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1. Strikingly Different Roles of SARS-CoV-2 Fusion Peptides Uncovered by Neutron Scattering

Author

Santamaria, A., Batchu, K.C., Matsarskaia, O., Prévost, S.F., Russo, D., Natali, F., Seydel, T., Hoffmann, I., Laux, V., Haertlein, M., Darwish, T.A., Russell, R.A., Corucci, G., Fragneto, G., Maestro, A., Zaccai Nathan, R., Zaccai, N.R., Science and Technology Facilities Council (UK), Wellcome Trust, Agence Nationale de la Recherche (France), National Science Foundation (US), National Collaborative Research Infrastructure Strategy (Australia), Santamaria, Andreas [0000-0002-6151-4406], Matsarskaia, Olga [0000-0002-7293-7287], Seydel, Tilo [0000-0001-9630-1630], Hoffmann, Ingo [0000-0001-7178-6467], Darwish, Tamim A [0000-0001-7704-1837], Maestro, Armando [0000-0002-7791-8130], Zaccai, Nathan R [0000-0002-1476-2044], Apollo - University of Cambridge Repository, and Zaccai, Nathan [0000-0002-1476-2044]

Subjects
Membrane Fluidity, viruses, Lipid Bilayers, chemistry.chemical_element, Neutron scattering, Calcium, medicine.disease_cause, Biochemistry, Catalysis, Colloid and Surface Chemistry, Protein Domains, Scattering, Small Angle, medicine, Amino Acid Sequence, Unilamellar Liposomes, Coronavirus, Fusion, Chemistry, SARS-CoV-2, Lipid bilayer fusion, General Chemistry, Small-angle neutron scattering, Peptide Fragments, Neutron Diffraction, Membrane, Cholesterol, Spike Glycoprotein, Coronavirus, Biophysics, Neutron reflectometry
Abstract

Funder: National Collaborative Research Infrastructure Strategy (NCRIS), Funder: ANR/NSF-PIRE, Funder: Science and Technology Facilities Council, Funder: Institut Laue Langevin, Coronavirus disease-2019 (COVID-19), a potentially lethal respiratory illness caused by the coronavirus SARS-CoV-2, emerged in the end of 2019 and has since spread aggressively across the globe. A thorough understanding of the molecular mechanisms of cellular infection by coronaviruses is therefore of utmost importance. A critical stage in infection is the fusion between viral and host membranes. Here, we present a detailed investigation of the role of selected SARS-CoV-2 Spike fusion peptides, and the influence of calcium and cholesterol, in this fusion process. Structural information from specular neutron reflectometry and small angle neutron scattering, complemented by dynamics information from quasi-elastic and spin-echo neutron spectroscopy, revealed strikingly different functions encoded in the Spike fusion domain. Calcium drives the N-terminal of the Spike fusion domain to fully cross the host plasma membrane. Removing calcium, however, reorients the peptide back to the lipid leaflet closest to the virus, leading to significant changes in lipid fluidity and rigidity. In conjunction with other regions of the fusion domain, which are also positioned to bridge and dehydrate viral and host membranes, the molecular events leading to cell entry by SARS-CoV-2 are proposed.

Published
2022

2. Towards a molecular understanding of the water purification properties of Moringa seed proteins

Author

Moulin, M, Mossou, E, Signor, L, Kieffer-Jaquinod, S, Kwaambwa, HM, Nermark, F, Gutfreund, P, Mitchell, EP, Haertlein, M, Forsyth, VT, Rennie, AR, Institut Laue-Langevin (ILL), ILL, Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Namibia University of Science and Technology (NUST), University of Botswana, Keele University [Keele], Uppsala University, Leriche, Marianne, Infrastructure Française pour la Biologie Structurale Intégrée - - FRISBI2010 - ANR-10-INBS-0005 - INBS - VALID, Grenoble Alliance for Integrated Structural Cell Biology - - GRAL2010 - ANR-10-LABX-0049 - LABX - VALID, Institut de biologie structurale (IBS - UMR 5075 ), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratoire de Biologie à Grande Échelle (BGE - UMR S1038), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Uppsala Universitet [Uppsala], FRISBI within the Grenoble Partnership for Structural Biology (PSB) [ANR-10-INBS-05-02], GRAL within the Grenoble Partnership for Structural Biology (PSB) [ANR-10-LABX-49-01], 'Investissement d'Avenir Infrastructures Nationales en Biologie et Sante' programme (ProFI project), Swedish Research CouncilSwedish Research Council [348-2011-7241], EPSRCEngineering and Physical Sciences Research Council (EPSRC) [GR/R99393/01, EP/C015452/1], ANR-10-INBS-0005,FRISBI,Infrastructure Française pour la Biologie Structurale Intégrée(2010), ANR-10-LABX-0049,GRAL,Grenoble Alliance for Integrated Structural Cell Biology(2010), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])

Subjects
Models, Molecular, Moringa oleifera, Fysikalisk kemi, Neutron reflectometry, Mass spectrometry, Protein Conformation, Flocculation, Silicon Dioxide, Moringa oleifera seeds, Physical Chemistry, Water Purification, X-ray diffraction, QH301, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], Seeds, Aluminum Oxide, [INFO.INFO-DL]Computer Science [cs]/Digital Libraries [cs.DL], Water treatment, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Adsorption, Amino Acid Sequence, [INFO.INFO-DL] Computer Science [cs]/Digital Libraries [cs.DL], QC, ComputingMilieux_MISCELLANEOUS, Plant Proteins
Abstract

International audience; Seed extracts from Moringa oleifera are of wide interest for use in water purification where they can play an important role in flocculation; they also have potential as anti-microbial agents. Previous work has focused on the crude protein extract. Here we describe the detailed biophysical characterization of individual proteins from these seeds. The results provide new insights relating to the active compounds involved. One fraction, designated Mo-CBP3, has been characterized at a molecular level using a range of biochemical and biophysical techniques including liquid chromatography, X-ray diffraction, mass spectrometry, and neutron reflection. The interfacial behavior is of particular interest in considering water purification applications and interactions with both charged (e.g. silica) and uncharged (alumina) surfaces were studied. The reflection studies show that, in marked contrast to the crude extract, only a single layer of the purified Mo-CBP3 binds to a silica interface and that there is no binding to an alumina interface. These observations are consistent with the crystallographic structure of Mo-CBP3-4, which is one of the main isoforms of the Mo-CBP3 fraction. The results are put in context of previous studies of the properties of the crude extract. This work shows possible routes to development of separation processes that would be based on the specific properties of individual proteins.

Published
2019
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3. Neutron radiobiology studies with a pure cold neutron beam: application to the measurement of the thermal neutron RBE of A375 melanoma cells for Boron Neutron Capture Therapy

Author

Pedrosa-Rivera, María, Ruiz-Magaña, María José, Porras Sánchez, José Ignacio, Praena Rodríguez, Antonio Javier, Torres Sánchez, Pablo, Sabariego Quintanilla, Manuel, Köster, U., Forsyth, T., Soldner, T., Haertlein, M., and Ruiz Ruiz, María Carmen

Subjects
Boron neutron capture therapy, Neutron radiobiology, Astrophysics::High Energy Astrophysical Phenomena, Nuclear Theory, Physics::Medical Physics, Nuclear Experiment, Neutron sources
Abstract

Data on the radiobiological effects of thermal neutrons are usually obtained from irradiations in a mixed field of neutrons of different energies and gamma rays or from conversion of proton data with similar energies to those created in the neutron capture on nitrogen. Experimental data from irradiations in a pure thermal or cold neutron beam can help to find new values for neutron relative biological effectiveness (RBE) factors, which are useful for BNCT (Boron Neutron Capture Therapy) and radiation protection applications. We present a new experimental setup for radiobiological studies at a cold neutron beam at Institut Laue-Langevin, a beam without fast neutron component and almost no gamma ray contribution. After the irradiation, survival assays are performed to obtain the survival curves. Finally, comparing with a reference photon irradiation, the thermal neutron RBE factors can be calculated. The methodology is outlined at the example of A375 melanoma cells for which new radiobiological data were obtained., Institut Laue-Langevin, Avenue des Martyrs, 38042 Grenoble, France. Departamento de Física Atómica Molecular y Nuclear, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain. Departamento de Bioquímica y Biología Molecular III e Inmunología, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain., We acknowledge financial support for this work from the Fundación Científica de la Asociación Española Contra el Cáncer (AECC) under grant PS16163811PORR, Junta de Andalucía (Andalusian Regional Government), under contract P11-FQM-8229, Spanish MINECO and FEDER funds under contract FIS2015-69941-C2-1-P, and the founders of the University of Granada Chair Neutrons for Medicine: Spanish Fundación ACS and Capitán Antonio. M.P. acknowledges a grant under the program Becas de Iniciación a la Investigación from the Universidad de Granada (Plan Propio de Investigación).

Published
2019

4. Dynamic self-assembly of DNA minor groove-binding ligand DB921 into nanotubes triggered by an alkali halide

Author

Mizuta, R., Devos, J.M., Webster, J., Ling, W.L., Narayanan, T., Round, A., Munnur, D., Mossou, E., Farahat, A.A., Boykin, D.W., Wilson, W.D., Neidle, S., Schweins, R., Rannou, P., Haertlein, M., Forsyth, V.T., Mitchell, E.P., European Synchrotron Radiation Facility (ESRF), European Molecular Biology Laboratory [Grenoble] (EMBL), Inst Max Von Laue Paul Langevin, F-38042 Grenoble, France, Institut Laue-Langevin (ILL), ILL, SYstèmes Moléculaires et nanoMatériaux pour l’Energie et la Santé (SYMMES), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), ILL-EMBL, and Swiss Federal Research Institute

Subjects
[PHYS]Physics [physics], [CHIM.POLY]Chemical Sciences/Polymers, [CHIM]Chemical Sciences, QD, [CHIM.MATE]Chemical Sciences/Material chemistry, [PHYS.COND]Physics [physics]/Condensed Matter [cond-mat], [SPI.NANO]Engineering Sciences [physics]/Micro and nanotechnologies/Microelectronics, ComputingMilieux_MISCELLANEOUS
Abstract

We describe a novel self-assembling supramolecular nanotube system formed by a heterocyclic cationic molecule which was originally designed for its potential as an antiparasitic and DNA sequence recognition agent. Our structural characterisation work indicates that the nanotubes form via a hierarchical assembly mechanism that can be triggered and tuned by well-defined concentrations of simple alkali halide salts in water. The nanotubes assembled in NaCl have inner and outer diameters of ca. 22 nm and 26 nm respectively, with lengths that reach into several microns. Our results suggest the tubes consist of DB921 molecules stacked along the direction of the nanotube long axis. The tubes are stabilised by face-to-face π–π stacking and ionic interactions between the charged amidinium groups of the ligand and the negative halide ions. The assembly process of the nanotubes was followed using small-angle X-ray and neutron scattering, transmission electron microscopy and ultraviolet/visible spectroscopy. Our data demonstrate that assembly occurs through the formation of intermediate ribbon-like structures that in turn form helices that tighten and compact to form the final stable filament. This assembly process was tested using different alkali–metal salts, showing a strong preference for chloride or bromide anions and with little dependency on the type of cation. Our data further demonstrates the existence of a critical anion concentration above which the rate of self-assembly is greatly enhanced.

Published
2018
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5. Dynamic self-assembly of DNA minor groove-binding ligand DB921 into nanotubes triggered by an alkali halide

Author

Mizuta, R, Devos, J, Webster, J, Ling, W, Narayanan, T, Round, A, Munnur, D, Mossou, E, Farahat, A, Boykin, D, Wilson, W, Neidle, S, Schweins, R, Rannou, P, Haertlein, M, Forsyth, V, Mitchell, E, Institut Laue-Langevin (ILL), ILL, European Synchrotron Radiation Facility (ESRF), Institut de biologie structurale (IBS - UMR 5075 ), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), European Molecular Biology Laboratory [Grenoble] (EMBL), Georgia State University, University System of Georgia (USG), UCL School of Pharmacy, Synthèse, Structure et Propriétés de Matériaux Fonctionnels (STEP), SYstèmes Moléculaires et nanoMatériaux pour l’Energie et la Santé (SYMMES), Institut de Chimie du CNRS (INC)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Institut Nanosciences et Cryogénie (INAC), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), ANR-10-INBS-0005,FRISBI,Infrastructure Française pour la Biologie Structurale Intégrée(2010), ANR-10-LABX-0049,GRAL,Grenoble Alliance for Integrated Structural Cell Biology(2010), Institut Laue-Langevin ( ILL ), Institut de biologie structurale ( IBS - UMR 5075 ), Université Joseph Fourier - Grenoble 1 ( UJF ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Centre National de la Recherche Scientifique ( CNRS ) -Université Grenoble Alpes ( UGA ), European Synchrotron Radiation Facility ( ESRF ), European Molecular Biology Laboratory [Grenoble] ( EMBL ), Synthèse, Structure et Propriétés de Matériaux Fonctionnels ( STEP ), SYstèmes Moléculaires et nanoMatériaux pour l’Energie et la Santé ( SYMMES ), Institut Nanosciences et Cryogénie ( INAC ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Grenoble Alpes ( UGA ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Grenoble Alpes ( UGA ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut Nanosciences et Cryogénie ( INAC ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Grenoble Alpes ( UGA ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Grenoble Alpes ( UGA ) -Centre National de la Recherche Scientifique ( CNRS ), ANR-10-INBS-05-01/10-INBS-0005,FRISBI,Infrastructure Française pour la Biologie Structurale Intégrée ( 2010 ), ANR-10-LABX-0049/10-LABX-0049,GRAL,Grenoble Alliance for Integrated Structural Cell Biology ( 2010 ), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])

Subjects
PI STACKING, Physics::Biological Physics, Quantitative Biology::Biomolecules, Nanotubes, Amidines, RECOGNITION, DNA, Alkalies, Condensed Matter::Mesoscopic Systems and Quantum Hall Effect, Ligands, HELICAL RIBBONS, PEPTIDE NANOTUBES, ORGANIC SEMICONDUCTOR, Quantitative Biology::Subcellular Processes, NANOFABRICATION, Condensed Matter::Materials Science, Chemistry, MOLECULES, Halogens, WATER, [CHIM]Chemical Sciences, Benzimidazoles, AGENTS, [ SDV.BBM.BS ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], BUILDING-BLOCKS
Abstract

We describe the preparation of a novel self-assembling supramolecular nanotube system., We describe a novel self-assembling supramolecular nanotube system formed by a heterocyclic cationic molecule which was originally designed for its potential as an antiparasitic and DNA sequence recognition agent. Our structural characterisation work indicates that the nanotubes form via a hierarchical assembly mechanism that can be triggered and tuned by well-defined concentrations of simple alkali halide salts in water. The nanotubes assembled in NaCl have inner and outer diameters of ca. 22 nm and 26 nm respectively, with lengths that reach into several microns. Our results suggest the tubes consist of DB921 molecules stacked along the direction of the nanotube long axis. The tubes are stabilised by face-to-face π–π stacking and ionic interactions between the charged amidinium groups of the ligand and the negative halide ions. The assembly process of the nanotubes was followed using small-angle X-ray and neutron scattering, transmission electron microscopy and ultraviolet/visible spectroscopy. Our data demonstrate that assembly occurs through the formation of intermediate ribbon-like structures that in turn form helices that tighten and compact to form the final stable filament. This assembly process was tested using different alkali–metal salts, showing a strong preference for chloride or bromide anions and with little dependency on the type of cation. Our data further demonstrates the existence of a critical anion concentration above which the rate of self-assembly is greatly enhanced.

Published
2018
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7. Crowding of membrane proteins and peptides

Author

Grage, S, Afonin, S, Wadhwani, P, Mykhailiuk, P, Berditsch, M, Turdzeladze, T, May, R, Haertlein, M, Callow, P, Watts, A, Huang, K, Martinac, B, and Ulrich, A

Published
2011

10. Expression, purification, assay, and crystal structure of perdeuterated human arginase I

Author

David W. Christianson, Michael Haertlein, Flora Meilleur, Luigi Di Costanzo, Martine Moulin, DI COSTANZO, Luigi, Moulin, M., Haertlein, M., Meilleur, F., and Christianson, D. W.

Subjects
Models, Molecular, Protein Conformation, Stereochemistry, Neutron diffraction, Biophysics, Crystal structure, Protein Engineering, Biochemistry, Article, Substrate Specificity, Isotopic labeling, Protein structure, Hydrolase, Escherichia coli, Humans, Computer Simulation, Molecular Biology, chemistry.chemical_classification, Arginase, Protein crystallography, Recombinant Protein, Deuterium, Recombinant Proteins, Crystallography, Enzyme, Enzyme-inhibitor complex, Models, Chemical, chemistry, Yield (chemistry), Human
Abstract

Arginase is a manganese metalloenzyme that catalyzes the hydrolysis of l-arginine to yield l-ornithine and urea. In order to establish a foundation for future neutron diffraction studies that will provide conclusive structural information regarding proton/deuteron positions in enzyme-inhibitor complexes, we have expressed, purified, assayed, and determined the X-ray crystal structure of perdeuterated (i.e., fully deuterated) human arginase I complexed with 2(S)-amino-6-boronohexanoic acid (ABH) at 1.90A resolution. Prior to the neutron diffraction experiment, it is important to establish that perdeuteration does not cause any unanticipated structural or functional changes. Accordingly, we find that perdeuterated human arginase I exhibits catalytic activity essentially identical to that of the unlabeled enzyme. Additionally, the structure of the perdeuterated human arginase I-ABH complex is identical to that of the corresponding complex with the unlabeled enzyme. Therefore, we conclude that crystals of the perdeuterated human arginase I-ABH complex are suitable for neutron crystallographic study.

Published
2007
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