Malard
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, LabEx LERMIT, 1 avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | - Christina Sizun
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, LabEx LERMIT, 1 avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | | | - Ludovic Carlier
- Laboratoire Des Biomolécules, LBM, Sorbonne Université, Ecole Normale Supérieure, PSL University, CNRS, Paris, France
| | - Ewen Lescop
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, LabEx LERMIT, 1 avenue de la Terrasse, 91190 Gif-sur-Yvette, France.
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12
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Pimenta BV, Madrid RRM, Mathews PD, Riske KA, Loh W, Angelov B, Angelova A, Mertins O. Interaction of polyelectrolyte-shell cubosomes with serum albumin for triggering drug release in gastrointestinal cancer. J Mater Chem B 2023; 11:2490-2503. [PMID: 36852541 DOI: 10.1039/d2tb02670h] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Nano-structured and functionalized materials for encapsulation, transport, targeting and controlled release of drugs are of high interest to overcome low bioavailability in oral administration. We develop lipid-based cubosomes, which are surface-functionalized with biocompatible chitosan-N-arginine and alginate, displaying internal liquid crystalline structures. Polyelectrolyte-shell (PS) cubosomes have pH-responsive characteristics profitable for oral delivery. The obtained PScubosomes can strongly interact with serum albumin, a protein which is released in the stomach under gastric cancer conditions. An effective thermodynamic PScubosome-protein interaction was characterized at pH 2.0 and 7.4 by isothermal titration calorimetry at 37 °C. A high increment of the albumin conformation transition temperature was evidenced by differential scanning calorimetry upon incubation with PScubosomes. The performed structural studies by synchrotron small-angle X-ray scattering (SAXS) revealed essential alterations in the internal liquid crystalline topology of the nanocarriers including an Im3m to Pn3m transition and a reduction of the cubic lattice parameters. The PScubosome nanoparticle interaction with serum albumin, leading to inner structural changes in a range of temperatures, promoted the release of water from the cubosomal nanochannels. Altogether, the results revealed effective interactions of the PScubosomes with albumin under simulated gastrointestinal pH conditions and suggested promising nanocarrier characteristics for triggered oral drug release.
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Affiliation(s)
- Barbara V Pimenta
- Laboratory of Nano Bio Materials (LNBM), Department of Biophysics, Paulista Medical School, Federal University of Sao Paulo (UNIFESP), 04023-062 Sao Paulo, Brazil.
| | - Rafael R M Madrid
- Laboratory of Nano Bio Materials (LNBM), Department of Biophysics, Paulista Medical School, Federal University of Sao Paulo (UNIFESP), 04023-062 Sao Paulo, Brazil.
| | - Patrick D Mathews
- Laboratory of Nano Bio Materials (LNBM), Department of Biophysics, Paulista Medical School, Federal University of Sao Paulo (UNIFESP), 04023-062 Sao Paulo, Brazil.
| | - Karin A Riske
- Laboratory of Nano Bio Materials (LNBM), Department of Biophysics, Paulista Medical School, Federal University of Sao Paulo (UNIFESP), 04023-062 Sao Paulo, Brazil.
| | - Watson Loh
- Institute of Chemistry, State University of Campinas (UNICAMP), 13083-970 Campinas, Brazil
| | - Borislav Angelov
- Institute of Physics, ELI Beamlines, Academy of Sciences of the Czech Republic, CZ-18221 Prague, Czech Republic
| | - Angelina Angelova
- Université Paris-Saclay, CNRS, Institut Galien Paris-Saclay, 91400 Orsay, France.
| | - Omar Mertins
- Laboratory of Nano Bio Materials (LNBM), Department of Biophysics, Paulista Medical School, Federal University of Sao Paulo (UNIFESP), 04023-062 Sao Paulo, Brazil. .,Université Paris-Saclay, CNRS, Institut Galien Paris-Saclay, 91400 Orsay, France.
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13
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Decrypting the programming of β-methylation in virginiamycin M biosynthesis. Nat Commun 2023; 14:1327. [PMID: 36899003 PMCID: PMC10006238 DOI: 10.1038/s41467-023-36974-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 02/27/2023] [Indexed: 03/12/2023] Open
Abstract
During biosynthesis by multi-modular trans-AT polyketide synthases, polyketide structural space can be expanded by conversion of initially-formed electrophilic β-ketones into β-alkyl groups. These multi-step transformations are catalysed by 3-hydroxy-3-methylgluratryl synthase cassettes of enzymes. While mechanistic aspects of these reactions have been delineated, little information is available concerning how the cassettes select the specific polyketide intermediate(s) to target. Here we use integrative structural biology to identify the basis for substrate choice in module 5 of the virginiamycin M trans-AT polyketide synthase. Additionally, we show in vitro that module 7, at minimum, is a potential additional site for β-methylation. Indeed, analysis by HPLC-MS coupled with isotopic labelling and pathway inactivation identifies a metabolite bearing a second β-methyl at the expected position. Collectively, our results demonstrate that several control mechanisms acting in concert underpin β-branching programming. Furthermore, variations in this control - whether natural or by design - open up avenues for diversifying polyketide structures towards high-value derivatives.
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14
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Lopez C, David-Briand E, Lollier V, Mériadec C, Bizien T, Pérez J, Artzner F. Solubilization of free β-sitosterol in milk sphingomyelin and polar lipid vesicles as carriers: Structural characterization of the membranes and sphingosome morphology. Food Res Int 2023; 165:112496. [PMID: 36869506 DOI: 10.1016/j.foodres.2023.112496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 11/29/2022] [Accepted: 01/20/2023] [Indexed: 02/05/2023]
Abstract
High consumption of plant sterols reduces the risk of cardiovascular diseases in humans and provides health benefits. Increasing the amount of plant sterols in the diet is therefore necessary to reach the recommended daily dietary intake. However, food supplementation with free plant sterols is challenging because of their low solubility in fats and water. The objectives of this study were to investigate the capacity of milk-sphingomyelin (milk-SM) and milk polar lipids to solubilise β-sitosterol molecules in bilayer membranes organised as vesicles called sphingosomes. The thermal and structural properties of milk-SM containing bilayers composed of various amounts of β-sitosterol were examined by differential scanning calorimetry (DSC) and temperature-controlled X-ray diffraction (XRD), the molecular interactions were studied using the Langmuir film technique, the morphologies of sphingosomes and β-sitosterol crystals were observed by microscopy. We showed that the milk-SM bilayers devoid of β-sitosterol exhibited a gel to fluid Lα phase transition for Tm = 34.5 °C and formed facetted spherical sphingosomes below Tm. The solubilisation of β-sitosterol within milk-SM bilayers induced a liquid-ordered Lo phaseabove 25 %mol (1.7 %wt) β-sitosterol and a softening of the membranes leading to the formation of elongated sphingosomes. Attractive molecular interactions revealed a condensing effect of β-sitosterol on milk-SM Langmuir monolayers. Above 40 %mol (25.7 %wt) β-sitosterol, partitioning occured with the formation of β-sitosterol microcrystals in the aqueous phase. Similar results were obtained with the solubilization of β-sitosterol within milk polar lipid vesicles. For the first time, this study highlighted the efficient solubilization of free β-sitosterol within milk-SM based vesicles, which opens new market opportunities for the formulation of functional foods enriched in non-crystalline free plant sterols.
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Affiliation(s)
- Christelle Lopez
- INRAE, BIA, F-44316 Nantes, France; INRAE, STLO, F-35000 Rennes, France.
| | | | - Virginie Lollier
- INRAE, BIA, F-44316 Nantes, France; INRAE, PROBE Research Infrastructure, BIBS Facility, F-44316 Nantes, France
| | | | - Thomas Bizien
- Synchrotron Soleil, L'Orme des Merisiers, Saint-Aubin BP48, F-91192 Gif-sur-Yvette, France
| | - Javier Pérez
- Synchrotron Soleil, L'Orme des Merisiers, Saint-Aubin BP48, F-91192 Gif-sur-Yvette, France
| | - Franck Artzner
- IPR, UMR 6251, CNRS, University of Rennes 1, F-35042 Rennes, France
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15
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Prolič-Kalinšek M, Volkov AN, Hadži S, Van Dyck J, Bervoets I, Charlier D, Loris R. Structural basis of DNA binding by YdaT, a functional equivalent of the CII repressor in the cryptic prophage CP-933P from Escherichia coli O157:H7. Acta Crystallogr D Struct Biol 2023; 79:245-258. [PMID: 36876434 PMCID: PMC9986795 DOI: 10.1107/s2059798323001249] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 02/10/2023] [Indexed: 03/01/2023] Open
Abstract
YdaT is a functional equivalent of the CII repressor in certain lambdoid phages and prophages. YdaT from the cryptic prophage CP-933P in the genome of Escherichia coli O157:H7 is functional as a DNA-binding protein and recognizes a 5'-TTGATTN6AATCAA-3' inverted repeat. The DNA-binding domain is a helix-turn-helix (HTH)-containing POU domain and is followed by a long α-helix (α6) that forms an antiparallel four-helix bundle, creating a tetramer. The loop between helix α2 and the recognition helix α3 in the HTH motif is unusually long compared with typical HTH motifs, and is highly variable in sequence and length within the YdaT family. The POU domains have a large degree of freedom to move relative to the helix bundle in the free structure, but their orientation becomes fixed upon DNA binding.
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Affiliation(s)
- Maruša Prolič-Kalinšek
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussel, Belgium
| | - Alexander N Volkov
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussel, Belgium
| | - San Hadži
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, 1000 Ljubljana, Slovenia
| | - Jeroen Van Dyck
- Department of Chemistry, Universiteit Antwerpen, Groenenborgerlaan 171, 2020 Antwerpen, Belgium
| | - Indra Bervoets
- Research Group of Microbiology, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussel, Belgium
| | - Daniel Charlier
- Research Group of Microbiology, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussel, Belgium
| | - Remy Loris
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussel, Belgium
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16
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Analysis and modeling of SDS and DPC micelle SAXS data for membrane protein solution structure characterization. Data Brief 2023; 47:108915. [PMID: 36747984 PMCID: PMC9898585 DOI: 10.1016/j.dib.2023.108915] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/10/2023] [Accepted: 01/12/2023] [Indexed: 01/22/2023] Open
Abstract
Herein, we present analysis and analytical modeling of Small Angle X-ray Scattering (SAXS) data on two surfactants forming micelles (i.e., sodium dodecyl sulfate and dodecyl phosphocholine) and used for the study in solution of mTSPO, the translocator membrane protein from Mus musculus, as supporting data of the research article published in Biochimie (Combet et al., 2022). For both surfactants, concentration series were measured at two Synchrotron SAXS-beamlines. After reduction, buffer subtraction and water calibration of the data, SAXS curves were normalized to surfactant concentration to highlight possible changes in micelle shape or presence of inter-micellar weak interactions. They were then analyzed in terms of radius of gyration (R G), absolute forward intensity (I0) to access the surfactant aggregation number (Na ) and pair-distance distribution function (P(r)), which gives information on the shape and dimensions of the micelles. Finally, an analytical modeling using SasView - a SAS analysis software package (https://www.sasview.org/) - was performed to describe structural features of the two surfactant micelles at a concentration at which no change in the micelle shape nor weak interactions are observed. A core-shell ellipsoidal model was used to fit the SAXS curves, which provided geometrical parameters of the micelles (equatorial and polar radii, shell thickness) and also scattering length densities (SLD) of both the hydrophobic core and the hydrophilic shell. Hydration of polar heads into the micelle shell could be estimated from micelle volume calculations (V core and V shell). These parameters are particularly useful when modeling SAXS curves of membrane protein-surfactant complexes as described in Combet et al. (2022).
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17
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Gérard FCA, Bourhis JM, Mas C, Branchard A, Vu DD, Varhoshkova S, Leyrat C, Jamin M. Structure and Dynamics of the Unassembled Nucleoprotein of Rabies Virus in Complex with Its Phosphoprotein Chaperone Module. Viruses 2022; 14:v14122813. [PMID: 36560817 PMCID: PMC9786881 DOI: 10.3390/v14122813] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/02/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022] Open
Abstract
As for all non-segmented negative RNA viruses, rabies virus has its genome packaged in a linear assembly of nucleoprotein (N), named nucleocapsid. The formation of new nucleocapsids during virus replication in cells requires the production of soluble N protein in complex with its phosphoprotein (P) chaperone. In this study, we reconstituted a soluble heterodimeric complex between an armless N protein of rabies virus (RABV), lacking its N-terminal subdomain (NNT-ARM), and a peptide encompassing the N0 chaperon module of the P protein. We showed that the chaperone module undergoes a disordered-order transition when it assembles with N0 and measured an affinity in the low nanomolar range using a competition assay. We solved the crystal structure of the complex at a resolution of 2.3 Å, unveiling the details of the conserved interfaces. MD simulations showed that both the chaperon module of P and RNA-mediated polymerization reduced the ability of the RNA binding cavity to open and close. Finally, by reconstituting a complex with full-length P protein, we demonstrated that each P dimer could independently chaperon two N0 molecules.
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Affiliation(s)
- Francine C. A. Gérard
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Jean-Marie Bourhis
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Caroline Mas
- Integrated Structural Biology Grenoble (ISBG), Université Grenoble Alpes, CNRS, CEA, EMBL, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Anaïs Branchard
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Duc Duy Vu
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Sylvia Varhoshkova
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Cédric Leyrat
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, 34094 Montpellier, France
- Correspondence: (C.L.); (M.J.)
| | - Marc Jamin
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, 71 Avenue des Martyrs, 38000 Grenoble, France
- Correspondence: (C.L.); (M.J.)
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18
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Dorival J, Moraïs S, Labourel A, Rozycki B, Cazade PA, Dabin J, Setter-Lamed E, Mizrahi I, Thompson D, Thureau A, Bayer EA, Czjzek M. Mapping the deformability of natural and designed cellulosomes in solution. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:68. [PMID: 35725490 PMCID: PMC9210761 DOI: 10.1186/s13068-022-02165-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 06/08/2022] [Indexed: 12/02/2022]
Abstract
Background Natural cellulosome multi-enzyme complexes, their components, and engineered ‘designer cellulosomes’ (DCs) promise an efficient means of breaking down cellulosic substrates into valuable biofuel products. Their broad uptake in biotechnology relies on boosting proximity-based synergy among the resident enzymes, but the modular architecture challenges structure determination and rational design. Results We used small angle X-ray scattering combined with molecular modeling to study the solution structure of cellulosomal components. These include three dockerin-bearing cellulases with distinct substrate specificities, original scaffoldins from the human gut bacterium Ruminococcus champanellensis (ScaA, ScaH and ScaK) and a trivalent cohesin-bearing designer scaffoldin (Scaf20L), followed by cellulosomal complexes comprising these components, and the nonavalent fully loaded Clostridium thermocellum CipA in complex with Cel8A from the same bacterium. The size analysis of Rg and Dmax values deduced from the scattering curves and corresponding molecular models highlight their variable aspects, depending on composition, size and spatial organization of the objects in solution. Conclusions Our data quantifies variability of form and compactness of cellulosomal components in solution and confirms that this native plasticity may well be related to speciation with respect to the substrate that is targeted. By showing that scaffoldins or components display enhanced compactness compared to the free objects, we provide new routes to rationally enhance their stability and performance in their environment of action. Supplementary Information The online version contains supplementary material available at 10.1186/s13068-022-02165-3.
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Intrinsically Disordered Proteins: An Overview. Int J Mol Sci 2022; 23:ijms232214050. [PMID: 36430530 PMCID: PMC9693201 DOI: 10.3390/ijms232214050] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022] Open
Abstract
Many proteins and protein segments cannot attain a single stable three-dimensional structure under physiological conditions; instead, they adopt multiple interconverting conformational states. Such intrinsically disordered proteins or protein segments are highly abundant across proteomes, and are involved in various effector functions. This review focuses on different aspects of disordered proteins and disordered protein regions, which form the basis of the so-called "Disorder-function paradigm" of proteins. Additionally, various experimental approaches and computational tools used for characterizing disordered regions in proteins are discussed. Finally, the role of disordered proteins in diseases and their utility as potential drug targets are explored.
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20
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Delhommel F, Martínez-Lumbreras S, Sattler M. Combining NMR, SAXS and SANS to characterize the structure and dynamics of protein complexes. Methods Enzymol 2022; 678:263-297. [PMID: 36641211 DOI: 10.1016/bs.mie.2022.09.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Understanding the structure and dynamics of biological macromolecules is essential to decipher the molecular mechanisms that underlie cellular functions. The description of structure and conformational dynamics often requires the integration of complementary techniques. In this review, we highlight the utility of combining nuclear magnetic resonance (NMR) spectroscopy with small angle scattering (SAS) to characterize these challenging biomolecular systems. NMR can assess the structure and conformational dynamics of multidomain proteins, RNAs and biomolecular complexes. It can efficiently provide information on interaction surfaces, long-distance restraints and relative domain orientations at residue-level resolution. Such information can be readily combined with high-resolution structural data available on subcomponents of biomolecular assemblies. Moreover, NMR is a powerful tool to characterize the dynamics of biomolecules on a wide range of timescales, from nanoseconds to seconds. On the other hand, SAS approaches provide global information on the size and shape of biomolecules and on the ensemble of all conformations present in solution. Therefore, NMR and SAS provide complementary data that are uniquely suited to investigate dynamic biomolecular assemblies. Here, we briefly review the type of data that can be obtained by both techniques and describe different approaches that can be used to combine them to characterize biomolecular assemblies. We then provide guidelines on which experiments are best suited depending on the type of system studied, ranging from fully rigid complexes, dynamic structures that interconvert between defined conformations and systems with very high structural heterogeneity.
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Affiliation(s)
- Florent Delhommel
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany; Bavarian NMR Center, Department of Chemistry, Technical University of Munich, Garching, Germany
| | - Santiago Martínez-Lumbreras
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany; Bavarian NMR Center, Department of Chemistry, Technical University of Munich, Garching, Germany
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany; Bavarian NMR Center, Department of Chemistry, Technical University of Munich, Garching, Germany.
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21
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Shemesh A, Dharan N, Ginsburg A, Dharan R, Levi-Kalisman Y, Ringel I, Raviv U. Mechanism of the Initial Tubulin Nucleation Phase. J Phys Chem Lett 2022; 13:9725-9735. [PMID: 36222421 DOI: 10.1021/acs.jpclett.2c02619] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Tubulin nucleation is a highly frequent event in microtubule (MT) dynamics but is poorly understood. In this work, we characterized the structural changes during the initial nucleation phase of dynamic tubulin. Using size-exclusion chromatography-eluted tubulin dimers in an assembly buffer solution free of glycerol and tubulin aggregates enabled us to start from a well-defined initial thermodynamic ensemble of isolated dynamic tubulin dimers and short oligomers. Following a temperature increase, time-resolved X-ray scattering and cryo-transmission electron microscopy during the initial nucleation phase revealed an isodesmic assembly mechanism of one-dimensional (1D) tubulin oligomers (where dimers were added and/or removed one at a time), leading to sufficiently stable two-dimensional (2D) dynamic nanostructures, required for MT assembly. A substantial amount of tubulin octamers accumulated before two-dimensional lattices appeared. Under subcritical assembly conditions, we observed a slower isodesmic assembly mechanism, but the concentration of 1D oligomers was insufficient to form the multistranded 2D nucleus required for MT formation.
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Affiliation(s)
- Asaf Shemesh
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Nadiv Dharan
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Avi Ginsburg
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Raviv Dharan
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Yael Levi-Kalisman
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
- Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Israel Ringel
- Institute for Drug Research, School of Pharmacy, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Uri Raviv
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
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22
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San Emeterio J, Pabit SA, Pollack L. Contrast variation SAXS: Sample preparation protocols, experimental procedures, and data analysis. Methods Enzymol 2022; 677:41-83. [PMID: 36410957 PMCID: PMC10015503 DOI: 10.1016/bs.mie.2022.08.007] [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] [Indexed: 11/19/2022]
Abstract
Proteins and nucleic acids, alone and in complex are among the essential building blocks of living organisms. Obtaining a molecular level understanding of their structures, and the changes that occur as they interact, is critical for expanding our knowledge of life processes or disease progression. Here, we motivate and describe an application of solution small angle X-ray scattering (SAXS) which provides valuable information about the structures, ensembles, compositions and dynamics of protein-nucleic acid complexes in solution, in equilibrium and time-resolved studies. Contrast variation (CV-) SAXS permits the visualization of the distinct molecular constituents (protein and/or nucleic acid) within a complex. CV-SAXS can be implemented in two modes. In the simplest, the protein within the complex is effectively rendered invisible by the addition of an inert contrast agent at an appropriate concentration. Under these conditions, the structure, or structural changes of only the nucleic acid component of the complex can be studied in detail. The second mode permits observation of both components of the complex: the protein and the nucleic acid. This approach requires the acquisition of SAXS profiles on the complex at different concentrations of a contrast agent. Here, we review CV-SAXS as applied to protein-nucleic acid complexes in both modes. We provide some theoretical framework for CV-SAXS but focus primarily on providing the necessary information required to implement a successful experiment including experimental design, sample quality assessment, and data analysis.
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Affiliation(s)
- Josue San Emeterio
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY, United States
| | - Suzette A Pabit
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY, United States
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY, United States.
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23
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Gabel F, Engilberge S, Schmitt E, Thureau A, Mechulam Y, Pérez J, Girard E. Medical contrast agents as promising tools for biomacromolecular SAXS experiments. Acta Crystallogr D Struct Biol 2022; 78:1120-1130. [PMID: 36048152 PMCID: PMC9435597 DOI: 10.1107/s2059798322007392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 07/18/2022] [Indexed: 11/18/2022] Open
Abstract
Lanthanide-based complexes are presented as a promising class of molecules for efficient SAXS contrast-variation experiments. Their interactions and contrast properties are analyzed for an oligomeric protein and a protein–RNA complex. Small-angle X-ray scattering (SAXS) has become an indispensable tool in structural biology, complementing atomic-resolution techniques. It is sensitive to the electron-density difference between solubilized biomacromolecules and the buffer, and provides information on molecular masses, particle dimensions and interactions, low-resolution conformations and pair distance-distribution functions. When SAXS data are recorded at multiple contrasts, i.e. at different solvent electron densities, it is possible to probe, in addition to their overall shape, the internal electron-density profile of biomacromolecular assemblies. Unfortunately, contrast-variation SAXS has been limited by the range of solvent electron densities attainable using conventional co-solutes (for example sugars, glycerol and salt) and by the fact that some biological systems are destabilized in their presence. Here, SAXS contrast data from an oligomeric protein and a protein–RNA complex are presented in the presence of iohexol and Gd-HPDO3A, two electron-rich molecules that are used in biomedical imaging and that belong to the families of iodinated and lanthanide-based complexes, respectively. Moderate concentrations of both molecules allowed solvent electron densities matching those of proteins to be attained. While iohexol yielded higher solvent electron densities (per mole), it interacted specifically with the oligomeric protein and precipitated the protein–RNA complex. Gd-HPDO3A, while less efficient (per mole), did not disrupt the structural integrity of either system, and atomic models could be compared with the SAXS data. Due to their elevated solubility and electron density, their chemical inertness, as well as the possibility of altering their physico-chemical properties, lanthanide-based complexes represent a class of molecules with promising potential for contrast-variation SAXS experiments on diverse biomacromolecular systems.
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24
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Léger C, Pitard I, Sadi M, Carvalho N, Brier S, Mechaly A, Raoux-Barbot D, Davi M, Hoos S, Weber P, Vachette P, Durand D, Haouz A, Guijarro JI, Ladant D, Chenal A. Dynamics and structural changes of calmodulin upon interaction with the antagonist calmidazolium. BMC Biol 2022; 20:176. [PMID: 35945584 PMCID: PMC9361521 DOI: 10.1186/s12915-022-01381-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 07/29/2022] [Indexed: 11/11/2022] Open
Abstract
Background Calmodulin (CaM) is an evolutionarily conserved eukaryotic multifunctional protein that functions as the major sensor of intracellular calcium signaling. Its calcium-modulated function regulates the activity of numerous effector proteins involved in a variety of physiological processes in diverse organs, from proliferation and apoptosis, to memory and immune responses. Due to the pleiotropic roles of CaM in normal and pathological cell functions, CaM antagonists are needed for fundamental studies as well as for potential therapeutic applications. Calmidazolium (CDZ) is a potent small molecule antagonist of CaM and one the most widely used inhibitors of CaM in cell biology. Yet, CDZ, as all other CaM antagonists described thus far, also affects additional cellular targets and its lack of selectivity hinders its application for dissecting calcium/CaM signaling. A better understanding of CaM:CDZ interaction is key to design analogs with improved selectivity. Here, we report a molecular characterization of CaM:CDZ complexes using an integrative structural biology approach combining SEC-SAXS, X-ray crystallography, HDX-MS, and NMR. Results We provide evidence that binding of a single molecule of CDZ induces an open-to-closed conformational reorientation of the two domains of CaM and results in a strong stabilization of its structural elements associated with a reduction of protein dynamics over a large time range. These CDZ-triggered CaM changes mimic those induced by CaM-binding peptides derived from physiological protein targets, despite their distinct chemical natures. CaM residues in close contact with CDZ and involved in the stabilization of the CaM:CDZ complex have been identified. Conclusion Our results provide molecular insights into CDZ-induced dynamics and structural changes of CaM leading to its inhibition and open the way to the rational design of more selective CaM antagonists. Graphical abstract Calmidazolium is a potent and widely used inhibitor of calmodulin, a major mediator of calcium-signaling in eukaryotic cells. Structural characterization of calmidazolium-binding to calmodulin reveals that it triggers open-to-closed conformational changes similar to those induced by calmodulin-binding peptides derived from enzyme targets. These results provide molecular insights into CDZ-induced dynamics and structural changes of CaM leading to its inhibition and open the way to the rational design of more selective CaM antagonists.![]() Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01381-5.
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Affiliation(s)
- Corentin Léger
- Biochemistry of Macromolecular Interactions Unit, Department of Structural Biology and Chemistry, CNRS UMR3528, Institut Pasteur, Paris, 75015, France
| | - Irène Pitard
- Biological NMR and HDX-MS Technological Platform, CNRS UMR3528, Université Paris Cité, Institut Pasteur, Paris, 75015, France
| | - Mirko Sadi
- Biochemistry of Macromolecular Interactions Unit, Department of Structural Biology and Chemistry, CNRS UMR3528, Institut Pasteur, Paris, 75015, France.,Université Paris Cité, Paris, France
| | - Nicolas Carvalho
- Biochemistry of Macromolecular Interactions Unit, Department of Structural Biology and Chemistry, CNRS UMR3528, Institut Pasteur, Paris, 75015, France.,Université Paris Cité, Paris, France
| | - Sébastien Brier
- Biological NMR and HDX-MS Technological Platform, CNRS UMR3528, Université Paris Cité, Institut Pasteur, Paris, 75015, France
| | - Ariel Mechaly
- Plate-forme de Cristallographie-C2RT, Université Paris Cité, CNRS UMR3528, Institut Pasteur, Paris, France
| | - Dorothée Raoux-Barbot
- Biochemistry of Macromolecular Interactions Unit, Department of Structural Biology and Chemistry, CNRS UMR3528, Institut Pasteur, Paris, 75015, France
| | - Maryline Davi
- Biochemistry of Macromolecular Interactions Unit, Department of Structural Biology and Chemistry, CNRS UMR3528, Institut Pasteur, Paris, 75015, France
| | - Sylviane Hoos
- Plateforme de Biophysique Moléculaire, Université Paris Cité, CNRS UMR3528, Institut Pasteur, Paris, France
| | - Patrick Weber
- Plate-forme de Cristallographie-C2RT, Université Paris Cité, CNRS UMR3528, Institut Pasteur, Paris, France
| | - Patrice Vachette
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Dominique Durand
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Ahmed Haouz
- Plate-forme de Cristallographie-C2RT, Université Paris Cité, CNRS UMR3528, Institut Pasteur, Paris, France
| | - J Iñaki Guijarro
- Biological NMR and HDX-MS Technological Platform, CNRS UMR3528, Université Paris Cité, Institut Pasteur, Paris, 75015, France
| | - Daniel Ladant
- Biochemistry of Macromolecular Interactions Unit, Department of Structural Biology and Chemistry, CNRS UMR3528, Institut Pasteur, Paris, 75015, France.
| | - Alexandre Chenal
- Biochemistry of Macromolecular Interactions Unit, Department of Structural Biology and Chemistry, CNRS UMR3528, Institut Pasteur, Paris, 75015, France.
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25
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Dai Y, Guo H, Liu N, Chen W, Ai X, Li H, Sun B, Hou X, Rety S, Xi X. Structural mechanism underpinning Thermus oshimai Pif1-mediated G-quadruplex unfolding. EMBO Rep 2022; 23:e53874. [PMID: 35736675 PMCID: PMC9253758 DOI: 10.15252/embr.202153874] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 05/04/2022] [Accepted: 05/16/2022] [Indexed: 08/05/2023] Open
Abstract
G-quadruplexes (G4s) are unusual stable DNA structures that cause genomic instability. To overcome the potential barriers formed by G4s, cells have evolved different families of proteins that unfold G4s. Pif1 is a DNA helicase from superfamily 1 (SF1) conserved from bacteria to humans with high G4-unwinding activity. Here, we present the first X-ray crystal structure of the Thermus oshimai Pif1 (ToPif1) complexed with a G4. Our structure reveals that ToPif1 recognizes the entire native G4 via a cluster of amino acids at domains 1B/2B which constitute a G4-Recognizing Surface (GRS). The overall structure of the G4 maintains its three-layered propeller-type G4 topology, without significant reorganization of G-tetrads upon protein binding. The three G-tetrads in G4 are recognized by GRS residues mainly through electrostatic, ionic interactions, and hydrogen bonds formed between the GRS residues and the ribose-phosphate backbone. Compared with previously solved structures of SF2 helicases in complex with G4, our structure reveals how helicases from distinct superfamilies adopt different strategies for recognizing and unfolding G4s.
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Affiliation(s)
- Yang‐Xue Dai
- College of Life SciencesNorthwest A&F UniversityYanglingChina
| | - Hai‐Lei Guo
- College of Life SciencesNorthwest A&F UniversityYanglingChina
| | - Na‐Nv Liu
- College of Life SciencesNorthwest A&F UniversityYanglingChina
| | - Wei‐Fei Chen
- College of Life SciencesNorthwest A&F UniversityYanglingChina
| | - Xia Ai
- College of Life SciencesNorthwest A&F UniversityYanglingChina
| | - Hai‐Hong Li
- College of Life SciencesNorthwest A&F UniversityYanglingChina
| | - Bo Sun
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Xi‐Miao Hou
- College of Life SciencesNorthwest A&F UniversityYanglingChina
| | - Stephane Rety
- LBMCENS de LyonCNRS UMR 5239INSERM U1293Universite Claude Bernard Lyon 1LyonFrance
| | - Xu‐Guang Xi
- College of Life SciencesNorthwest A&F UniversityYanglingChina
- Laboratoire de Biologie et Pharmacologie Appliquée (LBPA)UMR8113 CNRSENS Paris‐SaclayUniversité Paris‐SaclayGif‐sur‐YvetteFrance
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26
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Markússon S, Hallin EI, Bustad HJ, Raasakka A, Xu J, Muruganandam G, Loris R, Martinez A, Bramham CR, Kursula P. High-affinity anti-Arc nanobodies provide tools for structural and functional studies. PLoS One 2022; 17:e0269281. [PMID: 35671319 PMCID: PMC9173642 DOI: 10.1371/journal.pone.0269281] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 05/17/2022] [Indexed: 11/19/2022] Open
Abstract
Activity-regulated cytoskeleton-associated protein (Arc) is a multidomain protein of retroviral origin with a vital role in the regulation of synaptic plasticity and memory formation in mammals. However, the mechanistic and structural basis of Arc function is poorly understood. Arc has an N-terminal domain (NTD) involved in membrane binding and a C-terminal domain (CTD) that binds postsynaptic protein ligands. In addition, the NTD and CTD both function in Arc oligomerisation, including assembly of retrovirus-like capsids involved in intercellular signalling. To obtain new tools for studies on Arc structure and function, we produced and characterised six high-affinity anti-Arc nanobodies (Nb). The CTD of rat and human Arc were both crystallised in ternary complexes with two Nbs. One Nb bound deep into the stargazin-binding pocket of Arc CTD and suggested competitive binding with Arc ligand peptides. The crystallisation of the human Arc CTD in two different conformations, accompanied by SAXS data and molecular dynamics simulations, paints a dynamic picture of the mammalian Arc CTD. The collapsed conformation closely resembles Drosophila Arc in capsids, suggesting that we have trapped a capsid-like conformation of the human Arc CTD. Our data obtained with the help of anti-Arc Nbs suggest that structural dynamics of the CTD and dimerisation of the NTD may promote the formation of capsids. Taken together, the recombinant high-affinity anti-Arc Nbs are versatile tools that can be further developed for studying mammalian Arc structure and function, as well as mechanisms of Arc capsid formation, both in vitro and in vivo. For example, the Nbs could serve as a genetically encoded tools for inhibition of endogenous Arc interactions in the study of neuronal function and plasticity.
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Affiliation(s)
| | - Erik I. Hallin
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | | | - Arne Raasakka
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Ju Xu
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Gopinath Muruganandam
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium
- Department of Bioengineering Sciences, Structural Biology Brussels, Vrije Universiteit Brussel, Brussel, Belgium
| | - Remy Loris
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium
- Department of Bioengineering Sciences, Structural Biology Brussels, Vrije Universiteit Brussel, Brussel, Belgium
| | - Aurora Martinez
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | | | - Petri Kursula
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
- * E-mail:
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27
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A comparative study of unpasteurized and pasteurized frozen whole hen eggs using size-exclusion chromatography and small-angle X-ray scattering. Sci Rep 2022; 12:9218. [PMID: 35654960 PMCID: PMC9163139 DOI: 10.1038/s41598-022-12885-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 05/18/2022] [Indexed: 11/08/2022] Open
Abstract
Hen eggs are rich in proteins and are an important source of protein for humans. Pasteurized frozen whole hen eggs are widely used in cooking and confectionery and can be stored for long periods. However, processed eggs differ from raw eggs in properties such as viscosity, foaming ability, and thermal aggregation. To develop pasteurized frozen whole egg products with properties similar to those of unpasteurized whole eggs, it is necessary to establish a method that can differentiate between the two egg types with respect to the structures of their proteins. In this study, size-exclusion chromatography (SEC) and SEC coupled with small-angle X-ray scattering (SEC-SAXS) were successfully used to differentiate between the proteins in unpasteurized and pasteurized frozen whole eggs. We found that proteins in the plasma fraction of egg yolk, especially apovitellenins I and II, formed large aggregates in the pasteurized eggs, indicating that their structures are sensitive to temperature changes during pasteurization, freezing, and thawing. The results suggest that SEC and SEC-SAXS can be used to differentiate between unpasteurized and pasteurized frozen whole eggs. Additionally, they may be useful in determining molecular sizes and shapes of multiple components in various complex biological systems such as whole eggs.
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28
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Barclay A, Tidemand Johansen N, Tidemand FG, Arleth L, Pedersen MC. Global fitting of multiple data frames from SEC–SAXS to investigate the structure of next-generation nanodiscs. ACTA CRYSTALLOGRAPHICA SECTION D STRUCTURAL BIOLOGY 2022; 78:483-493. [PMID: 35362471 PMCID: PMC8972807 DOI: 10.1107/s2059798322001838] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 02/16/2022] [Indexed: 11/10/2022]
Abstract
The combination of online size-exclusion chromatography and small-angle X-ray scattering (SEC–SAXS) is rapidly becoming a key technique for structural investigations of elaborate biophysical samples in solution. Here, a novel model-refinement strategy centred around the technique is outlined and its utility is demonstrated by analysing data series from several SEC–SAXS experiments on phospholipid bilayer nanodiscs. Using this method, a single model was globally refined against many frames from the same data series, thereby capturing the frame-to-frame tendencies of the irradiated sample. These are compared with models refined in the traditional manner, in which refinement is based on the average profile of a set of consecutive frames from the same data series without an in-depth comparison of individual frames. This is considered to be an attractive model-refinement scheme as it considerably lowers the total number of parameters refined from the data series, produces tendencies that are automatically consistent between frames, and utilizes a considerably larger portion of the recorded data than is often performed in such experiments. Additionally, a method is outlined for correcting a measured UV absorption signal by accounting for potential peak broadening by the experimental setup.
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29
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Yunoki Y, Matsumoto A, Morishima K, Martel A, Porcar L, Sato N, Yogo R, Tominaga T, Inoue R, Yagi-Utsumi M, Okuda A, Shimizu M, Urade R, Terauchi K, Kono H, Yagi H, Kato K, Sugiyama M. Overall structure of fully assembled cyanobacterial KaiABC circadian clock complex by an integrated experimental-computational approach. Commun Biol 2022; 5:184. [PMID: 35273347 PMCID: PMC8913699 DOI: 10.1038/s42003-022-03143-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 02/08/2022] [Indexed: 12/24/2022] Open
Abstract
In the cyanobacterial circadian clock system, KaiA, KaiB and KaiC periodically assemble into a large complex. Here we determined the overall structure of their fully assembled complex by integrating experimental and computational approaches. Small-angle X-ray and inverse contrast matching small-angle neutron scatterings coupled with size-exclusion chromatography provided constraints to highlight the spatial arrangements of the N-terminal domains of KaiA, which were not resolved in the previous structural analyses. Computationally built 20 million structural models of the complex were screened out utilizing the constrains and then subjected to molecular dynamics simulations to examine their stabilities. The final model suggests that, despite large fluctuation of the KaiA N-terminal domains, their preferential positionings mask the hydrophobic surface of the KaiA C-terminal domains, hindering additional KaiA-KaiC interactions. Thus, our integrative approach provides a useful tool to resolve large complex structures harboring dynamically fluctuating domains. The revealed full KaiA12B6C6 complex is assembled including the dynamic and asynchronous KaiA N-terminal domains that have been missing in cryo-EM structures.
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Affiliation(s)
- Yasuhiro Yunoki
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, 444-8787, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuhoku, Nagoya, 467-8603, Japan.,Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2-1010 Asashironishi, Kumatori, Sennan-gun, Osaka, 590-0494, Japan
| | - Atsushi Matsumoto
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology (QST), Umemidai, Kizu, Kyoto, 619-0215, Japan
| | - Ken Morishima
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2-1010 Asashironishi, Kumatori, Sennan-gun, Osaka, 590-0494, Japan
| | - Anne Martel
- Institut Laue-Langevin, 71, avenue des martyrs, 38042, Grenoble, France
| | - Lionel Porcar
- Institut Laue-Langevin, 71, avenue des martyrs, 38042, Grenoble, France
| | - Nobuhiro Sato
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2-1010 Asashironishi, Kumatori, Sennan-gun, Osaka, 590-0494, Japan
| | - Rina Yogo
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, 444-8787, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuhoku, Nagoya, 467-8603, Japan.,Biomedical Research Centre, School of Biomedical Engineering, The University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Taiki Tominaga
- Neutron Science and Technology Center, Comprehensive Research Organization for Science and Society (CROSS), Tokai, Ibaraki, 319-1106, Japan
| | - Rintaro Inoue
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2-1010 Asashironishi, Kumatori, Sennan-gun, Osaka, 590-0494, Japan
| | - Maho Yagi-Utsumi
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, 444-8787, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuhoku, Nagoya, 467-8603, Japan
| | - Aya Okuda
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2-1010 Asashironishi, Kumatori, Sennan-gun, Osaka, 590-0494, Japan
| | - Masahiro Shimizu
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2-1010 Asashironishi, Kumatori, Sennan-gun, Osaka, 590-0494, Japan
| | - Reiko Urade
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2-1010 Asashironishi, Kumatori, Sennan-gun, Osaka, 590-0494, Japan
| | - Kazuki Terauchi
- Graduate School of Life Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga, 525-8577, Japan
| | - Hidetoshi Kono
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology (QST), Umemidai, Kizu, Kyoto, 619-0215, Japan.
| | - Hirokazu Yagi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuhoku, Nagoya, 467-8603, Japan.
| | - Koichi Kato
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, 444-8787, Japan. .,Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuhoku, Nagoya, 467-8603, Japan.
| | - Masaaki Sugiyama
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2-1010 Asashironishi, Kumatori, Sennan-gun, Osaka, 590-0494, Japan.
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30
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Trewhella J. Recent advances in small-angle scattering and its expanding impact in structural biology. Structure 2022; 30:15-23. [PMID: 34995477 DOI: 10.1016/j.str.2021.09.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/23/2021] [Accepted: 09/20/2021] [Indexed: 10/19/2022]
Abstract
Applications of small-angle scattering (SAS) in structural biology have benefited from continuing developments in instrumentation, tools for data analysis, modeling capabilities, standards for data and model presentation, and data archiving. The interplay of these capabilities has enabled SAS to contribute to advances in structural biology as the field pushes the boundaries in studies of biomolecular complexes and assemblies as large as whole cells, membrane proteins in lipid environments, and dynamic systems on time scales ranging from femtoseconds to hours. This review covers some of the important advances in biomolecular SAS capabilities for structural biology focused on over the last 5 years and presents highlights of recent applications that demonstrate how the technique is exploring new territories.
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Affiliation(s)
- Jill Trewhella
- School of Life and Environmental Sciences, The University of Sydney, Camperdown, NSW 2006, Australia.
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SEC-SAXS: Experimental set-up and software developments build up a powerful tool. Methods Enzymol 2022; 677:221-249. [DOI: 10.1016/bs.mie.2022.08.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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32
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Graewert MA, Svergun DI. Advanced sample environments and sample requirements for biological SAXS. Methods Enzymol 2022; 677:1-39. [DOI: 10.1016/bs.mie.2022.08.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Zhang F, Richter G, Bourgeois B, Spreitzer E, Moser A, Keilbach A, Kotnik P, Madl T. A General Small-Angle X-ray Scattering-Based Screening Protocol for Studying Physical Stability of Protein Formulations. Pharmaceutics 2021; 14:69. [PMID: 35056965 PMCID: PMC8778066 DOI: 10.3390/pharmaceutics14010069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 11/16/2022] Open
Abstract
A fundamental step in developing a protein drug is the selection of a stable storage formulation that ensures efficacy of the drug and inhibits physiochemical degradation or aggregation. Here, we designed and evaluated a general workflow for screening of protein formulations based on small-angle X-ray scattering (SAXS). Our SAXS pipeline combines automated sample handling, temperature control, and fast data analysis and provides protein particle interaction information. SAXS, together with different methods including turbidity analysis, dynamic light scattering (DLS), and SDS-PAGE measurements, were used to obtain different parameters to provide high throughput screenings. Using a set of model proteins and biopharmaceuticals, we show that SAXS is complementary to dynamic light scattering (DLS), which is widely used in biopharmaceutical research and industry. We found that, compared to DLS, SAXS can provide a more sensitive measure for protein particle interactions, such as protein aggregation and repulsion. Moreover, we show that SAXS is compatible with a broader range of buffers, excipients, and protein concentrations and that in situ SAXS provides a sensitive measure for long-term protein stability. This workflow can enable future high-throughput analysis of proteins and biopharmaceuticals and can be integrated with well-established complementary physicochemical analysis pipelines in (biopharmaceutical) research and industry.
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Affiliation(s)
- Fangrong Zhang
- Key Laboratory of Gastrointestinal Cancer, Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350122, China;
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, 8010 Graz, Austria; (G.R.); (B.B.); (E.S.)
| | - Gesa Richter
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, 8010 Graz, Austria; (G.R.); (B.B.); (E.S.)
| | - Benjamin Bourgeois
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, 8010 Graz, Austria; (G.R.); (B.B.); (E.S.)
| | - Emil Spreitzer
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, 8010 Graz, Austria; (G.R.); (B.B.); (E.S.)
| | - Armin Moser
- Anton Paar GmbH, 8054 Graz, Austria; (A.M.); (A.K.); (P.K.)
| | | | - Petra Kotnik
- Anton Paar GmbH, 8054 Graz, Austria; (A.M.); (A.K.); (P.K.)
| | - Tobias Madl
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, 8010 Graz, Austria; (G.R.); (B.B.); (E.S.)
- BioTechMed-Graz, 8010 Graz, Austria
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Shemesh A, Ginsburg A, Dharan R, Levi-Kalisman Y, Ringel I, Raviv U. Structure and Energetics of GTP- and GDP-Tubulin Isodesmic Self-Association. ACS Chem Biol 2021; 16:2212-2227. [PMID: 34643366 DOI: 10.1021/acschembio.1c00369] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Tubulin self-association is a critical process in microtubule dynamics. The early intermediate structures, energetics, and their regulation by fluxes of chemical energy, associated with guanosine triphosphate (GTP) hydrolysis, are poorly understood. We reconstituted an in vitro minimal model system, mimicking the key elements of the nontemplated tubulin assembly. To resolve the distribution of GTP- and guanosine diphosphate (GDP)-tubulin structures, at low temperatures (∼10 °C) and below the critical concentration for the microtubule assembly, we analyzed in-line size-exclusion chromatography-small-angle X-ray scattering (SEC-SAXS) chromatograms of GTP- and GDP-tubulin solutions. Both solutions rapidly attained steady state. The SEC-SAXS data were consistent with an isodesmic thermodynamic model of longitudinal tubulin self-association into 1D oligomers, terminated by the formation of tubulin single rings. The analysis showed that free dimers coexisted with tetramers and hexamers. Tubulin monomers and lateral association between dimers were not detected. The dimer-dimer longitudinal self-association standard Helmholtz free energies were -14.2 ± 0.4 kBT (-8.0 ± 0.2 kcal mol-1) and -13.1 ± 0.5 kBT (-7.4 ± 0.3 kcal mol-1) for GDP- and GTP-tubulin, respectively. We then determined the mass fractions of dimers, tetramers, and hexamers as a function of the total tubulin concentration. A small fraction of stable tubulin single rings, with a radius of 19.2 ± 0.2 nm, was detected in the GDP-tubulin solution. In the GTP-tubulin solution, this fraction was significantly lower. Cryo-TEM images and SEC-multiangle light-scattering analysis corroborated these findings. Our analyses provide an accurate structure-stability description of cold tubulin solutions.
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Affiliation(s)
- Asaf Shemesh
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
- The Harvey M. Krueger Family Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat
Ram, Jerusalem 9190401, Israel
| | - Avi Ginsburg
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Raviv Dharan
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Yael Levi-Kalisman
- The Harvey M. Krueger Family Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat
Ram, Jerusalem 9190401, Israel
- Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Israel Ringel
- Institute for Drug Research, The School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Ein Karem, Jerusalem 9112102, Israel
| | - Uri Raviv
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
- The Harvey M. Krueger Family Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat
Ram, Jerusalem 9190401, Israel
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Abstract
Small-angle X-ray scattering (SAXS) of proteins in solution has become a key tool for biochemists and structural biologists, thanks especially to the availability of beamlines with high-throughput capabilities at synchrotron sources. Despite the large spectrum of scientific disciplines tackled on the SWING beamline since its opening in 2008, there has always been a strong commitment to offering state-of-the-art biological SAXS (BioSAXS) instrumentation and data reduction methods to the scientific community. The extremely reliable in-vacuum EigerX-4M detector allows collection of an unlimited number of frames without noise. A small beamstop including a diamond diode-based monitor enables measurements of the transmitted intensity with 0.1% precision as well as a q
max/q
min ratio as large as 140 at a single distance. The parasitic scattering has been strongly reduced by the installation of new hybrid blades. A new thermally controlled in-vacuum capillary holder including fibre-optics-based spectroscopic functionalities allows the simultaneous use of three spectroscopic techniques in addition to SAXS measurements. The addition of a second high-performance liquid chromatography (HPLC) circuit has virtually eliminated the waiting time associated with column equilibration. The easy in-line connection of a multi-angle light scattering spectrometer and a refractometer allows for an independent determination of the molecular mass and of the concentration of low-UV-absorption samples such as detergents and sugars, respectively. These instrumental improvements are combined with important software developments. The HPLC injection Agilent software is controlled by the SAXS beamline acquisition software, allowing a virtually unlimited series of automated SAXS measurements to be synchronized with the sample injections. All data-containing files and reports are automatically stored in the same folders, with names related to both the user and sample. In addition, all raw SAXS images are processed automatically on the fly, and the analysed data are stored in the ISPyB database and made accessible via a web page.
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36
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de Wijn R, Rollet K, Ernst FGM, Wellner K, Betat H, Mörl M, Sauter C. CCA-addition in the cold: Structural characterization of the psychrophilic CCA-adding enzyme from the permafrost bacterium Planococcus halocryophilus. Comput Struct Biotechnol J 2021; 19:5845-5855. [PMID: 34765099 PMCID: PMC8563995 DOI: 10.1016/j.csbj.2021.10.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 10/12/2021] [Accepted: 10/12/2021] [Indexed: 11/25/2022] Open
Abstract
A high-resolution structure of a psychrophilic RNA polymerase contributes to our knowledge of cold adaptation. While catalytic core motifs are conserved, at least one shows cold adaptation. Loss of helix-capping increases structural flexibility in a catalytic core motif. Overall reduction of alpha-helical elements appears as a strategy for cold adaptation.
CCA-adding enzymes are highly specific RNA polymerases that add and maintain the sequence C-C-A at tRNA 3‘-ends. Recently, we could reveal that cold adaptation of such a polymerase is not only achieved at the expense of enzyme stability, but also at the cost of polymerization fidelity. Enzymes from psychrophilic organisms usually show an increased structural flexibility to enable catalysis at low temperatures. Here, polymerases face a dilemma, as there is a discrepancy between the need for a tightly controlled flexibility during polymerization and an increased flexibility as strategy for cold adaptation. Based on structural and biochemical analyses, we contribute to clarify the cold adaptation strategy of the psychrophilic CCA-adding enzyme from Planococcus halocryophilus, a gram-positive bacterium thriving in the arctic permafrost at low temperatures down to −15 °C. A comparison with the closely related enzyme from the thermophilic bacterium Geobacillus stearothermophilus reveals several features of cold adaptation - a significantly reduced amount of alpha-helical elements in the C-terminal tRNA-binding region and a structural adaptation in one of the highly conserved catalytic core motifs located in the N-terminal catalytic core of the enzyme.
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Affiliation(s)
- Raphaël de Wijn
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 67084 Strasbourg, France
| | - Kévin Rollet
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 67084 Strasbourg, France.,Institute for Biochemistry, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany
| | - Felix G M Ernst
- Institute for Biochemistry, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany
| | - Karolin Wellner
- Institute for Biochemistry, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany
| | - Heike Betat
- Institute for Biochemistry, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany
| | - Mario Mörl
- Institute for Biochemistry, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany
| | - Claude Sauter
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 67084 Strasbourg, France
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Ryzhykau YL, Vlasov AV, Orekhov PS, Rulev MI, Rogachev AV, Vlasova AD, Kazantsev AS, Verteletskiy DP, Skoi VV, Brennich ME, Pernot P, Murugova TN, Gordeliy VI, Kuklin AI. Ambiguities in and completeness of SAS data analysis of membrane proteins: the case of the sensory rhodopsin II-transducer complex. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2021; 77:1386-1400. [PMID: 34726167 DOI: 10.1107/s2059798321009542] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 09/14/2021] [Indexed: 01/14/2023]
Abstract
Membrane proteins (MPs) play vital roles in the function of cells and are also major drug targets. Structural information on proteins is vital for understanding their mechanism of function and is critical for the development of drugs. However, obtaining high-resolution structures of membrane proteins, in particular, under native conditions is still a great challenge. In such cases, the low-resolution methods small-angle X-ray and neutron scattering (SAXS and SANS) might provide valuable structural information. However, in some cases small-angle scattering (SAS) provides ambiguous ab initio structural information if complementary measurements are not performed and/or a priori information on the protein is not taken into account. Understanding the nature of the limitations may help to overcome these problems. One of the main problems of SAS data analysis of solubilized membrane proteins is the contribution of the detergent belt surrounding the MP. Here, a comprehensive analysis of how the detergent belt contributes to the SAS data of a membrane-protein complex of sensory rhodopsin II with its cognate transducer from Natronomonas pharaonis (NpSRII-NpHtrII) was performed. The influence of the polydispersity of NpSRII-NpHtrII oligomerization is the second problem that is addressed here. It is shown that inhomogeneity in the scattering length density of the detergent belt surrounding a membrane part of the complex and oligomerization polydispersity significantly impacts on SAXS and SANS profiles, and therefore on 3D ab initio structures. It is described how both problems can be taken into account to improve the quality of SAS data treatment. Since SAS data for MPs are usually obtained from solubilized proteins, and their detergent belt and, to a certain extent, oligomerization polydispersity are sufficiently common phenomena, the approaches proposed in this work might be used in SAS studies of different MPs.
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Affiliation(s)
- Yury L Ryzhykau
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russian Federation
| | - Alexey V Vlasov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russian Federation
| | - Philipp S Orekhov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russian Federation
| | - Maksim I Rulev
- Structural Biology Group, European Synchrotron Radiation Facility, 38000 Grenoble, France
| | - Andrey V Rogachev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russian Federation
| | - Anastasia D Vlasova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russian Federation
| | - Alexander S Kazantsev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russian Federation
| | - Dmitry P Verteletskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russian Federation
| | - Vadim V Skoi
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russian Federation
| | - Martha E Brennich
- Synchrotron Crystallography Team, EMBL Grenoble Outstation, 38042 Grenoble, France
| | - Petra Pernot
- Structural Biology Group, European Synchrotron Radiation Facility, 38000 Grenoble, France
| | - Tatiana N Murugova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russian Federation
| | - Valentin I Gordeliy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russian Federation
| | - Alexander I Kuklin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russian Federation
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38
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Mathews PD, Mertins O, Angelov B, Angelova A. Cubosomal lipid nanoassemblies with pH-sensitive shells created by biopolymer complexes: A synchrotron SAXS study. J Colloid Interface Sci 2021; 607:440-450. [PMID: 34509118 DOI: 10.1016/j.jcis.2021.08.187] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/19/2021] [Accepted: 08/28/2021] [Indexed: 12/19/2022]
Abstract
We report a strategy for sustainable development of pH-responsive cubic liquid crystalline nanoparticles (cubosomes), in which the structure-defining lyotropic nonlamellar lipid and the eventually encapsulated guest molecules can be protected by pH-sensitive polyelectrolyte shells with mucoadhesive properties. Bulk non-lamellar phases as well as pH-responsive polyelectrolyte-modified nanocarriers were formed by spontaneous assembly of the nonlamellar lipid monoolein and two biopolymers tailored in nanocomplexes with pH-dependent net charge. The mesophase particles involved positively charged N-arginine-modified chitosan (CHarg) and negatively charged alginate (ALG) chains assembled at different biopolymer concentrations and charge ratios into a series of pH-responsive complexes. The roles of Pluronic F127 as a dispersing agent and a stabilizer of the nanoscale dispersions were examined. Synchrotron small-angle X-ray scattering (SAXS) investigations were performed at several N-arginine-modified chitosan/alginate ratios (CHarg/ALG with 10, 15 and 20 wt% ALG relative to CHarg) and varying pH values mimicking the pH conditions of the gastrointestinal route. The structural parameters characterizing the inner cubic liquid crystalline organizations of the nanocarriers were determined as well as the particle sizes and stability on storage. The surface charge variations, influencing the measured zeta-potentials, evidenced the inclusion of the CHarg/ALG biopolymer complexes into the lipid nanoassemblies. The polyelectrolyte shells rendered the hybrid cubosome nanocarriers pH-sensitive and influenced the swelling of their lipid-phase core as revealed by the acquired SAXS patterns. The pH-responsiveness and the mucoadhesive features of the cubosomal lipid/polyelectrolyte nanocomplexes may be of interest for in vivo drug delivery applications.
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Affiliation(s)
- Patrick D Mathews
- Laboratory of Nano Bio Materials (LNBM), Department of Biophysics, Paulista Medical School, Federal University of Sao Paulo (UNIFESP), 04023-062 Sao Paulo, Brazil
| | - Omar Mertins
- Laboratory of Nano Bio Materials (LNBM), Department of Biophysics, Paulista Medical School, Federal University of Sao Paulo (UNIFESP), 04023-062 Sao Paulo, Brazil; Institut Galien Paris-Saclay UMR8612, Université Paris-Saclay, CNRS, F-92296 Châtenay-Malabry, France.
| | - Borislav Angelov
- Institute of Physics, ELI Beamlines, Academy of Sciences of the Czech Republic, CZ-18221 Prague, Czech Republic
| | - Angelina Angelova
- Institut Galien Paris-Saclay UMR8612, Université Paris-Saclay, CNRS, F-92296 Châtenay-Malabry, France.
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39
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Rengifo-Gonzalez JC, El Hage K, Clément MJ, Steiner E, Joshi V, Craveur P, Durand D, Pastré D, Bouhss A. The cooperative binding of TDP-43 to GU-rich RNA repeats antagonizes TDP-43 aggregation. eLife 2021; 10:67605. [PMID: 34490845 PMCID: PMC8523171 DOI: 10.7554/elife.67605] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 09/03/2021] [Indexed: 01/01/2023] Open
Abstract
TDP-43 is a nuclear RNA-binding protein that forms neuronal cytoplasmic inclusions in two major neurodegenerative diseases, ALS and FTLD. While the self-assembly of TDP-43 by its structured N-terminal and intrinsically disordered C-terminal domains has been widely studied, the mechanism by which mRNA preserves TDP-43 solubility in the nucleus has not been addressed. Here, we demonstrate that tandem RNA recognition motifs of TDP-43 bind to long GU-repeats in a cooperative manner through intermolecular interactions. Moreover, using mutants whose cooperativity is impaired, we found that the cooperative binding of TDP-43 to mRNA may be critical to maintain the solubility of TDP-43 in the nucleus and the miscibility of TDP-43 in cytoplasmic stress granules. We anticipate that the knowledge of a higher order assembly of TDP-43 on mRNA may clarify its role in intron processing and provide a means of interfering with the cytoplasmic aggregation of TDP-43.
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Affiliation(s)
- Juan Carlos Rengifo-Gonzalez
- Université Paris-Saclay, INSERM U1204, Univ Evry, Structure-Activité des Biomolécules Normales et Pathologiques (SABNP), Evry-Courcouronnes, France
| | - Krystel El Hage
- Université Paris-Saclay, INSERM U1204, Univ Evry, Structure-Activité des Biomolécules Normales et Pathologiques (SABNP), Evry-Courcouronnes, France
| | - Marie-Jeanne Clément
- Université Paris-Saclay, INSERM U1204, Univ Evry, Structure-Activité des Biomolécules Normales et Pathologiques (SABNP), Evry-Courcouronnes, France
| | - Emilie Steiner
- Université Paris-Saclay, INSERM U1204, Univ Evry, Structure-Activité des Biomolécules Normales et Pathologiques (SABNP), Evry-Courcouronnes, France
| | - Vandana Joshi
- Université Paris-Saclay, INSERM U1204, Univ Evry, Structure-Activité des Biomolécules Normales et Pathologiques (SABNP), Evry-Courcouronnes, France
| | | | - Dominique Durand
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - David Pastré
- Université Paris-Saclay, INSERM U1204, Univ Evry, Structure-Activité des Biomolécules Normales et Pathologiques (SABNP), Evry-Courcouronnes, France
| | - Ahmed Bouhss
- Université Paris-Saclay, INSERM U1204, Univ Evry, Structure-Activité des Biomolécules Normales et Pathologiques (SABNP), Evry-Courcouronnes, France
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40
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Malard F, Jacquet E, Nhiri N, Sizun C, Chabrier A, Messaoudi S, Dejeu J, Betzi S, Zhang X, Thureau A, Lescop E. Revisiting the Molecular Interactions between the Tumor Protein TCTP and the Drugs Sertraline/Thioridazine. ChemMedChem 2021; 17:e202100528. [PMID: 34472703 DOI: 10.1002/cmdc.202100528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Indexed: 11/07/2022]
Abstract
TCTP protein is a pharmacological target in cancer and TCTP inhibitors such as sertraline have been evaluated in clinical trials. The direct interaction of TCTP with the drugs sertraline and thioridazine has been reported in vitro by SPR experiments to be in the ∼30-50 μM Kd range (Amson et al. Nature Med 2012), supporting a TCTP-dependent mode of action of the drugs on tumor cells. However, the molecular details of the interaction remain elusive although they are crucial to improve the efforts of on-going medicinal chemistry. In addition, TCTP can be phosphorylated by the Plk-1 kinase, which is indicative of poor prognosis in several cancers. The impact of phosphorylation on TCTP structure/dynamics and binding with therapeutical ligands remains unexplored. Here, we combined NMR, TSA, SPR, BLI and ITC techniques to probe the molecular interactions between TCTP with the drugs sertraline and thioridazine. We reveal that drug binding is much weaker than reported with an apparent ∼mM Kd and leads to protein destabilization that obscured the analysis of the published SPR data. We further demonstrate by NMR and SAXS that TCTP S46 phosphorylation does not promote tighter interaction between TCTP and sertraline. Accordingly, we question the supported model in which sertraline and thioridazine directly interact with isolated TCTP in tumor cells and discuss alternative modes of action for the drugs in light of current literature.
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Affiliation(s)
- Florian Malard
- Institut de Chimie des Substances Naturelles, CNRS, Université Paris-Saclay, 1 av. de la terrasse, 91198, Gif-sur-Yvette, France
| | - Eric Jacquet
- Institut de Chimie des Substances Naturelles, CNRS, Université Paris-Saclay, 1 av. de la terrasse, 91198, Gif-sur-Yvette, France
| | - Naima Nhiri
- Institut de Chimie des Substances Naturelles, CNRS, Université Paris-Saclay, 1 av. de la terrasse, 91198, Gif-sur-Yvette, France
| | - Christina Sizun
- Institut de Chimie des Substances Naturelles, CNRS, Université Paris-Saclay, 1 av. de la terrasse, 91198, Gif-sur-Yvette, France
| | - Amélie Chabrier
- Université Paris-Saclay, BioCIS, Faculté de Pharmacie, CNRS, 92290, Châtenay-Malabry, France
| | - Samir Messaoudi
- Université Paris-Saclay, BioCIS, Faculté de Pharmacie, CNRS, 92290, Châtenay-Malabry, France
| | - Jérôme Dejeu
- Univ. Grenoble Alpes, CNRS, DCM, 38000, Grenoble, France
| | - Stéphane Betzi
- Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS, Aix-Marseille Université, Inserm, Institut Paoli-Calmettes, 27 bd Lei Roure, 13273, Marseille CEDEX 9, France
| | - Xu Zhang
- Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS, Aix-Marseille Université, Inserm, Institut Paoli-Calmettes, 27 bd Lei Roure, 13273, Marseille CEDEX 9, France
| | | | - Ewen Lescop
- Institut de Chimie des Substances Naturelles, CNRS, Université Paris-Saclay, 1 av. de la terrasse, 91198, Gif-sur-Yvette, France
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41
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Cardone C, Caseau CM, Bardiaux B, Thureaux A, Galloux M, Bajorek M, Eléouët JF, Litaudon M, Bontems F, Sizun C. A Structural and Dynamic Analysis of the Partially Disordered Polymerase-Binding Domain in RSV Phosphoprotein. Biomolecules 2021; 11:biom11081225. [PMID: 34439894 PMCID: PMC8392014 DOI: 10.3390/biom11081225] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/10/2021] [Accepted: 08/13/2021] [Indexed: 12/11/2022] Open
Abstract
The phosphoprotein P of Mononegavirales (MNV) is an essential co-factor of the viral RNA polymerase L. Its prime function is to recruit L to the ribonucleocapsid composed of the viral genome encapsidated by the nucleoprotein N. MNV phosphoproteins often contain a high degree of disorder. In Pneumoviridae phosphoproteins, the only domain with well-defined structure is a small oligomerization domain (POD). We previously characterized the differential disorder in respiratory syncytial virus (RSV) phosphoprotein by NMR. We showed that outside of RSV POD, the intrinsically disordered N-and C-terminal regions displayed a structural and dynamic diversity ranging from random coil to high helical propensity. Here we provide additional insight into the dynamic behavior of PCα, a domain that is C-terminal to POD and constitutes the RSV L-binding region together with POD. By using small phosphoprotein fragments centered on or adjacent to POD, we obtained a structural picture of the POD–PCα region in solution, at the single residue level by NMR and at lower resolution by complementary biophysical methods. We probed POD–PCα inter-domain contacts and showed that small molecules were able to modify the dynamics of PCα. These structural properties are fundamental to the peculiar binding mode of RSV phosphoprotein to L, where each of the four protomers binds to L in a different way.
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Affiliation(s)
- Christophe Cardone
- Institut de Chimie des Substances Naturelles, CNRS, Université Paris Saclay, 91190 Gif-sur-Yvette, France; (C.C.); (C.-M.C.); (M.L.); (F.B.)
| | - Claire-Marie Caseau
- Institut de Chimie des Substances Naturelles, CNRS, Université Paris Saclay, 91190 Gif-sur-Yvette, France; (C.C.); (C.-M.C.); (M.L.); (F.B.)
| | - Benjamin Bardiaux
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, 78015 Paris, France;
| | | | - Marie Galloux
- Unité de Virologie et Immunologie Moléculaires, INRAE, Université Paris Saclay, 78352 Jouy-en-Josas, France; (M.G.); (M.B.); (J.-F.E.)
| | - Monika Bajorek
- Unité de Virologie et Immunologie Moléculaires, INRAE, Université Paris Saclay, 78352 Jouy-en-Josas, France; (M.G.); (M.B.); (J.-F.E.)
| | - Jean-François Eléouët
- Unité de Virologie et Immunologie Moléculaires, INRAE, Université Paris Saclay, 78352 Jouy-en-Josas, France; (M.G.); (M.B.); (J.-F.E.)
| | - Marc Litaudon
- Institut de Chimie des Substances Naturelles, CNRS, Université Paris Saclay, 91190 Gif-sur-Yvette, France; (C.C.); (C.-M.C.); (M.L.); (F.B.)
| | - François Bontems
- Institut de Chimie des Substances Naturelles, CNRS, Université Paris Saclay, 91190 Gif-sur-Yvette, France; (C.C.); (C.-M.C.); (M.L.); (F.B.)
| | - Christina Sizun
- Institut de Chimie des Substances Naturelles, CNRS, Université Paris Saclay, 91190 Gif-sur-Yvette, France; (C.C.); (C.-M.C.); (M.L.); (F.B.)
- Correspondence:
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Bystranowska D, Skorupska A, Sołtys K, Padjasek M, Krężel A, Żak A, Kaus-Drobek M, Taube M, Kozak M, Ożyhar A. Nucleobindin-2 consists of two structural components: The Zn 2+-sensitive N-terminal half, consisting of nesfatin-1 and -2, and the Ca 2+-sensitive C-terminal half, consisting of nesfatin-3. Comput Struct Biotechnol J 2021; 19:4300-4318. [PMID: 34429849 PMCID: PMC8361300 DOI: 10.1016/j.csbj.2021.07.036] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 12/01/2022] Open
Abstract
Nucleobindin-2 (Nucb2) is a protein that has been suggested to play roles in a variety of biological processes. Nucb2 contains two Ca2+/Mg2+-binding EF-hand domains separated by an acidic amino acid residue-rich region and a leucine zipper. All of these domains are located within the C-terminal half of the protein. At the N-terminal half, Nucb2 also possesses a putative Zn2+-binding motif. In our recent studies, we observed that Nucb2 underwent Ca2+-dependent compaction and formed a mosaic-like structure consisting of intertwined disordered and ordered regions at its C-terminal half. The aim of this study was to investigate the impact of two other potential ligands: Mg2+, which possesses chemical properties similar to those of Ca2+, and Zn2+, for which a putative binding motif was identified. In this study, we demonstrated that the binding of Mg2+ led to oligomerization state changes with no significant secondary or tertiary structural alterations of Nucb2. In contrast, Zn2+ binding had a more pronounced effect on the structure of Nucb2, leading to the local destabilization of its N-terminal half while also inducing changes within its C-terminal half. These structural rearrangements resulted in the oligomerization and/or aggregation of Nucb2 molecules. Taken together, the results of our previous and current research help to elucidate the structure of the Nucb2, which can be divided into two parts: the Zn2+-sensitive N-terminal half (consisting of nesfatin-1 and -2) and the Ca2+-sensitive C-terminal half (consisting of nesfatin-3). These results may also help to open a new discussion regarding the diverse roles that metal cations play in regulating the structure of Nucb2 and the various physiological functions of this protein.
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Affiliation(s)
- Dominika Bystranowska
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Anna Skorupska
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Katarzyna Sołtys
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Michał Padjasek
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Artur Krężel
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Andrzej Żak
- Faculty of Mechanical Engineering, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Magdalena Kaus-Drobek
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Michał Taube
- Department of Macromolecular Physics, Faculty of Physics, Adam Mickiewicz University, Umultowska 85, 61-614 Poznań, Poland
| | - Maciej Kozak
- Department of Macromolecular Physics, Faculty of Physics, Adam Mickiewicz University, Umultowska 85, 61-614 Poznań, Poland
- National Synchrotron Radiation Centre SOLARIS, Jagiellonian University, Czerwone Maki 98, 30-392 Kraków, Poland
| | - Andrzej Ożyhar
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
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Violot S, Galisson F, Carrique L, Jugnarain V, Conchou L, Robert X, Thureau A, Helbert W, Aghajari N, Ballut L. Exploring molecular determinants of polysaccharide Lyase family 6-1 enzyme activity. Glycobiology 2021; 31:1557-1570. [PMID: 34245266 DOI: 10.1093/glycob/cwab073] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/24/2021] [Accepted: 07/07/2021] [Indexed: 11/14/2022] Open
Abstract
The Polysaccharide Lyase Family 6 (PL6) represents one of the 41 polysaccharide lyase families classified in the CAZy database with the vast majority of its members being alginate lyases grouped into three subfamilies, PL6_1-3. To decipher the mode of recognition and action of the enzymes belonging to subfamily PL6_1, we solved the crystal structures of Pedsa0632, Patl3640, Pedsa3628 and Pedsa3807, which all show different substrate specificities and mode of action (endo-/exo-lyase). Thorough exploration of the structures of Pedsa0632 and Patl3640 in complex with their substrates as well as docking experiments confirm that the conserved residues in subsites -1 to +3 of the catalytic site form a common platform which can accommodate various types of alginate in a very similar manner but with a series of original adaptations bringing them their specificities of action. From comparative studies with existing structures of PL6_1 alginate lyases, we observe that in the right-handed parallel β-helix fold shared by all these enzymes, the substrate binding site harbors the same overall conserved structures and organization. Despite this apparent similarity, it appears that members of the PL6_1 subfamily specifically accommodate and catalyze the degradation of different alginates suggesting that this common platform is actually a highly adaptable and specific tool.
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Affiliation(s)
- Sébastien Violot
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS Université de Lyon, 7 passage du Vercors, 69367 Lyon, France
| | - Frédéric Galisson
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS Université de Lyon, 7 passage du Vercors, 69367 Lyon, France
| | - Loïc Carrique
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS Université de Lyon, 7 passage du Vercors, 69367 Lyon, France
| | - Vinesh Jugnarain
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS Université de Lyon, 7 passage du Vercors, 69367 Lyon, France
| | - Léa Conchou
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS Université de Lyon, 7 passage du Vercors, 69367 Lyon, France
| | - Xavier Robert
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS Université de Lyon, 7 passage du Vercors, 69367 Lyon, France
| | | | - William Helbert
- Centre de Recherches sur les Macromolécules Végétales (CERMAV), Université Grenoble Alpes, CNRS, 38000 Grenoble, France
| | - Nushin Aghajari
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS Université de Lyon, 7 passage du Vercors, 69367 Lyon, France
| | - Lionel Ballut
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS Université de Lyon, 7 passage du Vercors, 69367 Lyon, France
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44
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Dai YX, Chen WF, Liu NN, Teng FY, Guo HL, Hou XM, Dou SX, Rety S, Xi XG. Structural and functional studies of SF1B Pif1 from Thermus oshimai reveal dimerization-induced helicase inhibition. Nucleic Acids Res 2021; 49:4129-4143. [PMID: 33784404 PMCID: PMC8053095 DOI: 10.1093/nar/gkab188] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 03/03/2021] [Accepted: 03/05/2021] [Indexed: 01/06/2023] Open
Abstract
Pif1 is an SF1B helicase that is evolutionarily conserved from bacteria to humans and plays multiple roles in maintaining genome stability in both nucleus and mitochondria. Though highly conserved, Pif1 family harbors a large mechanistic diversity. Here, we report crystal structures of Thermus oshimai Pif1 (ToPif1) alone and complexed with partial duplex or single-stranded DNA. In the apo state and in complex with a partial duplex DNA, ToPif1 is monomeric with its domain 2B/loop3 adopting a closed and an open conformation, respectively. When complexed with a single-stranded DNA, ToPif1 forms a stable dimer with domain 2B/loop3 shifting to a more open conformation. Single-molecule and biochemical assays show that domain 2B/loop3 switches repetitively between the closed and open conformations when a ToPif1 monomer unwinds DNA and, in contrast with other typical dimeric SF1A helicases, dimerization has an inhibitory effect on its helicase activity. This mechanism is not general for all Pif1 helicases but illustrates the diversity of regulation mechanisms among different helicases. It also raises the possibility that although dimerization results in activation for SF1A helicases, it may lead to inhibition for some of the other uncharacterized SF1B helicases, an interesting subject warranting further studies.
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Affiliation(s)
- Yang-Xue Dai
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Wei-Fei Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Na-Nv Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Fang-Yuan Teng
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hai-Lei Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xi-Miao Hou
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Shuo-Xing Dou
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.,School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Stephane Rety
- Univ. Lyon, ENS de Lyon, Univ. Claude Bernard CNRS UMR 5239, INSERM U1210, LBMC, 46 allée d'Italie Site Jacques Monod, F-69007, Lyon, France
| | - Xu-Guang Xi
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China.,Laboratoire de Biologie et de Pharmacologie Appliquée (LBPA), UMR 8113 CNRS, Institut D'Alembert, École Normale Supérieure Paris-Saclay, Université Paris-Saclay, 4, Avenue des Sciences, 91190 Gif sur Yvette, France
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45
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Lipa-Castro A, Nicolas V, Angelova A, Mekhloufi G, Prost B, Chéron M, Faivre V, Barratt G. Cochleate formulations of Amphotericin b designed for oral administration using a naturally occurring phospholipid. Int J Pharm 2021; 603:120688. [PMID: 33965540 DOI: 10.1016/j.ijpharm.2021.120688] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 04/23/2021] [Accepted: 05/04/2021] [Indexed: 12/21/2022]
Abstract
The purpose of this work was to formulate the poor soluble antifungal and antiparasitic agent Amphotericin B (AmB) in cost-effective lipid-based formulations suitable for oral use in developing countries, overcoming the limitations of poor water solubility, nephrotoxicity and low oral bioavailability. The antifungal agent was formulated, at different molar proportions, in cochleate nanocarriers prepared using an accessible naturally occurring phospholipid rich in phosphatidylserine (Lipoid PSP70). These nanoassemblies were prepared by condensation of negatively charged phospholipid membrane vesicles with divalent cations (Ca2+). Small-angle X-ray scattering studies revealed the Ca2+-triggered condensation of loosely packed multilamellar vesicles into tightly packed bilayers of strongly dehydrated multilamellar organization characterized by narrow Bragg peaks. Transmission electron microscopy and quasi-elastic light scattering studies demonstrated the formation of nanosized particles. AmB drug loading was above 55% in all formulations. Circular dichroism demonstrated the prevalence of monomeric and complexed forms of AmB over toxic aggregates. The stability of AmB in gastric medium was improved by loading in cochleates and its release in gastrointestinal media was retarded. Confocal microscopy studies revealed the in-vitro interactions of Lipoid PSP70-based cochleates with Caco2 intestinal cell monolayers. The results suggest that the low-cost AmB-loaded cochleates may increase the therapeutic range of this drug.
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Affiliation(s)
- Antonio Lipa-Castro
- Université Paris-Saclay, CNRS, Institut Galien Paris-Saclay, 92290 Châtenay-Malabry, France
| | - Valérie Nicolas
- Université Paris-Saclay, Inserm, IPSIT, Plateforme MIPSIT, 92290 Châtenay-Malabry, France
| | - Angelina Angelova
- Université Paris-Saclay, CNRS, Institut Galien Paris-Saclay, 92290 Châtenay-Malabry, France
| | - Ghozlene Mekhloufi
- Université Paris-Saclay, CNRS, Institut Galien Paris-Saclay, 92290 Châtenay-Malabry, France
| | - Bastien Prost
- Université Paris-Saclay, Inserm, IPSIT, Plateforme SAMM, 92290 Châtenay-Malabry, France
| | - Monique Chéron
- Faculté de Pharmacie, Université Paris-Saclay, 92290 Châtenay-Malabry, France
| | - Vincent Faivre
- Université Paris-Saclay, CNRS, Institut Galien Paris-Saclay, 92290 Châtenay-Malabry, France
| | - Gillian Barratt
- Université Paris-Saclay, CNRS, Institut Galien Paris-Saclay, 92290 Châtenay-Malabry, France.
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46
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Zhai LT, Rety S, Chen WF, Song ZY, Auguin D, Sun B, Dou SX, Xi XG. Crystal structures of N-terminally truncated telomerase reverse transcriptase from fungi‡. Nucleic Acids Res 2021; 49:4768-4781. [PMID: 33856462 PMCID: PMC8096264 DOI: 10.1093/nar/gkab261] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 03/28/2021] [Accepted: 04/05/2021] [Indexed: 12/12/2022] Open
Abstract
Telomerase plays critical roles in cellular aging, in the emergence and/or development of cancer, and in the capacity for stem-cell renewal, consists of a catalytic telomerase reverse transcriptase (TERT) and a template-encoding RNA (TER). TERs from diverse organisms contain two conserved structural elements: the template-pseudoknot (T-PK) and a helical three-way junction (TWJ). Species-specific features of the structure and function of telomerase make obtaining a more in-depth understanding of the molecular mechanism of telomerase particularly important. Here, we report the first structural studies of N-terminally truncated TERTs from Candida albicans and Candida tropicalis in apo form and complexed with their respective TWJs in several conformations. We found that Candida TERT proteins perform only one round of telomere addition in the presence or absence of PK/TWJ and display standard reverse transcriptase activity. The C-terminal domain adopts at least two extreme conformations and undergoes conformational interconversion, which regulates the catalytic activity. Most importantly, we identified a conserved tertiary structural motif, called the U-motif, which interacts with the reverse transcriptase domain and is crucial for catalytic activity. Together these results shed new light on the structure and mechanics of fungal TERTs, which show common TERT characteristics, but also display species-specific features.
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Affiliation(s)
- Liu-Tao Zhai
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Stephane Rety
- University Lyon, ENS de Lyon, University Claude Bernard, CNRS UMR 5239, INSERM U1210, LBMC, 46 Allée d’Italie Site Jacques Monod, F-69007 Lyon, France
| | - Wei-Fei Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ze-Yu Song
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Daniel Auguin
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), Université d’Orléans, INRA, USC1328, 45067 Orléans; Structural Motility, Institut Curie, CNRS, UMR 144 Paris, France
| | - Bo Sun
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Shuo-Xing Dou
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xu-Guang Xi
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
- Laboratoire de Biologie et de Pharmacologie Appliquée (LBPA), UMR 8113 CNRS, Institut D’Alembert, École Normale Supérieure Paris-Saclay, Université Paris-Saclay, 4, Avenue des Sciences, 91190 Gif sur Yvette, France
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47
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Kettisen K, Dicko C, Smeds E, Bülow L. Site-Specific Introduction of Negative Charges on the Protein Surface for Improving Global Functions of Recombinant Fetal Hemoglobin. Front Mol Biosci 2021; 8:649007. [PMID: 33859997 PMCID: PMC8042259 DOI: 10.3389/fmolb.2021.649007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Accepted: 03/04/2021] [Indexed: 11/13/2022] Open
Abstract
Due to its compatible oxygen-transporting abilities, hemoglobin (Hb) is a protein of interest in the development of artificial oxygen therapeutics. Despite continuous formulation attempts, extracellular Hb solution often exhibits undesirable reactions when applied in vivo. Therefore, protein engineering is frequently used to examine alternative ways of controlling the unwanted reactions linked to cell-free Hb solutions. In this study, three mutants of human fetal hemoglobin (HbF) are evaluated; single mutants αA12D and αA19D, and a double mutant αA12D/A19D. These variants were obtained by site-directed mutagenesis and recombinant production in E. coli, and carry negative charges on the surface of the α-subunit at the designated mutation sites. Through characterization of the mutant proteins, we found that the substitutions affected the protein in several ways. As expected, the isoelectric points (pIs) were lowered, from 7.1 (wild-type) down to 6.6 (double mutant), which influenced the anion exchange chromatographic procedures by shifting conditions toward higher conductivity for protein elution. The biological and physiological properties of HbF could be improved by these small modifications on the protein surface. The DNA cleavage rate associated with native HbF could be reduced by 55%. In addition, the negatively charged HbF mutant had an extended circulation time when examined in a mouse model using top load Hb additions. At the same time, the mutations did not affect the overall structural integrity of the HbF molecule, as determined by small-angle X-ray scattering. In combination with circular dichroism and thermal stability, modest structural shifts imposed by the mutations could possibly be related to changes in secondary structure or reorganization. Such local deformations were too minor to be determined within the resolution of the structural data; and overall, unchanged oxidation and heme loss kinetics support the conclusion that the mutations did not adversely affect the basic structural properties of Hb. We confirm the value of adding negatively charged residues onto the surface of the protein to improve the global functions of recombinant Hb.
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Affiliation(s)
- Karin Kettisen
- Division of Pure and Applied Biochemistry, Department of Chemistry, Lund University, Lund, Sweden
| | - Cedric Dicko
- Division of Pure and Applied Biochemistry, Department of Chemistry, Lund University, Lund, Sweden
| | - Emanuel Smeds
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Leif Bülow
- Division of Pure and Applied Biochemistry, Department of Chemistry, Lund University, Lund, Sweden
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48
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Shao H, Huang W, Avilan L, Receveur-Bréchot V, Puppo C, Puppo R, Lebrun R, Gontero B, Launay H. A new type of flexible CP12 protein in the marine diatom Thalassiosira pseudonana. Cell Commun Signal 2021; 19:38. [PMID: 33761918 PMCID: PMC7992989 DOI: 10.1186/s12964-021-00718-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/09/2021] [Indexed: 12/11/2022] Open
Abstract
Background CP12 is a small chloroplast protein that is widespread in various photosynthetic organisms and is an actor of the redox signaling pathway involved in the regulation of the Calvin Benson Bassham (CBB) cycle. The gene encoding this protein is conserved in many diatoms, but the protein has been overlooked in these organisms, despite their ecological importance and their complex and still enigmatic evolutionary background. Methods A combination of biochemical, bioinformatics and biophysical methods including electrospray ionization-mass spectrometry, circular dichroism, nuclear magnetic resonance spectroscopy and small X ray scattering, was used to characterize a diatom CP12. Results Here, we demonstrate that CP12 is expressed in the marine diatom Thalassiosira pseudonana constitutively in dark-treated and in continuous light-treated cells as well as in all growth phases. This CP12 similarly to its homologues in other species has some features of intrinsically disorder protein family: it behaves abnormally under gel electrophoresis and size exclusion chromatography, has a high net charge and a bias amino acid composition. By contrast, unlike other known CP12 proteins that are monomers, this protein is a dimer as suggested by native electrospray ionization-mass spectrometry and small angle X-ray scattering. In addition, small angle X-ray scattering revealed that this CP12 is an elongated cylinder with kinks. Circular dichroism spectra indicated that CP12 has a high content of α-helices, and nuclear magnetic resonance spectroscopy suggested that these helices are unstable and dynamic within a millisecond timescale. Together with in silico predictions, these results suggest that T. pseudonana CP12 has both coiled coil and disordered regions. Conclusions These findings bring new insights into the large family of dynamic proteins containing disordered regions, thus increasing the diversity of known CP12 proteins. As it is a protein that is more abundant in many stresses, it is not devoted to one metabolism and in particular, it is not specific to carbon metabolism. This raises questions about the role of this protein in addition to the well-established regulation of the CBB cycle. Choregraphy of metabolism by CP12 proteins in Viridiplantae and Heterokonta. While the monomeric CP12 in Viridiplantae is involved in carbon assimilation, regulating phosphoribulokinase (PRK) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) through the formation of a ternary complex, in Heterokonta studied so far, the dimeric CP12 is associated with Ferredoxin-NADP reductase (FNR) and GAPDH. The Viridiplantae CP12 can bind metal ions and can be a chaperone, the Heterokonta CP12 is more abundant in all stresses (C, N, Si, P limited conditions) and is not specific to a metabolism. ![]()
Video Abstract
Supplementary Information The online version contains supplementary material available at 10.1186/s12964-021-00718-x.
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Affiliation(s)
- Hui Shao
- CNRS, BIP UMR 7281, Aix Marseille Univ, 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 20, France
| | - Wenmin Huang
- CNRS, BIP UMR 7281, Aix Marseille Univ, 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 20, France.,Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Luisana Avilan
- CNRS, BIP UMR 7281, Aix Marseille Univ, 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 20, France.,Centre for Enzyme Innovation, School of Biological Sciences, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, PO1 2DY, UK
| | | | - Carine Puppo
- CNRS, BIP UMR 7281, Aix Marseille Univ, 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 20, France
| | - Rémy Puppo
- CNRS FR 3479, Plate-Forme Protéomique de L'Institut de Microbiologie de La Méditerranée (IMM), Aix Marseille Univ, 13009, Marseille, France
| | - Régine Lebrun
- CNRS FR 3479, Plate-Forme Protéomique de L'Institut de Microbiologie de La Méditerranée (IMM), Aix Marseille Univ, 13009, Marseille, France
| | - Brigitte Gontero
- CNRS, BIP UMR 7281, Aix Marseille Univ, 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 20, France.
| | - Hélène Launay
- CNRS, BIP UMR 7281, Aix Marseille Univ, 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 20, France.
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49
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Solution structure of multi-domain protein ER-60 studied by aggregation-free SAXS and coarse-grained-MD simulation. Sci Rep 2021; 11:5655. [PMID: 33707747 PMCID: PMC7952739 DOI: 10.1038/s41598-021-85219-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/25/2021] [Indexed: 11/08/2022] Open
Abstract
Multi-domain proteins (MDPs) show a variety of domain conformations under physiological conditions, regulating their functions through such conformational changes. One of the typical MDPs, ER-60 which is a protein folding enzyme, has a U-shape with four domains and is thought to have different domain conformations in solution depending on the redox state at the active centres of the edge domains. In this work, an aggregation-free small-angle X-ray scattering revealed that the structures of oxidized and reduced ER-60 in solution are different from each other and are also different from those in the crystal. Furthermore, structural modelling with coarse-grained molecular dynamics simulation indicated that the distance between the two edge domains of oxidized ER-60 is longer than that of reduced ER-60. In addition, one of the edge domains has a more flexible conformation than the other.
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Angelova A, Angelov B, Drechsler M, Bizien T, Gorshkova YE, Deng Y. Plasmalogen-Based Liquid Crystalline Multiphase Structures Involving Docosapentaenoyl Derivatives Inspired by Biological Cubic Membranes. Front Cell Dev Biol 2021; 9:617984. [PMID: 33644054 PMCID: PMC7905036 DOI: 10.3389/fcell.2021.617984] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 01/04/2021] [Indexed: 12/29/2022] Open
Abstract
Structural properties of plasmenyl-glycerophospholipids (plasmalogens) have been scarcely studied for plasmalogens with long polyunsaturated fatty acid (PUFA) chains, despite of their significance for the organization and functions of the cellular membranes. Elaboration of supramolecular assemblies involving PUFA-chain plasmalogens in nanostructured mixtures with lyotropic lipids may accelerate the development of nanomedicines for certain severe pathologies (e.g., peroxisomal disorders, cardiometabolic impairments, and neurodegenerative Alzheimer's and Parkinson's diseases). Here, we investigate the spontaneous self-assembly of bioinspired, custom-produced docosapentaenoyl (DPA) plasmenyl (ether) and ester phospholipids in aqueous environment (pH 7) by synchrotron small-angle X-ray scattering (SAXS) and cryogenic transmission electron microscopy (cryo-TEM). A coexistence of a liquid crystalline primitive cubic Im3m phase and an inverted hexagonal (HII) phase is observed for the DPA-ethanolamine plasmalogen (C16:1p-22:5n6 PE) derivative. A double-diamond cubic Pn3m phase is formed in mixed assemblies of the phosphoethanolamine plasmalogen (C16:1p-22:5n6 PE) and monoolein (MO), whereas a coexistence of cubic and lamellar liquid crystalline phases is established for the DPA-plasmenyl phosphocholine (C16:1p-22:5n6 PC)/MO mixture at ambient temperature. The DPA-diacyl phosphoinositol (22:5n6-22:5n6 PI) ester lipid displays a propensity for a lamellar phase formation. Double membrane vesicles and multilamellar onion topologies with inhomogeneous distribution of interfacial curvature are formed upon incorporation of the phosphoethanolamine plasmalogen (C16:1p-22:5n6 PE) into dioleoylphosphocholine (DOPC) bilayers. Nanoparticulate formulations of plasmalogen-loaded cubosomes, hexosomes, and various multiphase cubosome- and hexosome-derived architectures and mixed type nano-objects (e.g., oil droplet-embedding vesicles or core-shell particles with soft corona) are produced with PUFA-chain phospholipids and lipophilic antioxidant-containing membrane compositions that are characterized by synchrotron SAXS and cryo-TEM imaging. The obtained multiphase nanostructures reflect the changes in the membrane curvature induced by the inclusion of DPA-based PE and PC plasmalogens, as well as DPA-PI ester derivative, and open new opportunities for exploration of these bioinspired nanoassemblies.
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Affiliation(s)
- Angelina Angelova
- Institut Galien Paris-Saclay UMR8612, Université Paris-Saclay, CNRS, Châtenay-Malabry, France
| | - Borislav Angelov
- Institute of Physics, ELI Beamlines, Academy of Sciences of the Czech Republic, Prague, Czech
| | - Markus Drechsler
- Keylab "Electron and Optical Microscopy", Bavarian Polymer Institute, University of Bayreuth, Bayreuth, Germany
| | - Thomas Bizien
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, France
| | - Yulia E Gorshkova
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna, Russia
| | - Yuru Deng
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, China
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