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Lauster D, Klenk S, Ludwig K, Nojoumi S, Behren S, Adam L, Stadtmüller M, Saenger S, Zimmler S, Hönzke K, Yao L, Hoffmann U, Bardua M, Hamann A, Witzenrath M, Sander LE, Wolff T, Hocke AC, Hippenstiel S, De Carlo S, Neudecker J, Osterrieder K, Budisa N, Netz RR, Böttcher C, Liese S, Herrmann A, Hackenberger CPR. Phage capsid nanoparticles with defined ligand arrangement block influenza virus entry. Nat Nanotechnol 2020; 15:373-379. [PMID: 32231271 DOI: 10.1038/s41565-020-0660-2] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 02/25/2020] [Indexed: 05/21/2023]
Abstract
Multivalent interactions at biological interfaces occur frequently in nature and mediate recognition and interactions in essential physiological processes such as cell-to-cell adhesion. Multivalency is also a key principle that allows tight binding between pathogens and host cells during the initial stages of infection. One promising approach to prevent infection is the design of synthetic or semisynthetic multivalent binders that interfere with pathogen adhesion1-4. Here, we present a multivalent binder that is based on a spatially defined arrangement of ligands for the viral spike protein haemagglutinin of the influenza A virus. Complementary experimental and theoretical approaches demonstrate that bacteriophage capsids, which carry host cell haemagglutinin ligands in an arrangement matching the geometry of binding sites of the spike protein, can bind to viruses in a defined multivalent mode. These capsids cover the entire virus envelope, thus preventing its binding to the host cell as visualized by cryo-electron tomography. As a consequence, virus infection can be inhibited in vitro, ex vivo and in vivo. Such highly functionalized capsids present an alternative to strategies that target virus entry by spike-inhibiting antibodies5 and peptides6 or that address late steps of the viral replication cycle7.
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Affiliation(s)
- Daniel Lauster
- Institut für Chemie und Biochemie, Organische Chemie, Freie Universität Berlin, Berlin, Germany
- Institut für Biologie, Molekulare Biophysik, IRI Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Simon Klenk
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
- Institut für Chemie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Kai Ludwig
- Forschungszentrum für Elektronenmikroskopie und Gerätezentrum BioSupraMol, Institut für Chemie und Biochemie, Freie Universität Berlin, Berlin, Germany
| | - Saba Nojoumi
- Institut für Chemie, Biokatalyse, Technische Universität Berlin, Berlin, Germany
- Department of Chemistry, University of Manitoba, Winnipeg, Canada
| | - Sandra Behren
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
- Institut für Chemie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Lutz Adam
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
- Institut für Chemie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Marlena Stadtmüller
- Robert Koch Institut, FG 17 Influenzaviren und weitere Viren des Respirationstraktes, Berlin, Germany
| | - Sandra Saenger
- Robert Koch Institut, FG 17 Influenzaviren und weitere Viren des Respirationstraktes, Berlin, Germany
| | - Stephanie Zimmler
- Robert Koch Institut, FG 17 Influenzaviren und weitere Viren des Respirationstraktes, Berlin, Germany
| | - Katja Hönzke
- Medizinische Klinik mit Schwerpunkt Infektiologie und Pneumologie, Charité, Universitätsmedizin Berlin, Partner von Freie Universität Berlin, Humboldt-Universität zu Berlin und Berlin Institute of Health, Berlin, Germany
| | - Ling Yao
- Medizinische Klinik mit Schwerpunkt Infektiologie und Pneumologie, Charité, Universitätsmedizin Berlin, Partner von Freie Universität Berlin, Humboldt-Universität zu Berlin und Berlin Institute of Health, Berlin, Germany
| | - Ute Hoffmann
- Experimentelle Rheumatologie, Deutsches Rheuma-Forschungszentrum Berlin, ein Leibniz-Institut, Berlin, Germany
| | - Markus Bardua
- Experimentelle Rheumatologie, Deutsches Rheuma-Forschungszentrum Berlin, ein Leibniz-Institut, Berlin, Germany
| | - Alf Hamann
- Experimentelle Rheumatologie, Deutsches Rheuma-Forschungszentrum Berlin, ein Leibniz-Institut, Berlin, Germany
| | - Martin Witzenrath
- Medizinische Klinik mit Schwerpunkt Infektiologie und Pneumologie, Charité, Universitätsmedizin Berlin, Partner von Freie Universität Berlin, Humboldt-Universität zu Berlin und Berlin Institute of Health, Berlin, Germany
| | - Leif E Sander
- Medizinische Klinik mit Schwerpunkt Infektiologie und Pneumologie, Charité, Universitätsmedizin Berlin, Partner von Freie Universität Berlin, Humboldt-Universität zu Berlin und Berlin Institute of Health, Berlin, Germany
| | - Thorsten Wolff
- Robert Koch Institut, FG 17 Influenzaviren und weitere Viren des Respirationstraktes, Berlin, Germany
| | - Andreas C Hocke
- Medizinische Klinik mit Schwerpunkt Infektiologie und Pneumologie, Charité, Universitätsmedizin Berlin, Partner von Freie Universität Berlin, Humboldt-Universität zu Berlin und Berlin Institute of Health, Berlin, Germany
| | - Stefan Hippenstiel
- Medizinische Klinik mit Schwerpunkt Infektiologie und Pneumologie, Charité, Universitätsmedizin Berlin, Partner von Freie Universität Berlin, Humboldt-Universität zu Berlin und Berlin Institute of Health, Berlin, Germany
| | | | - Jens Neudecker
- Chirurgische Klinik, Campus Mitte/Campus Virchow Klinikum, Charité, Universitätsmedizin Berlin, Partner von Freie Universität Berlin, Humboldt-Universität zu Berlin, und Berlin Institute of Health, Berlin, Germany
| | - Klaus Osterrieder
- Institut für Virologie, Robert von Ostertag-Haus, Zentrum für Infektionsmedizin, Freie Universität Berlin, Berlin, Germany
| | - Nediljko Budisa
- Institut für Chemie, Biokatalyse, Technische Universität Berlin, Berlin, Germany
- Department of Chemistry, University of Manitoba, Winnipeg, Canada
| | - Roland R Netz
- Fachbereich Physik, Theoretische Biophysik und Physik weicher Materie, Freie Universität Berlin, Berlin, Germany
| | - Christoph Böttcher
- Forschungszentrum für Elektronenmikroskopie und Gerätezentrum BioSupraMol, Institut für Chemie und Biochemie, Freie Universität Berlin, Berlin, Germany
| | - Susanne Liese
- Fachbereich Physik, Theoretische Biophysik und Physik weicher Materie, Freie Universität Berlin, Berlin, Germany.
- Department of Mathematics, University of Oslo (UiO), Oslo, Norway.
| | - Andreas Herrmann
- Institut für Biologie, Molekulare Biophysik, IRI Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany.
| | - Christian P R Hackenberger
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany.
- Institut für Chemie, Humboldt-Universität zu Berlin, Berlin, Germany.
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Schulze-Briese C, Förster A, Hofer P, De Carlo S, Piazza L, Wennmacher JTC, Grüne T. The death of powder – micro-electron diffraction with EIGER. Acta Crystallogr A Found Adv 2019. [DOI: 10.1107/s0108767319097447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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3
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Heidler J, Pantelic R, Wennmacher JTC, Zaubitzer C, Fecteau-Lefebvre A, Goldie KN, Müller E, Holstein JJ, van Genderen E, De Carlo S, Gruene T. Design guidelines for an electron diffractometer for structural chemistry and structural biology. Acta Crystallogr D Struct Biol 2019; 75:458-466. [PMID: 31063148 PMCID: PMC6503764 DOI: 10.1107/s2059798319003942] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 03/22/2019] [Indexed: 11/11/2022] Open
Abstract
3D electron diffraction has reached a stage where the structures of chemical compounds can be solved productively. Instrumentation is lagging behind this development, and to date dedicated electron diffractometers for data collection based on the rotation method do not exist. Current studies use transmission electron microscopes as a workaround. These are optimized for imaging, which is not optimal for diffraction studies. The beam intensity is very high, it is difficult to create parallel beam illumination and the detectors used for imaging are of only limited use for diffraction studies. In this work, the combination of an EIGER hybrid pixel detector with a transmission electron microscope to construct a productive electron diffractometer is described. The construction not only refers to the combination of hardware but also to the calibration of the system, so that it provides rapid access to the experimental parameters that are necessary for processing diffraction data. Until fully integrated electron diffractometers become available, this describes a setup for productive and efficient operation in chemical crystallography.
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Affiliation(s)
- Jonas Heidler
- Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | | | | | - Christian Zaubitzer
- Scientific Center for Optical and Electron Microscopy, ETH Zürich, 8093 Zürich, Switzerland
| | | | - Kenneth N. Goldie
- Center for Cellular Imaging and NanoAnalytics, University Basel, 4058 Basel, Switzerland
| | | | - Julian J. Holstein
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto Hahn Strasse 6, 44227 Dortmund, Germany
| | | | | | - Tim Gruene
- Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
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4
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Gruene T, Wennmacher JTC, Zaubitzer C, Holstein JJ, Heidler J, Fecteau-Lefebvre A, De Carlo S, Müller E, Goldie KN, Regeni I, Li T, Santiso-Quinones G, Steinfeld G, Handschin S, van Genderen E, van Bokhoven JA, Clever GH, Pantelic R. Rapid Structure Determination of Microcrystalline Molecular Compounds Using Electron Diffraction. Angew Chem Int Ed Engl 2018; 57:16313-16317. [PMID: 30325568 PMCID: PMC6468266 DOI: 10.1002/anie.201811318] [Citation(s) in RCA: 158] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Indexed: 12/02/2022]
Abstract
Chemists of all fields currently publish about 50 000 crystal structures per year, the vast majority of which are X‐ray structures. We determined two molecular structures by employing electron rather than X‐ray diffraction. For this purpose, an EIGER hybrid pixel detector was fitted to a transmission electron microscope, yielding an electron diffractometer. The structure of a new methylene blue derivative was determined at 0.9 Å resolution from a crystal smaller than 1×2 μm2. Several thousand active pharmaceutical ingredients (APIs) are only available as submicrocrystalline powders. To illustrate the potential of electron crystallography for the pharmaceutical industry, we also determined the structure of an API from its pill. We demonstrate that electron crystallography complements X‐ray crystallography and is the technique of choice for all unsolved cases in which submicrometer‐sized crystals were the limiting factor.
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Affiliation(s)
- Tim Gruene
- Department of Energy and Environment, Paul Scherrer Institut, Forschungsstrasse 111, 5232, Villigen PSI, Switzerland
| | - Julian T C Wennmacher
- Department of Energy and Environment, Paul Scherrer Institut, Forschungsstrasse 111, 5232, Villigen PSI, Switzerland
| | - Christan Zaubitzer
- Scientific Center for Optical and Electron Microscopy, ETH Zürich, Auguste-Piccard-Hof 1, 8093, Zürich, Switzerland
| | - Julian J Holstein
- Department of Chemical and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 6, 44227, Dortmund, Germany
| | - Jonas Heidler
- Department of Biology and Chemistry, Paul Scherrer Institut, Forschungsstrasse 111, 5232, Villigen PSI, Switzerland
| | - Ariane Fecteau-Lefebvre
- Center for Cellular Imaging and NanoAnalytics, University of Basel, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Sacha De Carlo
- DECTRIS Ltd., Taefernweg 1, 5405, Baden-Daettwil, Switzerland
| | - Elisabeth Müller
- Electron Microscopy Facility, Paul Scherrer Institut, Forschungsstrasse 111, 5232, Villigen PSI, Switzerland
| | - Kenneth N Goldie
- Center for Cellular Imaging and NanoAnalytics, University of Basel, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Irene Regeni
- Department of Chemical and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 6, 44227, Dortmund, Germany
| | - Teng Li
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, 8093, Zürich, Switzerland
| | | | | | - Stephan Handschin
- Scientific Center for Optical and Electron Microscopy, ETH Zürich, Auguste-Piccard-Hof 1, 8093, Zürich, Switzerland
| | - Eric van Genderen
- Department of Biology and Chemistry, Paul Scherrer Institut, Forschungsstrasse 111, 5232, Villigen PSI, Switzerland
| | - Jeroen A van Bokhoven
- Department of Energy and Environment, Paul Scherrer Institut, Forschungsstrasse 111, 5232, Villigen PSI, Switzerland.,Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, 8093, Zürich, Switzerland
| | - Guido H Clever
- Department of Chemical and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 6, 44227, Dortmund, Germany
| | - Radosav Pantelic
- Department of Biology and Chemistry, Paul Scherrer Institut, Forschungsstrasse 111, 5232, Villigen PSI, Switzerland.,DECTRIS Ltd., Taefernweg 1, 5405, Baden-Daettwil, Switzerland
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5
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Afanasyev P, Seer-Linnemayr C, Ravelli RBG, Matadeen R, De Carlo S, Alewijnse B, Portugal RV, Pannu NS, Schatz M, van Heel M. Single-particle cryo-EM using alignment by classification (ABC): the structure of Lumbricus terrestris haemoglobin. IUCrJ 2017; 4:678-694. [PMID: 28989723 PMCID: PMC5619859 DOI: 10.1107/s2052252517010922] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 07/24/2017] [Indexed: 05/12/2023]
Abstract
Single-particle cryogenic electron microscopy (cryo-EM) can now yield near-atomic resolution structures of biological complexes. However, the reference-based alignment algorithms commonly used in cryo-EM suffer from reference bias, limiting their applicability (also known as the 'Einstein from random noise' problem). Low-dose cryo-EM therefore requires robust and objective approaches to reveal the structural information contained in the extremely noisy data, especially when dealing with small structures. A reference-free pipeline is presented for obtaining near-atomic resolution three-dimensional reconstructions from heterogeneous ('four-dimensional') cryo-EM data sets. The methodologies integrated in this pipeline include a posteriori camera correction, movie-based full-data-set contrast transfer function determination, movie-alignment algorithms, (Fourier-space) multivariate statistical data compression and unsupervised classification, 'random-startup' three-dimensional reconstructions, four-dimensional structural refinements and Fourier shell correlation criteria for evaluating anisotropic resolution. The procedures exclusively use information emerging from the data set itself, without external 'starting models'. Euler-angle assignments are performed by angular reconstitution rather than by the inherently slower projection-matching approaches. The comprehensive 'ABC-4D' pipeline is based on the two-dimensional reference-free 'alignment by classification' (ABC) approach, where similar images in similar orientations are grouped by unsupervised classification. Some fundamental differences between X-ray crystallography versus single-particle cryo-EM data collection and data processing are discussed. The structure of the giant haemoglobin from Lumbricus terrestris at a global resolution of ∼3.8 Å is presented as an example of the use of the ABC-4D procedure.
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Affiliation(s)
- Pavel Afanasyev
- Institute of Biology Leiden, Leiden University, 2333 CC Leiden, The Netherlands
- Institute of Nanoscopy, Maastricht University, 6211 LK Maastricht, The Netherlands
| | | | | | - Rishi Matadeen
- Netherlands Centre for Electron Nanoscopy (NeCEN), Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Sacha De Carlo
- Netherlands Centre for Electron Nanoscopy (NeCEN), Einsteinweg 55, 2333 CC Leiden, The Netherlands
- FEI Company/Thermo Fisher Scientific, Eindhoven, The Netherlands
| | - Bart Alewijnse
- Institute of Biology Leiden, Leiden University, 2333 CC Leiden, The Netherlands
- FEI Company/Thermo Fisher Scientific, Eindhoven, The Netherlands
| | | | - Navraj S. Pannu
- Leiden Institute of Chemistry, Leiden University, 2333 CC Leiden, The Netherlands
| | | | - Marin van Heel
- Institute of Biology Leiden, Leiden University, 2333 CC Leiden, The Netherlands
- Brazilian Nanotechnology National Laboratory (LNNANO), Campinas, SP, Brazil
- Department of Life Sciences, Imperial College London, England
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Kuijper M, van Hoften G, Janssen B, Geurink R, De Carlo S, Vos M, van Duinen G, van Haeringen B, Storms M. FEI’s direct electron detector developments: Embarking on a revolution in cryo-TEM. J Struct Biol 2015; 192:179-87. [DOI: 10.1016/j.jsb.2015.09.014] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 09/23/2015] [Accepted: 09/25/2015] [Indexed: 10/23/2022]
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Afanasyev P, Ravelli RBG, Matadeen R, De Carlo S, van Duinen G, Alewijnse B, Peters PJ, Abrahams JP, Portugal RV, Schatz M, van Heel M. A posteriori correction of camera characteristics from large image data sets. Sci Rep 2015; 5:10317. [PMID: 26068909 PMCID: PMC4464200 DOI: 10.1038/srep10317] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 03/31/2015] [Indexed: 11/18/2022] Open
Abstract
Large datasets are emerging in many fields of image processing including: electron microscopy, light microscopy, medical X-ray imaging, astronomy, etc. Novel computer-controlled instrumentation facilitates the collection of very large datasets containing thousands of individual digital images. In single-particle cryogenic electron microscopy (“cryo-EM”), for example, large datasets are required for achieving quasi-atomic resolution structures of biological complexes. Based on the collected data alone, large datasets allow us to precisely determine the statistical properties of the imaging sensor on a pixel-by-pixel basis, independent of any “a priori” normalization routinely applied to the raw image data during collection (“flat field correction”). Our straightforward “a posteriori” correction yields clean linear images as can be verified by Fourier Ring Correlation (FRC), illustrating the statistical independence of the corrected images over all spatial frequencies. The image sensor characteristics can also be measured continuously and used for correcting upcoming images.
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Affiliation(s)
- Pavel Afanasyev
- 1] Leiden Institute of Chemistry, Leiden University, 2333 CC Leiden, The Netherlands [2] The Institute of Nanoscopy, Maastricht University, 6211 LK Maastricht, The Netherlands
| | - Raimond B G Ravelli
- The Institute of Nanoscopy, Maastricht University, 6211 LK Maastricht, The Netherlands
| | - Rishi Matadeen
- Netherlands Centre for Electron Nanoscopy (NeCEN), 2333 CC Leiden, The Netherlands
| | - Sacha De Carlo
- 1] Netherlands Centre for Electron Nanoscopy (NeCEN), 2333 CC Leiden, The Netherlands [2] FEI Company, 5651 GG Eindhoven, The Netherlands
| | | | - Bart Alewijnse
- 1] Leiden Institute of Chemistry, Leiden University, 2333 CC Leiden, The Netherlands [2] The Institute of Nanoscopy, Maastricht University, 6211 LK Maastricht, The Netherlands
| | - Peter J Peters
- The Institute of Nanoscopy, Maastricht University, 6211 LK Maastricht, The Netherlands
| | - Jan-Pieter Abrahams
- Leiden Institute of Chemistry, Leiden University, 2333 CC Leiden, The Netherlands
| | - Rodrigo V Portugal
- Brazilian Nanotechnology National Laboratory - LNNano, CNPEM, C.P. 6192, 13083-970 Campinas SP, Brasil
| | - Michael Schatz
- Image Science Software GmbH, Gillweg 3, D-14193 Berlin, Germany
| | - Marin van Heel
- 1] Leiden Institute of Chemistry, Leiden University, 2333 CC Leiden, The Netherlands [2] Brazilian Nanotechnology National Laboratory - LNNano, CNPEM, C.P. 6192, 13083-970 Campinas SP, Brasil [3] Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, UK
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Abstract
Negative staining is widely applicable to isolated viruses, protein molecules, macromolecular assemblies and fibrils, subcellular membrane fractions, liposomes and artificial membranes, synthetic DNA arrays, and also to polymer solutions and a variety of nanotechnology samples. Techniques are provided for the preparation of the necessary support films (continuous carbon and holey/perforated carbon). The range of suitable negative stains is presented, with some emphasis on the benefit of using ammonium molybdate and of negative stain-trehalose combinations. Protocols are provided for the single droplet negative staining technique (on continuous and holey carbon support films), the floating and carbon sandwich techniques in addition to the negative staining-carbon film (NS-CF) technique for randomly dispersed fragile molecules, 2D crystallization of proteins and for cleavage of cells and organelles. Immuno-negative staining and negative staining of affinity labeled complexes (e.g., biotin-streptavidin) are presented in some detail. The formation of immune complexes in solution for droplet negative staining is given, as is the use of carbon-plastic support films as an adsorption surface on which to perform immunolabeling or affinity experiments, prior to negative staining. Dynamic biological systems can be investigated by negative staining, where the time period is in excess of a few minutes, but there are possibilities to greatly reduce the time by rapid stabilization of molecular systems with uranyl acetate or tannic acid. The more recently developed cryo-negative staining procedures are also included: first, the high concentration ammonium molybdate procedure on holey carbon films and second, the carbon sandwich procedure using uranyl formate. Several electron micrographs showing examples of applications of negative staining techniques are included and the chapter is thoroughly referenced.
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Affiliation(s)
- J Robin Harris
- Institute of Zoology, University of Mainz, Mainz, Germany
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De Carlo S, Lin SC, Taatjes DJ, Hoenger A. Molecular basis of transcription initiation in Archaea. Transcription 2012; 1:103-11. [PMID: 21326901 DOI: 10.4161/trns.1.2.13189] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2010] [Revised: 07/19/2010] [Accepted: 07/27/2010] [Indexed: 01/24/2023] Open
Abstract
Compared with eukaryotes, the archaeal transcription initiation machinery-commonly known as the Pre-Initiation Complex-is relatively simple. The archaeal PIC consists of the TFIIB ortholog TFB, TBP, and an 11-subunit RNA polymerase (RNAP). The relatively small size of the entire archaeal PIC makes it amenable to structural analysis. Using purified RNAP, TFB, and TBP from the thermophile Pyrococcus furiosus, we assembled the biochemically active PIC at 65ºC. The intact archaeal PIC was isolated by implementing a cross-linking technique followed by size-exclusion chromatography, and the structure of this 440 kDa assembly was determined using electron microscopy and single-particle reconstruction techniques. Combining difference maps with crystal structure docking of various sub-domains, TBP and TFB were localized within the macromolecular PIC. TBP/TFB assemble near the large RpoB subunit and the RpoD/L "foot" domain behind the RNAP central cleft. This location mimics that of yeast TBP and TFIIB in complex with yeast RNAP II. Collectively, these results define the structural organization of the archaeal transcription machinery and suggest a conserved core PIC architecture.
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Affiliation(s)
- Sacha De Carlo
- Department of Chemistry, City College of the City University of New York, NY, USA.
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CHOWDHURY SAIKAT, De Carlo S, Diaz-Avalos R, Rice W, Nixon BT. Asymmetry in activator ring opens up Sigma54 dependent transcription in bacteria. FASEB J 2012. [DOI: 10.1096/fasebj.26.1_supplement.737.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- SAIKAT CHOWDHURY
- Biochemistry and Molecular BiologyThe Pennsylvania State UniversityUniversity ParkPA
| | | | | | | | - B Tracy Nixon
- Biochemistry and Molecular BiologyThe Pennsylvania State UniversityUniversity ParkPA
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Nixon BT, Sysoeva TA, Chen B, Chowdhury S, Guo L, De Carlo S, Hanson J, Yang H. AAA+ ATPase Mechanism. Biophys J 2011. [DOI: 10.1016/j.bpj.2010.12.412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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12
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De Carlo S, Harris JR. Negative staining and cryo-negative staining of macromolecules and viruses for TEM. Micron 2010; 42:117-31. [PMID: 20634082 DOI: 10.1016/j.micron.2010.06.003] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2010] [Revised: 06/14/2010] [Accepted: 06/15/2010] [Indexed: 10/19/2022]
Abstract
In this review we cover the technical background to negative staining of biomolecules and viruses, and then expand upon the different possibilities and limitations. Topics range from conventional air-dry negative staining of samples adsorbed to carbon support films, the variant termed the "negative staining-carbon film" technique and negative staining of samples spread across the holes of holey-carbon support films, to a consideration of dynamic/time-dependent negative staining. For each of these approaches examples of attainable data are given. The cryo-negative staining technique for the specimen preparation of frozen-hydrated/vitrified samples is also presented. A detailed protocol to successfully achieve cryo-negative staining with ammonium molybdate is given, as well as examples of data, which support the claim that cryo-negative staining provides a useful approach for the high-resolution study of macromolecular and viral structure.
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Affiliation(s)
- Sacha De Carlo
- Department of Chemistry, and Institute for Macro Molecular Assemblies, The City College of CUNY, 160 Convent Ave, New York, NY, USA.
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13
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Abstract
Cryoelectron microscopy (cryo-EM) combined with single-particle reconstruction methods is a powerful technique to study the structure of biological assemblies at molecular resolution (i.e., 3-10 Å). Since electron micrographs of frozen-hydrated biological particles are usually very noisy, improvement of the signal-to-noise ratio (SNR) is necessary and is usually achieved by image processing. We propose an alternative method to improve the contrast at the specimen preparation stage: cryonegative staining. Cryonegative staining aims to increase the SNR while preserving the biological samples in the frozen-hydrated state. Here, we present two alternative procedures to efficiently perform cryonegative staining on macromolecular assemblies. The first is very similar to conventional cryo-EM, the main difference being that the samples are observed in the presence of an additional contrasting agent, ammonium molybdate. The second is based on a carbon-sandwich method and is typically used with uranyl formate or acetate. Compared to air-dried negative staining at room temperature, the advantage of both cryonegative-staining procedures presented here is that the sample is kept hydrated at all steps and observed at liquid nitrogen temperature in the electron microscope. The advantage over conventional cryo-EM is that the SNR is improved by at least a factor of three. For each of these approaches, a few examples of attainable data are given. We cover the technical background to cryonegative staining of macromolecular assemblies, and then expand upon the different possibilities and limitations.
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Affiliation(s)
- Sacha De Carlo
- Department of Chemistry, Institute for Macromolecular Assemblies, City University of New York, City College Campus, New York, USA
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Batchelor JD, Doucleff M, Lee CJ, Matsubara K, De Carlo S, Heideker J, Lamers MH, Pelton JG, Wemmer DE. Structure and regulatory mechanism of Aquifex aeolicus NtrC4: variability and evolution in bacterial transcriptional regulation. J Mol Biol 2008; 384:1058-75. [PMID: 18955063 DOI: 10.1016/j.jmb.2008.10.024] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2008] [Revised: 10/06/2008] [Accepted: 10/06/2008] [Indexed: 10/21/2022]
Abstract
Genetic changes lead gradually to altered protein function, making deduction of the molecular basis for activity from a sequence difficult. Comparative studies provide insights into the functional consequences of specific changes. Here we present structural and biochemical studies of NtrC4, a sigma-54 activator from Aquifex aeolicus, and compare it with NtrC1 (a paralog) and NtrC (a homolog from Salmonella enterica) to provide insight into how a substantial change in regulatory mechanism may have occurred. Activity assays show that assembly of NtrC4's active oligomer is repressed by the N-terminal receiver domain, and that BeF3- addition (mimicking phosphorylation) removes this repression. Observation of assembly without activation for NtrC4 indicates that it is much less strongly repressed than NtrC1. The crystal structure of the unactivated receiver-ATPase domain combination shows a partially disrupted interface. NMR structures of the regulatory domain show that its activation mechanism is very similar to that of NtrC1. The crystal structure of the NtrC4 DNA-binding domain shows that it is dimeric and more similar in structure to NtrC than NtrC1. Electron microscope images of the ATPase-DNA-binding domain combination show formation of oligomeric rings. Sequence alignments provide insights into the distribution of activation mechanisms in this family of proteins.
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Affiliation(s)
- Joseph D Batchelor
- Graduate Group in Biophysics, Physical Biosciences Division, Lawrence Berkeley National Laboratory and the Department of Chemistry, University of California, Berkeley, CA 94720, USA
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15
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Chen B, Doucleff M, Wemmer DE, De Carlo S, Huang HH, Nogales E, Hoover TR, Kondrashkina E, Guo L, Nixon BT. ATP ground- and transition states of bacterial enhancer binding AAA+ ATPases support complex formation with their target protein, sigma54. Structure 2007; 15:429-40. [PMID: 17437715 PMCID: PMC2680074 DOI: 10.1016/j.str.2007.02.007] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2006] [Revised: 11/01/2006] [Accepted: 02/22/2007] [Indexed: 11/28/2022]
Abstract
Transcription initiation by the sigma54 form of bacterial RNA polymerase requires hydrolysis of ATP by an enhancer binding protein (EBP). We present SAS-based solution structures of the ATPase domain of the EBP NtrC1 from Aquifex aeolicus in different nucleotide states. Structures of apo protein and that bound to AMPPNP or ADP-BeF(x) (ground-state mimics), ADP-AlF(x) (a transition-state mimic), or ADP (product) show substantial changes in the position of the GAFTGA loops that contact polymerase, particularly upon conversion from the apo state to the ADP-BeF(x) state, and from the ADP-AlF(x) state to the ADP state. Binding of the ATP analogs stabilizes the oligomeric form of the ATPase and its binding to sigma54, with ADP-AlF(x) having the largest effect. These data indicate that ATP binding promotes a conformational change that stabilizes complexes between EBPs and sigma54, while subsequent hydrolysis and phosphate release drive the conformational change needed to open the polymerase/promoter complex.
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Affiliation(s)
- Baoyu Chen
- Integrative Biosciences Graduate Degree Program – Chemical Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Michaeleen Doucleff
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - David E. Wemmer
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Sacha De Carlo
- Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California at Berkeley, and Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Hector H. Huang
- Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California at Berkeley, and Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Eva Nogales
- Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California at Berkeley, and Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Timothy R. Hoover
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Elena Kondrashkina
- BioCAT at APS/Argonne National Lab, Illinois Institute of Technology, 9700 S. Cass Ave, Argonne, IL 60439, USA
| | - Liang Guo
- BioCAT at APS/Argonne National Lab, Illinois Institute of Technology, 9700 S. Cass Ave, Argonne, IL 60439, USA
| | - B. Tracy Nixon
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
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16
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Kostek SA, Grob P, De Carlo S, Lipscomb JS, Garczarek F, Nogales E. Molecular architecture and conformational flexibility of human RNA polymerase II. Structure 2007; 14:1691-700. [PMID: 17098194 DOI: 10.1016/j.str.2006.09.011] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2006] [Revised: 09/14/2006] [Accepted: 09/19/2006] [Indexed: 11/25/2022]
Abstract
Transcription by RNA polymerase II (RNAPII) is a central process in eukaryotic gene regulation. While atomic details exist for the yeast RNAPII, characterization of the human complex lags behind, mostly due to the inability to obtain large quantities of purified material. Although the complexes have the same protein composition and high sequence similarity, understanding of transcription and of transcription-coupled DNA repair (TCR) in humans will require the use of human proteins in structural studies. We have used cryo-electron microscopy, image reconstruction, and variance analysis to characterize the structure and dynamics of human RNAPII (hRNAPII). Our studies show that hRNAPII in solution parallels the conformational flexibility of the yeast structures crystallized in different states but also illustrate a more extensive conformational range with potential biological significance. This hRNAPII study will serve as a structural platform to build up higher-order transcription and TCR complexes and to gain information that may be unique to the human RNAPII system.
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Affiliation(s)
- Seth A Kostek
- Molecular and Cell Biology Department, University of California, Berkeley, Berkeley, California 94720, USA
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17
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De Carlo S, Chen B, Hoover TR, Kondrashkina E, Nogales E, Nixon BT. The structural basis for regulated assembly and function of the transcriptional activator NtrC. Genes Dev 2006; 20:1485-95. [PMID: 16751184 PMCID: PMC1475761 DOI: 10.1101/gad.1418306] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2006] [Accepted: 04/04/2006] [Indexed: 11/25/2022]
Abstract
In two-component signal transduction, an input triggers phosphorylation of receiver domains that regulate the status of output modules. One such module is the AAA+ ATPase domain in bacterial enhancer-binding proteins that remodel the sigma(54) form of RNA polymerase. We report X-ray solution scattering and electron microscopy structures of the activated, full-length nitrogen-regulatory protein C (NtrC) showing a novel mechanism for regulation of AAA+ ATPase assembly via the juxtaposition of the receiver domains and ATPase ring. Accompanying the hydrolysis cycle that is required for transcriptional activation, we observed major order-disorder changes in the GAFTGA loops involved in sigma(54) binding, as well as in the DNA-binding domains.
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Affiliation(s)
- Sacha De Carlo
- Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, USA
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18
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Jawhari A, Uhring M, De Carlo S, Crucifix C, Tocchini-Valentini G, Moras D, Schultz P, Poterszman A. Structure and oligomeric state of human transcription factor TFIIE. EMBO Rep 2006; 7:500-5. [PMID: 16547462 PMCID: PMC1479554 DOI: 10.1038/sj.embor.7400663] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2005] [Revised: 11/02/2005] [Accepted: 02/20/2006] [Indexed: 11/08/2022] Open
Abstract
The general RNA polymerase II transcription factor TFIIE, which is composed of two subunits, has essential roles in both transcription initiation and promoter escape. Electron microscopy analysis of negatively stained human TFIIE showed a large proportion of alpha/beta heterodimers as well as a small proportion of tetramers. Analytical ultracentrifugation, chemical crosslinking, pulldown experiments and cryo-electron microscopy confirmed that TFIIE is a alpha/beta heterodimer in solution. Three-dimensional envelopes of the alpha/beta particles showed an elongated structure composed of three distinct modules. Finally, a model for the quaternary architecture of the complex is proposed that provides a structural framework to discuss the function of TFIIE in the context of RNA polymerase II transcription initiation.
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Affiliation(s)
- Anass Jawhari
- Department of Structural Biology and Genomics, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, rue Laurent Fries, 67404 Illkirch, France
| | - Muriel Uhring
- Department of Structural Biology and Genomics, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, rue Laurent Fries, 67404 Illkirch, France
| | - Sacha De Carlo
- Department of Structural Biology and Genomics, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, rue Laurent Fries, 67404 Illkirch, France
| | - Corinne Crucifix
- Department of Structural Biology and Genomics, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, rue Laurent Fries, 67404 Illkirch, France
- Ecole Supérieure de Biotechnologie de Strasbourg, Pôle API, rue Sébastien Brand, 67404 Illkirch, France
| | - Guiseppe Tocchini-Valentini
- Department of Structural Biology and Genomics, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, rue Laurent Fries, 67404 Illkirch, France
| | - Dino Moras
- Department of Structural Biology and Genomics, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, rue Laurent Fries, 67404 Illkirch, France
| | - Patrick Schultz
- Department of Structural Biology and Genomics, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, rue Laurent Fries, 67404 Illkirch, France
- Ecole Supérieure de Biotechnologie de Strasbourg, Pôle API, rue Sébastien Brand, 67404 Illkirch, France
- Tel: +33 3 90 24 4800; Fax: +33 3 88 65 3201; E-mail:
| | - Arnaud Poterszman
- Department of Structural Biology and Genomics, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, rue Laurent Fries, 67404 Illkirch, France
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Abstract
The pharmacological activity of several amphiphilic drugs is often related to their ability to interact with biological membranes. Propranolol is an efficient multidrug resistance (MDR) modulator; it is a nonselective beta-blocker and is thought to reduce hypertension by decreasing the cardiac frequency and thus blood pressure. It is used in drug delivery studies in order to treat systemic hypertension. We are interested in the interaction of propranolol with artificial membranes, as liposomes of controllable size are used as biocompatible and protective structures to encapsulate labile molecules, such as proteins, nucleic acids or drugs, for pharmaceutical, cosmetic or chemical applications. We present here a study of the interaction of propranolol, a cationic surfactant, with pure egg phosphatidylcholine (EPC) vesicles. The gradual transition from liposome to micelle of EPC vesicles in the presence of propranolol was monitored by time-resolved electron cryo-microscopy (cryo-EM) under different experimental conditions. The liposome-drug interaction was studied with varying drug/lipid (D/L) ratios and different stages were captured by direct thin-film vitrification. The time-series cryo-EM data clearly illustrate the mechanism of action of propranolol on the liposome structure: the drug disrupts the lipid bilayer by perturbing the local organization of the phospholipids. This is followed by the formation of thread-like micelles, also called worm-like micelles (WLM), and ends with the formation of spherical (globular) micelles. The overall reaction is slow, with the process taking almost two hours to be completed. The effect of a monovalent salt was also investigated by repeating the lipid-surfactant interaction experiments in the presence of KCl as an additive to the lipid/drug suspension. When KCl was added in the presence of propranolol the overall reaction was the same but with slower kinetics, suggesting that this monovalent salt affects the general lipid-to-micelle transition by stabilizing the membrane, presumably by binding to the carbonyl chains of the phosphatidylcholine.
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Affiliation(s)
- Sacha De Carlo
- Molecular and Cell Biology Department, Howard Hughes Medical Institute, University of California, Berkeley, California, USA.
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20
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Abstract
The structure of the yeast DNA-dependent RNA polymerase I (RNA Pol I), prepared by cryo-negative staining, was studied by electron microscopy. A structural model of the enzyme at a resolution of 1.8 nm was determined from the analysis of isolated molecules and showed an excellent fit with the atomic structure of the RNA Pol II Delta4/7. The high signal-to-noise ratio (SNR) of the stained molecular images revealed a conformational flexibility within the image data set that could be recovered in three-dimensions after implementation of a novel strategy to sort the "open" and "closed" conformations in our heterogeneous data set. This conformational change mapped in the "wall/flap" domain of the second largest subunit (beta-like) and allows a better accessibility of the DNA-binding groove. This displacement of the wall/flap domain could play an important role in the transition between initiation and elongation state of the enzyme. Moreover, a protrusion was apparent in the cryo-negatively stained model, which was absent in the atomic structure and was not detected in previous 3D models of RNA Pol I. This structure could, however, be detected in unstained views of the enzyme obtained from frozen hydrated 2D crystals, indicating that this novel feature is not induced by the staining process. Unexpectedly, negatively charged molybdenum compounds were found to accumulate within the DNA-binding groove, which is best explained by the highly positive electrostatic potential of this region of the molecule, thus, suggesting that the stain distribution reflects the overall surface charge of the molecule.
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Affiliation(s)
- Sacha De Carlo
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, 1 rue Laurent Fries, BP163, F-67404 Illkirch Cedex, C.U. de Strasbourg, France.
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21
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Bellon PL, Cantele F, De Carlo S, Lanzavecchia S. A trajectory-based algorithm to determine and refine Euler angles of projections in three-dimensional microscopy. Improvements and tests. Ultramicroscopy 2002; 93:111-21. [PMID: 12425589 DOI: 10.1016/s0304-3991(02)00152-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An improvement of the trajectory matching algorithm is presented, which is based on the use of the derivative of trajectories and of the projection of experimental sinogram lines in the factor space determined by sinogram lines of projections of a model. The algorithm performance is illustrated by use of different phantom structures, to show the effect of symmetry on trajectory matching. A GroEL complex has also been reconstructed from both cryo-negatively stained and unstained frozen-hydrated samples. The refinement of this structure has been carried out by the trajectory matching algorithm as well as by conventional cross-correlation methods. Slight differences among the two results are discussed. The improved trajectory matching algorithm, based on chi2 distances, runs much faster than correlation analysis and looks satisfactory as for the quality of the reconstructed structures.
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Affiliation(s)
- Pier Luigi Bellon
- Dipartimento di Chimica Strutturale e Stereochimica Inorganica, Universita' degli Studi, Milano, Italy
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