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1. Structural basis for the inhibition of IAPP fibril formation by the co-chaperonin prefoldin

Author

Ricarda Törner, Tatsiana Kupreichyk, Lothar Gremer, Elisa Colas Debled, Daphna Fenel, Sarah Schemmert, Pierre Gans, Dieter Willbold, Guy Schoehn, Wolfgang Hoyer, Jerome Boisbouvier, Institut de biologie structurale (IBS - UMR 5075), Centre National de la Recherche Scientifique (CNRS)-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)-Université Grenoble Alpes (UGA), Institute of Biochemistry & Molecular Biology II, Heinrich Heine University Medical Center, Institut für Physikalische Biologie [Düsseldorfd], Heinrich Heine Universität Düsseldorf = Heinrich Heine University [Düsseldorf], and ANR-20-CE05-0016,DEAL,Amélioration de la durabilité des véhicules électriques à pile à combustible en explorant le contrôle basé sur l'apprentissage à plusieurs niveaux(2020)

Subjects
MESH: Amyloid, Amyloid, MESH: Chaperonins, MESH: Humans, Multidisciplinary, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Chaperonins, General Physics and Astronomy, General Chemistry, MESH: Islet Amyloid Polypeptide, General Biochemistry, Genetics and Molecular Biology, Islet Amyloid Polypeptide, Humans, ddc:500, MESH: Molecular Chaperones, prefoldin, metabolism [Molecular Chaperones], metabolism [Amyloid], Molecular Chaperones
Abstract

Chaperones, as modulators of protein conformational states, are key cellular actors to prevent the accumulation of fibrillar aggregates. Here, we integrated kinetic investigations with structural studies to elucidate how the ubiquitous co-chaperonin prefoldin inhibits diabetes associated islet amyloid polypeptide (IAPP) fibril formation. We demonstrated that both human and archaeal prefoldin interfere similarly with the IAPP fibril elongation and secondary nucleation pathways. Using archaeal prefoldin model, we combined nuclear magnetic resonance spectroscopy with electron microscopy to establish that the inhibition of fibril formation is mediated by the binding of prefoldin’s coiled-coil helices to the flexible IAPP N-terminal segment accessible on the fibril surface and fibril ends. Atomic force microscopy demonstrates that binding of prefoldin to IAPP leads to the formation of lower amounts of aggregates, composed of shorter fibrils, clustered together. Linking structural models with observed fibrillation inhibition processes opens perspectives for understanding the interference between natural chaperones and formation of disease-associated amyloids.

Published
2022
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2. True-atomic-resolution insights into the structure and functional role of linear chains and low-barrier hydrogen bonds in proteins

Author

Valentin Borshchevskiy, Kirill Kovalev, Ekaterina Round, Rouslan Efremov, Roman Astashkin, Gleb Bourenkov, Dmitry Bratanov, Taras Balandin, Igor Chizhov, Christian Baeken, Ivan Gushchin, Alexander Kuzmin, Alexey Alekseev, Andrey Rogachev, Dieter Willbold, Martin Engelhard, Ernst Bamberg, Georg Büldt, Valentin Gordeliy, Moscow Institute of Physics and Technology [Moscow] (MIPT), Institute of Complex Systems (ICS), Forschungszentrum Jülich GmbH | Centre de recherche de Juliers, Helmholtz-Gemeinschaft = Helmholtz Association-Helmholtz-Gemeinschaft = Helmholtz Association, European X-ray Free Electron Laser GmbH, Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), Institut de biologie structurale (IBS - UMR 5075), Centre National de la Recherche Scientifique (CNRS)-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)-Université Grenoble Alpes (UGA), DESY, European Mol Biol Lab, D-22607 Hamburg, Germany, Institute of Biological Information Processing [Jülich] (IBI-7), Institute for Biophysical Chemistry, Hannover Medical School [Hannover] (MHH), Jülich Center for Structural Biology [Jülich] (JuStruct), Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow, Institut für Physikalische Biologie [Düsseldorfd], Heinrich Heine Universität Düsseldorf = Heinrich Heine University [Düsseldorf], Max Planck Institute of Molecular Physiology, Max-Planck-Gesellschaft, and Department of Structural Biology, Max-Planck-Institute of Biophysics, Frankfurt, Germany

Subjects
[SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Structural Biology, Proteins, MESH: Proteins, Hydrogen Bonding, MESH: Hydrogen Bonding, MESH: Protons, Protons, Molecular Biology
Abstract

International audience; Hydrogen bonds are fundamental to the structure and function of biological macromolecules and have been explored in detail. The chains of hydrogen bonds (CHBs) and low-barrier hydrogen bonds (LBHBs) were proposed to play essential roles in enzyme catalysis and proton transport. However, high-resolution structural data from CHBs and LBHBs is limited. The challenge is that their 'visualization' requires ultrahigh-resolution structures of the ground and functionally important intermediate states to identify proton translocation events and perform their structural assignment. Our true-atomic-resolution structures of the light-driven proton pump bacteriorhodopsin, a model in studies of proton transport, show that CHBs and LBHBs not only serve as proton pathways, but also are indispensable for long-range communications, signaling and proton storage in proteins. The complete picture of CHBs and LBHBs discloses their multifunctional roles in providing protein functions and presents a consistent picture of proton transport and storage resolving long-standing debates and controversies.

Published
2021
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3. Daily global mapping of Mars ozone column abundances with MARCI UV band imaging

Author

Michael C. Malin, Bruce A. Cantor, Franck Lefèvre, Michael D. Smith, R. Todd Clancy, Michael J. Wolff, Space Science Institute [Boulder] (SSI), Institut für Physikalische Biologie [Düsseldorfd], Heinrich Heine Universität Düsseldorf = Heinrich Heine University [Düsseldorf], PLANETO - LATMOS, Laboratoire Atmosphères, Milieux, Observations Spatiales (LATMOS), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Malin Space Science Systems (MSSS), and NASA Goddard Space Flight Center (GSFC)

Subjects
Atmospheres, Ice cloud, 010504 meteorology & atmospheric sciences, Photochemistry, Atmosphere, [SDU.ASTR.EP]Sciences of the Universe [physics]/Astrophysics [astro-ph]/Earth and Planetary Astrophysics [astro-ph.EP], Mars, Astronomy and Astrophysics, Context (language use), Mars Exploration Program, Atmosphere of Mars, Atmospheric sciences, 01 natural sciences, Latitude, Chemistry, 13. Climate action, Space and Planetary Science, Dust storm, 0103 physical sciences, Ultraviolet Observations, 010303 astronomy & astrophysics, Water vapor, 0105 earth and related environmental sciences
Abstract

International audience; Since November of 2006, The Mars Color Imager (MARCI) onboard the Mars Reconnaissance Orbiter (MRO) has obtained multiple-filter daily global images of Mars centered upon a local time (LT) of 3pm. Ultraviolet imaging bands placed within (260 nm) and longward (320 nm) of Hartley band (240-300 nm) ozone (O3) absorption support retrievals of atmospheric ozone columns, with detection limits (∼ 1 μm-atm) appropriate to mapping elevated O3 abundances at low latitudes around Mars aphelion, and over mid-to-high latitudes during fall/winter/spring seasons. MARCI O3 maps for these regions reveal the detailed spatial (∼1° lat/long, for 8x8 pixel binned resolution) and temporal (daily, with substantial LT coverage at pole) behaviors of water vapor saturation conditions that force large variations in water vapor photolysis products (HOx- OH, HO2, and H) responsible for the catalytic destruction of O3 in the Mars atmosphere. A detailed description of the MARCI O3 data set, including measurement and retrieval characteristics, is provided in conjunction with comparisons to Mars Express SPICAM ozone measurements ( Perrier et al., 2006) and LMD GCM simulated O3 abundances ( Lefèvre et al., 2004). Presented aspects of the MARCI ozone mapping data set include aphelion increases in low latitude O3, dynamically evolving high latitude O3 maxima associated with planetary waves and weather fronts during northern early spring, and distinctive winter/spring O3 and CO increases within the Hellas basin associated with transport of condensation-enhanced south polar air mass. Comparisons of coincident MARCI measurements and LMD simulations for ice cloud and O3 columns are considered in the context of potential heterogeneous photochemical processes ( Lefèvre et al., 2008), which are not strongly evidenced in the MARCI observations. Modest interannual variations are exhibited, most notably a 20% reduction in aphelion low latitude O3 columns following the 2007 perihelic global dust storm.

Published
2016
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4. Mechanism of transmembrane signaling by sensor histidine kinases

Author

Gushchin, Ivan Yu., Melkinov, Igor, Polovinkin, Vitaly, Ishchenko, Andrii, Yuzhakova, Anastasia, Buslaev, Pavel, Bourenkov, Gleb, Grudinin, Sergei, Round, Ekaterina, Balandin, Taras, Borshchevskiy, Valentin, Willbold, Dieter, Leonard, Gordon, Büldt, Georg, Popov, Alexander, Gordeliy, Valentin I., Moscow Institute of Physics and Technology [Moscow] (MIPT), Institute of Complex Systems (ICS), Forschungszentrum Jülich GmbH | Centre de recherche de Juliers, Helmholtz-Gemeinschaft = Helmholtz Association-Helmholtz-Gemeinschaft = Helmholtz Association, 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), European Synchrotron Radiation Facility (ESRF), Institute of Crystallography [Aachen], Rheinisch-Westfälische Technische Hochschule Aachen University (RWTH), European Molecular Biology Laboratory [Hamburg] (EMBL), Algorithms for Modeling and Simulation of Nanosystems (NANO-D), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Laboratoire Jean Kuntzmann (LJK ), Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Institut für Physikalische Biologie [Düsseldorfd], Heinrich Heine Universität Düsseldorf = Heinrich Heine University [Düsseldorf], 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), and Rheinisch-Westfälische Technische Hochschule Aachen (RWTH)

Subjects
[SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], [PHYS.PHYS.PHYS-BIO-PH]Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph], Protein crystallography, Protein structure, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation
Abstract

International audience; One of the major and essential classes of transmembrane (TM) receptors, present in all domains of life, is sensor histidine kinases (HKs), parts of two-component signaling systems (TCS). The structural mechanisms of transmembrane signaling by these sensors are poorly understood. We present here crystal structures of the periplasmic sensor domain, the TM domain and the cytoplasmic HAMP domain of the Escherichia coli nitrate/nitrite sensor HK NarQ in the ligand-bound and mutated ligand-free states. The structures reveal that the ligand binding induces significant rearrangements and piston-like shifts of TM helices. The HAMP domain protomers undergo lever-like motions and convert the piston-like motions into helical rotations. Our findings provide the structural framework for complete understanding of TM TCS signaling and for development of antimicrobial treatments targeting TCS.

Published
2017
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5. Amyloid β Oligomeric Species Present in the Lag Phase of Amyloid Formation

Author

Martin, Wolff, Dmitry, Unuchek, Bo, Zhang, Valentin, Gordeliy, Dieter, Willbold, Luitgard, Nagel-Steger, Institut für Physikalische Biologie [Düsseldorfd], Heinrich Heine Universität Düsseldorf = Heinrich Heine University [Düsseldorf], Dep. of Molecular and Chemical Physics, Moscow Institute of Physics and Technology [Moscow] (MIPT), Institute of Complex Systems, Structural Biochemistry (ICS-6), Research Centre Julich, 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), Thomas, Frank, 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)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)

Subjects
Amyloid beta-Peptides, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], [SDV.BBM.BS] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], lcsh:R, lcsh:Medicine, Protein Aggregation, Pathological, Peptide Fragments, Protein Aggregates, Alzheimer Disease, Humans, lcsh:Q, ddc:500, lcsh:Science, Research Article
Abstract

International audience; Alzheimer's disease (AD)-associated amyloid β peptide (Aβ) is one of the main actors in AD pathogenesis. Aβ is characterized by its high tendency to self-associate, leading to the generation of oligomers and amyloid fibrils. The elucidation of pathways and intermediates is crucial for the understanding of protein assembly mechanisms in general and in conjunction with neurodegenerative diseases, e.g., for the identification of new therapeutic targets. Our study focused on Aβ42 and its oligomeric assemblies in the lag phase of amyloid formation, as studied by sedimentation velocity (SV) centrifugation. The assembly state of Aβ during the lag phase, the time required by an Aβ solution to reach the exponential growth phase of aggregation, was characterized by a dominant monomer fraction below 1 S and a population of oligomeric species between 4 and 16 S. From the oligomer population, two major species close to a 12-mer and an 18-mer with a globular shape were identified. The recurrence of these two species at different initial concentrations and experimental conditions as the smallest assemblies present in solution supports the existence of distinct, energetically favored assemblies in solution. The sizes of the two species suggest an Aβ42 aggregation pathway that is based on a basic hexameric building block. The study demonstrates the potential of SV analysis for the evaluation of protein aggregation pathways.

Published
2015
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6. The cspA mRNA is a thermosensor that modulates translation of the cold-shock protein CspA

Author

Benoît Masquida, Anna Maria Giuliodori, Claudio O. Gualerzi, Fabio Di Pietro, Cynthia L. Pon, Rolf Wagner, Pascale Romby, Stefano Marzi, Laboratory of Genetics, Department of Biology MCA, University of Camerino, Italy, Architecture et Réactivité de l'ARN (ARN), Institut de biologie moléculaire et cellulaire (IBMC), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut für Physikalische Biologie [Düsseldorfd], and Heinrich Heine Universität Düsseldorf = Heinrich Heine University [Düsseldorf]

Subjects
MESH: Cold Temperature, MESH: Acclimatization, MESH: Escherichia coli Proteins, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Biology, MESH: Heat-Shock Proteins, 03 medical and health sciences, Sense (molecular biology), MESH: Models, Genetic, Gene, Protein secondary structure, Molecular Biology, 030304 developmental biology, MESH: RNA, Messenger, 0303 health sciences, Messenger RNA, MESH: Gene Expression Regulation, Bacterial, 030306 microbiology, MESH: Escherichia coli, Mutagenesis, RNA, Translation (biology), [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Cell Biology, Cold-shock domain, Molecular biology, MESH: Nucleic Acid Conformation, MESH: Protein Biosynthesis, Biophysics, MESH: 5' Untranslated Regions
Abstract

International audience; Cold induction of cspA, the paradigm Escherichia coli cold-shock gene, is mainly subject to posttranscriptional control, partly promoted by cis-acting elements of its transcript, whose secondary structure at 37 degrees C and at cold-shock temperature has been elucidated here by enzymatic and chemical probing. The structures, which were also validated by mutagenesis, demonstrate that cspA mRNA undergoes a temperature-dependent structural rearrangement, likely resulting from stabilization in the cold of an otherwise thermodynamically unstable folding intermediate. At low temperature, the "cold-shock" structure is more efficiently translated and somewhat less susceptible to degradation than the 37 degrees C structure. Overall, our data shed light on a molecular mechanism at the basis of the cold-shock response, indicating that cspA mRNA is able to sense temperature downshifts, adopting functionally distinct structures at different temperatures, even without the aid of trans-acting factors. Unlike with other previously studied RNA thermometers, these structural rearrangements do not result from melting of hairpin structures.

Published
2010
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