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Linse JB, Hub JS. Scrutinizing the protein hydration shell from molecular dynamics simulations against consensus small-angle scattering data. Commun Chem 2023; 6:272. [PMID: 38086909 PMCID: PMC10716392 DOI: 10.1038/s42004-023-01067-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 11/20/2023] [Indexed: 06/09/2024] Open
Abstract
Biological macromolecules in solution are surrounded by a hydration shell, whose structure differs from the structure of bulk solvent. While the importance of the hydration shell for numerous biological functions is widely acknowledged, it remains unknown how the hydration shell is regulated by macromolecular shape and surface composition, mainly because a quantitative probe of the hydration shell structure has been missing. We show that small-angle scattering in solution using X-rays (SAXS) or neutrons (SANS) provide a protein-specific probe of the protein hydration shell that enables quantitative comparison with molecular simulations. Using explicit-solvent SAXS/SANS predictions, we derived the effect of the hydration shell on the radii of gyration Rg of five proteins using 18 combinations of protein force field and water model. By comparing computed Rg values from SAXS relative to SANS in D2O with consensus SAXS/SANS data from a recent worldwide community effort, we found that several but not all force fields yield a hydration shell contrast in remarkable agreement with experiments. The hydration shell contrast captured by Rg values depends strongly on protein charge and geometric shape, thus providing a protein-specific footprint of protein-water interactions and a novel observable for scrutinizing atomistic hydration shell models against experimental data.
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Affiliation(s)
- Johanna-Barbara Linse
- Theoretical Physics and Center for Biophysics, Saarland University, Saarbrücken, 66123, Germany
| | - Jochen S Hub
- Theoretical Physics and Center for Biophysics, Saarland University, Saarbrücken, 66123, Germany.
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2
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Delhommel F, Martínez-Lumbreras S, Sattler M. Combining NMR, SAXS and SANS to characterize the structure and dynamics of protein complexes. Methods Enzymol 2022; 678:263-297. [PMID: 36641211 DOI: 10.1016/bs.mie.2022.09.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Understanding the structure and dynamics of biological macromolecules is essential to decipher the molecular mechanisms that underlie cellular functions. The description of structure and conformational dynamics often requires the integration of complementary techniques. In this review, we highlight the utility of combining nuclear magnetic resonance (NMR) spectroscopy with small angle scattering (SAS) to characterize these challenging biomolecular systems. NMR can assess the structure and conformational dynamics of multidomain proteins, RNAs and biomolecular complexes. It can efficiently provide information on interaction surfaces, long-distance restraints and relative domain orientations at residue-level resolution. Such information can be readily combined with high-resolution structural data available on subcomponents of biomolecular assemblies. Moreover, NMR is a powerful tool to characterize the dynamics of biomolecules on a wide range of timescales, from nanoseconds to seconds. On the other hand, SAS approaches provide global information on the size and shape of biomolecules and on the ensemble of all conformations present in solution. Therefore, NMR and SAS provide complementary data that are uniquely suited to investigate dynamic biomolecular assemblies. Here, we briefly review the type of data that can be obtained by both techniques and describe different approaches that can be used to combine them to characterize biomolecular assemblies. We then provide guidelines on which experiments are best suited depending on the type of system studied, ranging from fully rigid complexes, dynamic structures that interconvert between defined conformations and systems with very high structural heterogeneity.
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Affiliation(s)
- Florent Delhommel
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany; Bavarian NMR Center, Department of Chemistry, Technical University of Munich, Garching, Germany
| | - Santiago Martínez-Lumbreras
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany; Bavarian NMR Center, Department of Chemistry, Technical University of Munich, Garching, Germany
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany; Bavarian NMR Center, Department of Chemistry, Technical University of Munich, Garching, Germany.
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3
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Trewhella J, Vachette P, Bierma J, Blanchet C, Brookes E, Chakravarthy S, Chatzimagas L, Cleveland TE, Cowieson N, Crossett B, Duff AP, Franke D, Gabel F, Gillilan RE, Graewert M, Grishaev A, Guss JM, Hammel M, Hopkins J, Huang Q, Hub JS, Hura GL, Irving TC, Jeffries CM, Jeong C, Kirby N, Krueger S, Martel A, Matsui T, Li N, Pérez J, Porcar L, Prangé T, Rajkovic I, Rocco M, Rosenberg DJ, Ryan TM, Seifert S, Sekiguchi H, Svergun D, Teixeira S, Thureau A, Weiss TM, Whitten AE, Wood K, Zuo X. A round-robin approach provides a detailed assessment of biomolecular small-angle scattering data reproducibility and yields consensus curves for benchmarking. Acta Crystallogr D Struct Biol 2022; 78:1315-1336. [PMID: 36322416 PMCID: PMC9629491 DOI: 10.1107/s2059798322009184] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 09/15/2022] [Indexed: 12/14/2022] Open
Abstract
Through an expansive international effort that involved data collection on 12 small-angle X-ray scattering (SAXS) and four small-angle neutron scattering (SANS) instruments, 171 SAXS and 76 SANS measurements for five proteins (ribonuclease A, lysozyme, xylanase, urate oxidase and xylose isomerase) were acquired. From these data, the solvent-subtracted protein scattering profiles were shown to be reproducible, with the caveat that an additive constant adjustment was required to account for small errors in solvent subtraction. Further, the major features of the obtained consensus SAXS data over the q measurement range 0-1 Å-1 are consistent with theoretical prediction. The inherently lower statistical precision for SANS limited the reliably measured q-range to <0.5 Å-1, but within the limits of experimental uncertainties the major features of the consensus SANS data were also consistent with prediction for all five proteins measured in H2O and in D2O. Thus, a foundation set of consensus SAS profiles has been obtained for benchmarking scattering-profile prediction from atomic coordinates. Additionally, two sets of SAXS data measured at different facilities to q > 2.2 Å-1 showed good mutual agreement, affirming that this region has interpretable features for structural modelling. SAS measurements with inline size-exclusion chromatography (SEC) proved to be generally superior for eliminating sample heterogeneity, but with unavoidable sample dilution during column elution, while batch SAS data collected at higher concentrations and for longer times provided superior statistical precision. Careful merging of data measured using inline SEC and batch modes, or low- and high-concentration data from batch measurements, was successful in eliminating small amounts of aggregate or interparticle interference from the scattering while providing improved statistical precision overall for the benchmarking data set.
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Affiliation(s)
- Jill Trewhella
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Patrice Vachette
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Paris, 91198 Gif-sur-Yvette, France
| | - Jan Bierma
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Clement Blanchet
- European Molecular Biology Laboratory (EMBL) Hamburg Unit, Notkestrasse 85, c/o Deutsches Elektronen-Synchrotron, 22607 Hamburg, Germany
| | - Emre Brookes
- Chemistry and Biochemistry, University of Montana, 32 Campus Drive, Missoula, MT 59812, USA
| | - Srinivas Chakravarthy
- BioCAT, Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Leonie Chatzimagas
- Theoretical Physics and Center for Biophysics, Saarland University, Campus E2.6, 66123 Saarbrücken, Germany
| | - Thomas E. Cleveland
- Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850, USA
- National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD 20899, USA
| | - Nathan Cowieson
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Ben Crossett
- Sydney Mass Spectrometry, The University of Sydney, Sydney, NSW 2006, Australia
| | - Anthony P. Duff
- Australian Nuclear Science and Technology Organisation, New Illawara Road, Lucas Heights, NSW 2234, Australia
| | - Daniel Franke
- European Molecular Biology Laboratory (EMBL) Hamburg Unit, Notkestrasse 85, c/o Deutsches Elektronen-Synchrotron, 22607 Hamburg, Germany
| | - Frank Gabel
- Institut de Biologie Structurale, CEA, CNRS, Université Grenoblé Alpes, 41 Rue Jules Horowitz, 38027 Grenoble, France
| | - Richard E. Gillilan
- Cornell High-Energy Synchrotron Source, 161 Synchrotron Drive, Ithaca, NY 14853, USA
| | - Melissa Graewert
- European Molecular Biology Laboratory (EMBL) Hamburg Unit, Notkestrasse 85, c/o Deutsches Elektronen-Synchrotron, 22607 Hamburg, Germany
| | - Alexander Grishaev
- Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850, USA
- National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD 20899, USA
| | - J. Mitchell Guss
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Michal Hammel
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Jesse Hopkins
- BioCAT, Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Qingqui Huang
- Cornell High-Energy Synchrotron Source, 161 Synchrotron Drive, Ithaca, NY 14853, USA
| | - Jochen S. Hub
- Theoretical Physics and Center for Biophysics, Saarland University, Campus E2.6, 66123 Saarbrücken, Germany
| | - Greg L. Hura
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Thomas C. Irving
- BioCAT, Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Cy Michael Jeffries
- European Molecular Biology Laboratory (EMBL) Hamburg Unit, Notkestrasse 85, c/o Deutsches Elektronen-Synchrotron, 22607 Hamburg, Germany
| | - Cheol Jeong
- Department of Physics, Wesleyan University, Middletown, CT 06459, USA
| | - Nigel Kirby
- Australian Synchrotron, ANSTO, 800 Blackburn Road, Clayton, VIC 3158, Australia
| | - Susan Krueger
- National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD 20899, USA
| | - Anne Martel
- Institut Laue–Langevin, 71 Avenue des Martyrs, 38042 Grenoble CEDEX 9, France
| | - Tsutomu Matsui
- Stanford Synchrotron Radiation Lightsource, Stanford University, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Na Li
- National Facility for Protein Science in Shanghai, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Road No. 333, Haike Road, Shanghai 201210, People’s Republic of China
| | - Javier Pérez
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint-Aubin BP 48, 91192 Gif-sur-Yvette, France
| | - Lionel Porcar
- Institut Laue–Langevin, 71 Avenue des Martyrs, 38042 Grenoble CEDEX 9, France
| | - Thierry Prangé
- CITCoM (UMR 8038 CNRS), Faculté de Pharmacie, 4 Avenue de l’Observatoire, 75006 Paris, France
| | - Ivan Rajkovic
- Stanford Synchrotron Radiation Lightsource, Stanford University, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Mattia Rocco
- Proteomica e Spettrometria di Massa, IRCCS Ospedale Policlinico San Martino, Largo R. Benzi 10, 16132 Genova, Italy
| | - Daniel J. Rosenberg
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Timothy M. Ryan
- Australian Synchrotron, ANSTO, 800 Blackburn Road, Clayton, VIC 3158, Australia
| | - Soenke Seifert
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Hiroshi Sekiguchi
- SPring-8, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyōgo 679-5198, Japan
| | - Dmitri Svergun
- European Molecular Biology Laboratory (EMBL) Hamburg Unit, Notkestrasse 85, c/o Deutsches Elektronen-Synchrotron, 22607 Hamburg, Germany
| | - Susana Teixeira
- National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD 20899, USA
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, DE 19716, USA
| | - Aurelien Thureau
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint-Aubin BP 48, 91192 Gif-sur-Yvette, France
| | - Thomas M. Weiss
- Stanford Synchrotron Radiation Lightsource, Stanford University, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Andrew E. Whitten
- Australian Nuclear Science and Technology Organisation, New Illawara Road, Lucas Heights, NSW 2234, Australia
| | - Kathleen Wood
- Australian Nuclear Science and Technology Organisation, New Illawara Road, Lucas Heights, NSW 2234, Australia
| | - Xiaobing Zuo
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Lemont, IL 60439, USA
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4
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Martel A, Gabel F. Time-resolved small-angle neutron scattering (TR-SANS) for structural biology of dynamic systems: Principles, recent developments, and practical guidelines. Methods Enzymol 2022; 677:263-290. [DOI: 10.1016/bs.mie.2022.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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5
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Kuklin AI, Ivankov OI, Rogachev AV, Soloviov DV, Islamov AK, Skoi VV, Kovalev YS, Vlasov AV, Ryzykau YL, Soloviev AG, Kucerka N, Gordeliy VI. Small-Angle Neutron Scattering at the Pulsed Reactor IBR-2: Current Status and Prospects. CRYSTALLOGR REP+ 2021. [DOI: 10.1134/s1063774521020085] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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6
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Delhommel F, Gabel F, Sattler M. Current approaches for integrating solution NMR spectroscopy and small-angle scattering to study the structure and dynamics of biomolecular complexes. J Mol Biol 2020; 432:2890-2912. [DOI: 10.1016/j.jmb.2020.03.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 02/27/2020] [Accepted: 03/10/2020] [Indexed: 01/24/2023]
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7
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Lapinaite A, Carlomagno T, Gabel F. Small-Angle Neutron Scattering of RNA-Protein Complexes. Methods Mol Biol 2020; 2113:165-188. [PMID: 32006315 DOI: 10.1007/978-1-0716-0278-2_13] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Small-angle neutron scattering (SANS) provides structural information on biomacromolecules and their complexes in dilute solutions at the nanometer length scale. The overall dimensions, shapes, and interactions can be probed and compared to information obtained by complementary structural biology techniques such as crystallography, NMR, and EM. SANS, in combination with solvent H2O/D2O exchange and/or deuteration, is particularly well suited to probe the internal structure of RNA-protein (RNP) complexes since neutrons are more sensitive than X-rays to the difference in scattering length densities of proteins and RNA, with respect to an aqueous solvent. In this book chapter we provide a practical guide on how to carry out SANS experiments on RNP complexes, as well as possibilities of data analysis and interpretation.
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Affiliation(s)
- Audrone Lapinaite
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Teresa Carlomagno
- Centre for Biomolecular Drug Research, Leibniz University Hannover, Hannover, Germany.,Helmholtz Centre for Infection Research, Group of Structural Chemistry, Braunschweig, Germany
| | - Frank Gabel
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France.
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8
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Sunday DF, Martin TB, Chang AB, Burns AB, Grubbs RH. Addressing the challenges of modeling the scattering from bottlebrush polymers in solution. JOURNAL OF POLYMER SCIENCE 2020; 58:10.1002/pol.20190289. [PMID: 33305292 PMCID: PMC7724922 DOI: 10.1002/pol.20190289] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 02/02/2020] [Indexed: 12/17/2022]
Abstract
Small-angle scattering measurements of complex macromolecules in solution are used to establish relationships between chemical structure and conformational properties. Interpretation of the scattering data requires an inverse approach where a model is chosen and the simulated scattering intensity from that model is iterated to match the experimental scattering intensity. This raises challenges in the case where the model is an imperfect approximation of the underlying structure, or where there are significant correlations between model parameters. We examine three bottlebrush polymers (consisting of polynorbornene backbone and polystyrene side chains) in a good solvent using a model commonly applied to this class of polymers: the flexible cylinder model. Applying a series of constrained Monte-Carlo Markov Chain analyses demonstrates the severity of the correlations between key parameters and the presence of multiple close minima in the goodness of fit space. We demonstrate that a shape-agnostic model can fit the scattering with significantly reduced parameter correlations and less potential for complex, multimodal parameter spaces. We provide recommendations to improve the analysis of complex macromolecules in solution, highlighting the value of Bayesian methods. This approach provides richer information for understanding parameter sensitivity compared to methods which produce a single, best fit.
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Affiliation(s)
- Daniel F. Sunday
- Materials Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, Maryland
| | - Tyler B. Martin
- Materials Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, Maryland
| | - Alice B. Chang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California
| | - Adam B. Burns
- Materials Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, Maryland
| | - Robert H. Grubbs
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California
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9
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Chen PC, Shevchuk R, Strnad FM, Lorenz C, Karge L, Gilles R, Stadler AM, Hennig J, Hub JS. Combined Small-Angle X-ray and Neutron Scattering Restraints in Molecular Dynamics Simulations. J Chem Theory Comput 2019; 15:4687-4698. [DOI: 10.1021/acs.jctc.9b00292] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Po-chia Chen
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Roman Shevchuk
- Institute for Microbiology and Genetics, Georg-August-Universität Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
| | - Felix M. Strnad
- Institute for Microbiology and Genetics, Georg-August-Universität Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
| | - Charlotte Lorenz
- Jülich Centre for Neutron Science (JCNS-1) and Institute for Complex Systems ICS (ICS-1), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- Institute of Physical Chemistry, RWTH Aachen University, Landoltweg 2, 52056 Aachen, Germany
| | - Lukas Karge
- Heinz Maier-Leibnitz Zentrum, Technische Universität München, Lichtenbergstrasse 1, 85748 Garching, Germany
| | - Ralph Gilles
- Heinz Maier-Leibnitz Zentrum, Technische Universität München, Lichtenbergstrasse 1, 85748 Garching, Germany
| | - Andreas M. Stadler
- Jülich Centre for Neutron Science (JCNS-1) and Institute for Complex Systems ICS (ICS-1), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- Institute of Physical Chemistry, RWTH Aachen University, Landoltweg 2, 52056 Aachen, Germany
| | - Janosch Hennig
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Jochen S. Hub
- Theoretical Physics and Center for Biophysics, Saarland University, Campus E2 6, 66123 Saarbrücken, Germany
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10
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Chen PC, Hennig J. The role of small-angle scattering in structure-based screening applications. Biophys Rev 2018; 10:1295-1310. [PMID: 30306530 PMCID: PMC6233350 DOI: 10.1007/s12551-018-0464-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 09/04/2018] [Indexed: 12/16/2022] Open
Abstract
In many biomolecular interactions, changes in the assembly states and structural conformations of participants can act as a complementary reporter of binding to functional and thermodynamic assays. This structural information is captured by a number of structural biology and biophysical techniques that are viable either as primary screens in small-scale applications or as secondary screens to complement higher throughput methods. In particular, small-angle X-ray scattering (SAXS) reports the average distance distribution between all atoms after orientational averaging. Such information is important when for example investigating conformational changes involved in inhibitory and regulatory mechanisms where binding events do not necessarily cause functional changes. Thus, we summarise here the current and prospective capabilities of SAXS-based screening in the context of other methods that yield structural information. Broad guidelines are also provided to assist readers in preparing screening protocols that are tailored to available X-ray sources.
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Affiliation(s)
- Po-Chia Chen
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Meyerhofstrasse 1, 69126, Heidelberg, Germany.
| | - Janosch Hennig
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Meyerhofstrasse 1, 69126, Heidelberg, Germany.
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11
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Abstract
Based on molecular dynamics simulations of four globular proteins in dilute aqueous solution, with three different water models, we examine several, essentially geometrical, aspects of the protein-water interface that remain controversial or incompletely understood. First, we compare different hydration shell definitions, based on spatial or topological proximity criteria. We find that the best method for constructing monolayer shells with nearly complete coverage is to use a 5 Å water-carbon cutoff and a 4 Å water-water cutoff. Using this method, we determine a mean interfacial water area of 11.1 Å2 which appears to be a universal property of the protein-water interface. We then analyze the local coordination and packing density of water molecules in the hydration shells and in subsets of the first shell. The mean polar water coordination number in the first shell remains within 1% of the bulk-water value, and it is 5% lower in the nonpolar part of the first shell. The local packing density is obtained from additively weighted Voronoi tessellation, arguably the most physically realistic method for allocating space between protein and water. We find that water in all parts of the first hydration shell, including the nonpolar part, is more densely packed than in the bulk, with a shell-averaged density excess of 6% for all four proteins. We suggest reasons why this value differs from previous experimental and computational results, emphasizing the importance of a realistic placement of the protein-water dividing surface and the distinction between spatial correlation and packing density. The protein-induced perturbation of water coordination and packing density is found to be short-ranged, with an exponential decay "length" of 0.6 shells. We also compute the protein partial volume, analyze its decomposition, and argue against the relevance of electrostriction.
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Affiliation(s)
- Filip Persson
- Division of Biophysical Chemistry, Department of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
| | - Pär Söderhjelm
- Division of Biophysical Chemistry, Department of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
| | - Bertil Halle
- Division of Biophysical Chemistry, Department of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
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12
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Ivanović MT, Bruetzel LK, Shevchuk R, Lipfert J, Hub JS. Quantifying the influence of the ion cloud on SAXS profiles of charged proteins. Phys Chem Chem Phys 2018; 20:26351-26361. [DOI: 10.1039/c8cp03080d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
MD simulations and Poisson–Boltzmann calculations predict ion cloud effects on SAXS experiments.
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Affiliation(s)
- Miloš T. Ivanović
- Georg-August-Universität Göttingen, Institute for Microbiology and Genetics
- 37077 Göttingen
- Germany
| | - Linda K. Bruetzel
- Ludwig-Maximilian-Universität München, Department of Physics
- 80799 München
- Germany
| | - Roman Shevchuk
- Georg-August-Universität Göttingen, Institute for Microbiology and Genetics
- 37077 Göttingen
- Germany
| | - Jan Lipfert
- Ludwig-Maximilian-Universität München, Department of Physics
- 80799 München
- Germany
| | - Jochen S. Hub
- Georg-August-Universität Göttingen, Institute for Microbiology and Genetics
- 37077 Göttingen
- Germany
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13
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Trewhella J. Small Angle Scattering and Structural Biology: Data Quality and Model Validation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1105:77-100. [PMID: 30617825 DOI: 10.1007/978-981-13-2200-6_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
This chapter provides a brief review of the current state-of-the-art in small-angle scattering (SAS) from biomolecules in solution in regard to: (1) sample preparation and instrumentation, (2) data reduction and analysis, and (3) three-dimensional structural modelling and validation. In this context, areas of ongoing research in regard to the interpretation of SAS data will be discussed with a particular focus on structural modelling using computational methods and data from different experimental techniques, including SAS (hybrid methods). Finally, progress made in establishing community accepted publication guidelines and a standard reporting framework that includes SAS data deposition in a public data bank will be described. Importantly, SAS data with associated meta-data can now be held in a format that supports exchange between data archives and seamless interoperability with the world-wide Protein Data Bank (wwPDB). Biomolecular SAS is thus well positioned to contribute to an envisioned federation of data archives in support of hybrid structural biology.
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Affiliation(s)
- Jill Trewhella
- School of Life and Environmental Sciences, The University of Sydney, NSW, Australia. .,Department of Chemistry, University of Utah, Salt Lake City, UT, USA.
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14
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Trewhella J, Duff AP, Durand D, Gabel F, Guss JM, Hendrickson WA, Hura GL, Jacques DA, Kirby NM, Kwan AH, Pérez J, Pollack L, Ryan TM, Sali A, Schneidman-Duhovny D, Schwede T, Svergun DI, Sugiyama M, Tainer JA, Vachette P, Westbrook J, Whitten AE. 2017 publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution: an update. Acta Crystallogr D Struct Biol 2017; 73:710-728. [PMID: 28876235 PMCID: PMC5586245 DOI: 10.1107/s2059798317011597] [Citation(s) in RCA: 181] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 08/07/2017] [Indexed: 12/02/2022] Open
Abstract
In 2012, preliminary guidelines were published addressing sample quality, data acquisition and reduction, presentation of scattering data and validation, and modelling for biomolecular small-angle scattering (SAS) experiments. Biomolecular SAS has since continued to grow and authors have increasingly adopted the preliminary guidelines. In parallel, integrative/hybrid determination of biomolecular structures is a rapidly growing field that is expanding the scope of structural biology. For SAS to contribute maximally to this field, it is essential to ensure open access to the information required for evaluation of the quality of SAS samples and data, as well as the validity of SAS-based structural models. To this end, the preliminary guidelines for data presentation in a publication are reviewed and updated, and the deposition of data and associated models in a public archive is recommended. These guidelines and recommendations have been prepared in consultation with the members of the International Union of Crystallography (IUCr) Small-Angle Scattering and Journals Commissions, the Worldwide Protein Data Bank (wwPDB) Small-Angle Scattering Validation Task Force and additional experts in the field.
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Affiliation(s)
- Jill Trewhella
- School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia
| | - Anthony P. Duff
- ANSTO, New Illawarra Road, Lucas Heights, NSW 2234, Australia
| | - Dominique Durand
- Institut de Biologie Intégrative de la Cellule, UMR 9198, Bâtiment 430, Université Paris-Sud, 91405 Orsay CEDEX, France
| | - Frank Gabel
- Université Grenoble Alpes, Commissariat à l’Energie Atomique (CEA), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Structurale (IBS), and Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - J. Mitchell Guss
- School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia
| | - Wayne A. Hendrickson
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Greg L. Hura
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - David A. Jacques
- University of Technology Sydney, ithree Institute, 15 Broadway, Ultimo, NSW 2007, Australia
| | - Nigel M. Kirby
- Australian Synchrotron, 800 Blackburn Road, Clayton, VIC 3168, Australia
| | - Ann H. Kwan
- School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia
| | - Javier Pérez
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint-Aubin BP48, 91192 Gif-sur-Yvette CEDEX, France
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853-2501, USA
| | - Timothy M. Ryan
- Australian Synchrotron, 800 Blackburn Road, Clayton, VIC 3168, Australia
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences (QB3), University of California San Francisco, San Francisco, California, USA
| | - Dina Schneidman-Duhovny
- School of Computer Science and Engineering, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Torsten Schwede
- Biozentrum, University of Basel and SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Dmitri I. Svergun
- European Molecular Biology Laboratory (EMBL) Hamburg, c/o DESY, Nokestrasse 85, 22607 Hamburg, Germany
| | - Masaaki Sugiyama
- Research Reactor Institute, Kyoto University, Kumatori, Sennan-gun, Osaka 590-0494, Japan
| | - John A. Tainer
- Basic Science Research Division, Molecular and Cellular Oncology, MD Anderson Cancer Center, University of Texas, Houston, Texas, USA
| | - Patrice Vachette
- Institut de Biologie Intégrative de la Cellule, UMR 9198, Bâtiment 430, Université Paris-Sud, 91405 Orsay CEDEX, France
| | - John Westbrook
- Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, NJ 07102, USA
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Ibrahim Z, Martel A, Moulin M, Kim HS, Härtlein M, Franzetti B, Gabel F. Time-resolved neutron scattering provides new insight into protein substrate processing by a AAA+ unfoldase. Sci Rep 2017; 7:40948. [PMID: 28102317 PMCID: PMC5244417 DOI: 10.1038/srep40948] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 12/12/2016] [Indexed: 01/24/2023] Open
Abstract
We present a combination of small-angle neutron scattering, deuterium labelling and contrast variation, temperature activation and fluorescence spectroscopy as a novel approach to obtain time-resolved, structural data individually from macromolecular complexes and their substrates during active biochemical reactions. The approach allowed us to monitor the mechanical unfolding of a green fluorescent protein model substrate by the archaeal AAA+ PAN unfoldase on the sub-minute time scale. Concomitant with the unfolding of its substrate, the PAN complex underwent an energy-dependent transition from a relaxed to a contracted conformation, followed by a slower expansion to its initial state at the end of the reaction. The results support a model in which AAA ATPases unfold their substrates in a reversible power stroke mechanism involving several subunits and demonstrate the general utility of this time-resolved approach for studying the structural molecular kinetics of multiple protein remodelling complexes and their substrates on the sub-minute time scale.
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Affiliation(s)
- Ziad Ibrahim
- Université Grenoble Alpes, Institut de Biologie Structurale, 38044 Grenoble, France.,Centre National de la Recherche Scientifique, Institut de Biologie Structurale, 38044 Grenoble, France.,Centre à l'Energie Atomique et aux Energies Alternatives, Institut de Biologie Structurale, 38044 Grenoble, France.,Institut Laue-Langevin, 38042 Grenoble, France
| | - Anne Martel
- Institut Laue-Langevin, 38042 Grenoble, France
| | | | - Henry S Kim
- Université Grenoble Alpes, Institut de Biologie Structurale, 38044 Grenoble, France.,Centre National de la Recherche Scientifique, Institut de Biologie Structurale, 38044 Grenoble, France.,Centre à l'Energie Atomique et aux Energies Alternatives, Institut de Biologie Structurale, 38044 Grenoble, France
| | | | - Bruno Franzetti
- Université Grenoble Alpes, Institut de Biologie Structurale, 38044 Grenoble, France.,Centre National de la Recherche Scientifique, Institut de Biologie Structurale, 38044 Grenoble, France.,Centre à l'Energie Atomique et aux Energies Alternatives, Institut de Biologie Structurale, 38044 Grenoble, France
| | - Frank Gabel
- Université Grenoble Alpes, Institut de Biologie Structurale, 38044 Grenoble, France.,Centre National de la Recherche Scientifique, Institut de Biologie Structurale, 38044 Grenoble, France.,Centre à l'Energie Atomique et aux Energies Alternatives, Institut de Biologie Structurale, 38044 Grenoble, France.,Institut Laue-Langevin, 38042 Grenoble, France
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16
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Structural studies of RNA-protein complexes: A hybrid approach involving hydrodynamics, scattering, and computational methods. Methods 2016; 118-119:146-162. [PMID: 27939506 DOI: 10.1016/j.ymeth.2016.12.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 12/01/2016] [Accepted: 12/05/2016] [Indexed: 01/01/2023] Open
Abstract
The diverse functional cellular roles played by ribonucleic acids (RNA) have emphasized the need to develop rapid and accurate methodologies to elucidate the relationship between the structure and function of RNA. Structural biology tools such as X-ray crystallography and Nuclear Magnetic Resonance are highly useful methods to obtain atomic-level resolution models of macromolecules. However, both methods have sample, time, and technical limitations that prevent their application to a number of macromolecules of interest. An emerging alternative to high-resolution structural techniques is to employ a hybrid approach that combines low-resolution shape information about macromolecules and their complexes from experimental hydrodynamic (e.g. analytical ultracentrifugation) and solution scattering measurements (e.g., solution X-ray or neutron scattering), with computational modeling to obtain atomic-level models. While promising, scattering methods rely on aggregation-free, monodispersed preparations and therefore the careful development of a quality control pipeline is fundamental to an unbiased and reliable structural determination. This review article describes hydrodynamic techniques that are highly valuable for homogeneity studies, scattering techniques useful to study the low-resolution shape, and strategies for computational modeling to obtain high-resolution 3D structural models of RNAs, proteins, and RNA-protein complexes.
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17
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Small-angle scattering and 3D structure interpretation. Curr Opin Struct Biol 2016; 40:1-7. [DOI: 10.1016/j.sbi.2016.05.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Revised: 05/12/2016] [Accepted: 05/12/2016] [Indexed: 12/29/2022]
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18
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Kim HS, Martel A, Girard E, Moulin M, Härtlein M, Madern D, Blackledge M, Franzetti B, Gabel F. SAXS/SANS on Supercharged Proteins Reveals Residue-Specific Modifications of the Hydration Shell. Biophys J 2016; 110:2185-94. [PMID: 27224484 PMCID: PMC4880798 DOI: 10.1016/j.bpj.2016.04.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 03/09/2016] [Accepted: 04/08/2016] [Indexed: 11/26/2022] Open
Abstract
Water molecules in the immediate vicinity of biomacromolecules, including proteins, constitute a hydration layer characterized by physicochemical properties different from those of bulk water and play a vital role in the activity and stability of these structures, as well as in intermolecular interactions. Previous studies using solution scattering, crystallography, and molecular dynamics simulations have provided valuable information about the properties of these hydration shells, including modifications in density and ionic concentration. Small-angle scattering of x-rays (SAXS) and neutrons (SANS) are particularly useful and complementary techniques to study biomacromolecular hydration shells due to their sensitivity to electronic and nuclear scattering-length density fluctuations, respectively. Although several sophisticated SAXS/SANS programs have been developed recently, the impact of physicochemical surface properties on the hydration layer remains controversial, and systematic experimental data from individual biomacromolecular systems are scarce. Here, we address the impact of physicochemical surface properties on the hydration shell by a systematic SAXS/SANS study using three mutants of a single protein, green fluorescent protein (GFP), with highly variable net charge (+36, -6, and -29). The combined analysis of our data shows that the hydration shell is locally denser in the vicinity of acidic surface residues, whereas basic and hydrophilic/hydrophobic residues only mildly modify its density. Moreover, the data demonstrate that the density modifications result from the combined effect of residue-specific recruitment of ions from the bulk in combination with water structural rearrangements in their vicinity. Finally, we find that the specific surface-charge distributions of the different GFP mutants modulate the conformational space of flexible parts of the protein.
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Affiliation(s)
- Henry S Kim
- University Grenoble Alpes, Grenoble, France; CNRS, Grenoble, France; CEA, IBS, Grenoble, France
| | | | - Eric Girard
- University Grenoble Alpes, Grenoble, France; CNRS, Grenoble, France; CEA, IBS, Grenoble, France
| | | | | | - Dominique Madern
- University Grenoble Alpes, Grenoble, France; CNRS, Grenoble, France; CEA, IBS, Grenoble, France; Institut Laue-Langevin, Grenoble, France
| | - Martin Blackledge
- University Grenoble Alpes, Grenoble, France; CNRS, Grenoble, France; CEA, IBS, Grenoble, France
| | - Bruno Franzetti
- University Grenoble Alpes, Grenoble, France; CNRS, Grenoble, France; CEA, IBS, Grenoble, France; Institut Laue-Langevin, Grenoble, France
| | - Frank Gabel
- University Grenoble Alpes, Grenoble, France; CNRS, Grenoble, France; CEA, IBS, Grenoble, France; Institut Laue-Langevin, Grenoble, France.
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19
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Application of advanced X-ray methods in life sciences. Biochim Biophys Acta Gen Subj 2016; 1861:3671-3685. [PMID: 27156488 DOI: 10.1016/j.bbagen.2016.05.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 05/03/2016] [Accepted: 05/04/2016] [Indexed: 12/19/2022]
Abstract
BACKGROUND Synchrotron radiation (SR) sources provide diverse X-ray methods for the investigation of structure-function relationships in biological macromolecules. SCOPE OF REVIEW Recent developments in SR sources and in the X-ray tools they offer for life sciences are reviewed. Specifically, advances in macromolecular crystallography, small angle X-ray solution scattering, X-ray absorption and fluorescence spectroscopy, and imaging are discussed with examples. MAJOR CONCLUSIONS SR sources offer a range of X-ray techniques that can be used in a complementary fashion in studies of biological systems at a wide range of resolutions from atomic to cellular scale. Emerging applications of X-ray techniques include the characterization of disordered proteins, noncrystalline and nonequilibrium systems, elemental imaging of tissues, cells and organs, and detection of time-resolved changes in molecular structures. GENERAL SIGNIFICANCE X-ray techniques are in the center of hybrid approaches that are used to gain insight into complex problems relating to biomolecular mechanisms, disease and possible therapeutic solutions. This article is part of a Special Issue entitled "Science for Life". Guest Editors: Dr. Austen Angell, Dr. Salvatore Magazù and Dr. Federica Migliardo.
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20
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Delaforge E, Milles S, Bouvignies G, Bouvier D, Boivin S, Salvi N, Maurin D, Martel A, Round A, Lemke EA, Ringkjøbing Jensen M, Hart DJ, Blackledge M. Large-Scale Conformational Dynamics Control H5N1 Influenza Polymerase PB2 Binding to Importin α. J Am Chem Soc 2015; 137:15122-34. [DOI: 10.1021/jacs.5b07765] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Elise Delaforge
- Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38044 Grenoble, France
- CEA, DSV, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
| | - Sigrid Milles
- Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38044 Grenoble, France
- CEA, DSV, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
| | - Guillaume Bouvignies
- Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38044 Grenoble, France
- CEA, DSV, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
| | - Denis Bouvier
- Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38044 Grenoble, France
- CEA, DSV, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- Univ. Grenoble Alpes, UVHCI, Grenoble, France
- CNRS, UVHCI, Grenoble, France
| | - Stephane Boivin
- Univ. Grenoble Alpes, UVHCI, Grenoble, France
- CNRS, UVHCI, Grenoble, France
- Unit for Virus Host Cell Interactions, Univ. Grenoble Alpes-EMBL-CNRS, Grenoble, France
| | - Nicola Salvi
- Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38044 Grenoble, France
- CEA, DSV, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
| | - Damien Maurin
- Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38044 Grenoble, France
- CEA, DSV, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
| | - Anne Martel
- Institut Laue-Langevin, F-38044 Grenoble, France
| | - Adam Round
- European Molecular Biology Laboratory, Grenoble Outstation, 38042 Grenoble, France
| | - Edward A. Lemke
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Malene Ringkjøbing Jensen
- Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38044 Grenoble, France
- CEA, DSV, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
| | - Darren J. Hart
- Univ. Grenoble Alpes, UVHCI, Grenoble, France
- CNRS, UVHCI, Grenoble, France
- Unit for Virus Host Cell Interactions, Univ. Grenoble Alpes-EMBL-CNRS, Grenoble, France
| | - Martin Blackledge
- Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38044 Grenoble, France
- CEA, DSV, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
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21
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Gabel F. Small-Angle Neutron Scattering for Structural Biology of Protein–RNA Complexes. Methods Enzymol 2015; 558:391-415. [DOI: 10.1016/bs.mie.2015.02.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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