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Molodenskiy DS, Svergun DI, Kikhney AG. Artificial neural networks for solution scattering data analysis. Structure 2022; 30:900-908.e2. [DOI: 10.1016/j.str.2022.03.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 01/24/2022] [Accepted: 03/16/2022] [Indexed: 11/27/2022]
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Gruzinov AY, Schroer MA, Manalastas-Cantos K, Kikhney AG, Hajizadeh NR, Schulz F, Franke D, Svergun DI, Blanchet CE. Anomalous SAXS at P12 beamline EMBL Hamburg: instrumentation and applications. J Synchrotron Radiat 2021; 28:812-823. [PMID: 33949989 PMCID: PMC8127372 DOI: 10.1107/s1600577521003404] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 03/30/2021] [Indexed: 05/09/2023]
Abstract
Small-angle X-ray scattering (SAXS) is an established method for studying nanostructured systems and in particular biological macromolecules in solution. To obtain element-specific information about the sample, anomalous SAXS (ASAXS) exploits changes of the scattering properties of selected atoms when the energy of the incident X-rays is close to the binding energy of their electrons. While ASAXS is widely applied to condensed matter and inorganic systems, its use for biological macromolecules is challenging because of the weak anomalous effect. Biological objects are often only available in small quantities and are prone to radiation damage, which makes biological ASAXS measurements very challenging. The BioSAXS beamline P12 operated by the European Molecular Biology Laboratory (EMBL) at the PETRA III storage ring (DESY, Hamburg) is dedicated to studies of weakly scattering objects. Here, recent developments at P12 allowing for ASAXS measurements are presented. The beamline control, data acquisition and data reduction pipeline of the beamline were adapted to conduct ASAXS experiments. Modelling tools were developed to compute ASAXS patterns from atomic models, which can be used to analyze the data and to help designing appropriate data collection strategies. These developments are illustrated with ASAXS experiments on different model systems performed at the P12 beamline.
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Affiliation(s)
- Andrey Yu. Gruzinov
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Martin A. Schroer
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Karen Manalastas-Cantos
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Center for Data and Computing in Natural Science, University of Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany
| | - Alexey G. Kikhney
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Nelly R. Hajizadeh
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Novartis, Novartis Campus, Fabrikstrasse 2, 4056 Basel, Switzerland
| | - Florian Schulz
- Institute of Physical Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Daniel Franke
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Dmitri I. Svergun
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Clement E. Blanchet
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
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Manalastas-Cantos K, Konarev PV, Hajizadeh NR, Kikhney AG, Petoukhov MV, Molodenskiy DS, Panjkovich A, Mertens HDT, Gruzinov A, Borges C, Jeffries CM, Svergun DI, Franke D. ATSAS 3.0: expanded functionality and new tools for small-angle scattering data analysis. J Appl Crystallogr 2021; 54:343-355. [PMID: 33833657 PMCID: PMC7941305 DOI: 10.1107/s1600576720013412] [Citation(s) in RCA: 363] [Impact Index Per Article: 121.0] [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: 06/04/2020] [Accepted: 10/06/2020] [Indexed: 11/11/2022] Open
Abstract
The ATSAS software suite encompasses a number of programs for the processing, visualization, analysis and modelling of small-angle scattering data, with a focus on the data measured from biological macromolecules. Here, new developments in the ATSAS 3.0 package are described. They include IMSIM, for simulating isotropic 2D scattering patterns; IMOP, to perform operations on 2D images and masks; DATRESAMPLE, a method for variance estimation of structural invariants through parametric resampling; DATFT, which computes the pair distance distribution function by a direct Fourier transform of the scattering data; PDDFFIT, to compute the scattering data from a pair distance distribution function, allowing comparison with the experimental data; a new module in DATMW for Bayesian consensus-based concentration-independent molecular weight estimation; DATMIF, an ab initio shape analysis method that optimizes the search model directly against the scattering data; DAMEMB, an application to set up the initial search volume for multiphase modelling of membrane proteins; ELLLIP, to perform quasi-atomistic modelling of liposomes with elliptical shapes; NMATOR, which models conformational changes in nucleic acid structures through normal mode analysis in torsion angle space; DAMMIX, which reconstructs the shape of an unknown intermediate in an evolving system; and LIPMIX and BILMIX, for modelling multilamellar and asymmetric lipid vesicles, respectively. In addition, technical updates were deployed to facilitate maintainability of the package, which include porting the PRIMUS graphical interface to Qt5, updating SASpy - a PyMOL plugin to run a subset of ATSAS tools - to be both Python 2 and 3 compatible, and adding utilities to facilitate mmCIF compatibility in future ATSAS releases. All these features are implemented in ATSAS 3.0, freely available for academic users at https://www.embl-hamburg.de/biosaxs/software.html.
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Affiliation(s)
- Karen Manalastas-Cantos
- European Molecular Biology Laboratory, Hamburg Site, Notkestrasse 85, Building 25 A, Hamburg, 22607, Germany
| | - Petr V. Konarev
- A.V. Shubnikov Institute of Crystallography, Federal Scientific Research Centre ‘Crystallography and Photonics’ of Russian Academy of Sciences, Leninsky prospekt 59, Moscow, 119333, Russian Federation
| | - Nelly R. Hajizadeh
- European Molecular Biology Laboratory, Hamburg Site, Notkestrasse 85, Building 25 A, Hamburg, 22607, Germany
| | - Alexey G. Kikhney
- European Molecular Biology Laboratory, Hamburg Site, Notkestrasse 85, Building 25 A, Hamburg, 22607, Germany
| | - Maxim V. Petoukhov
- A.V. Shubnikov Institute of Crystallography, Federal Scientific Research Centre ‘Crystallography and Photonics’ of Russian Academy of Sciences, Leninsky prospekt 59, Moscow, 119333, Russian Federation
| | - Dmitry S. Molodenskiy
- European Molecular Biology Laboratory, Hamburg Site, Notkestrasse 85, Building 25 A, Hamburg, 22607, Germany
| | - Alejandro Panjkovich
- European Molecular Biology Laboratory, Hamburg Site, Notkestrasse 85, Building 25 A, Hamburg, 22607, Germany
| | - Haydyn D. T. Mertens
- European Molecular Biology Laboratory, Hamburg Site, Notkestrasse 85, Building 25 A, Hamburg, 22607, Germany
| | - Andrey Gruzinov
- European Molecular Biology Laboratory, Hamburg Site, Notkestrasse 85, Building 25 A, Hamburg, 22607, Germany
| | - Clemente Borges
- European Molecular Biology Laboratory, Hamburg Site, Notkestrasse 85, Building 25 A, Hamburg, 22607, Germany
| | - Cy M. Jeffries
- European Molecular Biology Laboratory, Hamburg Site, Notkestrasse 85, Building 25 A, Hamburg, 22607, Germany
| | - Dmitri I. Svergun
- European Molecular Biology Laboratory, Hamburg Site, Notkestrasse 85, Building 25 A, Hamburg, 22607, Germany
| | - Daniel Franke
- European Molecular Biology Laboratory, Hamburg Site, Notkestrasse 85, Building 25 A, Hamburg, 22607, Germany
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4
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Kikhney AG, Borges CR, Molodenskiy DS, Jeffries CM, Svergun DI. SASBDB: Towards an automatically curated and validated repository for biological scattering data. Protein Sci 2019; 29:66-75. [PMID: 31576635 DOI: 10.1002/pro.3731] [Citation(s) in RCA: 132] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 09/14/2019] [Accepted: 09/16/2019] [Indexed: 02/03/2023]
Abstract
Small-angle scattering (SAS) of X-rays and neutrons is a fundamental tool to study the nanostructural properties, and in particular, biological macromolecules in solution. In structural biology, SAS recently transformed from a specialization into a general technique leading to a dramatic increase in the number of publications reporting structural models. The growing amount of data recorded and published has led to an urgent need for a global SAS repository that includes both primary data and models. In response to this, a small-angle scattering biological data bank (SASBDB) was designed in 2014 and is available for public access at www.sasbdb.org. SASBDB is a comprehensive, free and searchable repository of SAS experimental data and models deposited together with the relevant experimental conditions, sample details and instrument characteristics. SASBDB is rapidly growing, and presently has over 1,000 entries containing more than 1,600 models. We describe here the overall organization and procedures of SASBDB paying most attention to user-relevant information during submission. Perspectives of further developments, in particular, with OneDep system of the Protein Data Bank, and also widening of SASBDB including new types of data/models are discussed.
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Affiliation(s)
- Alexey G Kikhney
- European Molecular Biology Laboratory, Hamburg Outstation, Hamburg, Germany
| | - Clemente R Borges
- European Molecular Biology Laboratory, Hamburg Outstation, Hamburg, Germany
| | | | - Cy M Jeffries
- European Molecular Biology Laboratory, Hamburg Outstation, Hamburg, Germany
| | - Dmitri I Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, Hamburg, Germany
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Hajizadeh NR, Franke D, Kikhney AG, Svergun DI. Automation and inclusion of additional information for biological solution SAXS. Acta Crystallogr A Found Adv 2017. [DOI: 10.1107/s2053273317089173] [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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6
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Franke D, Petoukhov MV, Konarev PV, Panjkovich A, Tuukkanen A, Mertens HDT, Kikhney AG, Hajizadeh NR, Franklin JM, Jeffries CM, Svergun DI. ATSAS 2.8: a comprehensive data analysis suite for small-angle scattering from macromolecular solutions. J Appl Crystallogr 2017; 50:1212-1225. [PMID: 28808438 PMCID: PMC5541357 DOI: 10.1107/s1600576717007786] [Citation(s) in RCA: 953] [Impact Index Per Article: 136.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 05/25/2017] [Indexed: 11/16/2022] Open
Abstract
Developments and improvements of the ATSAS software suite (versions 2.5–2.8) for analysis of small-angle scattering data of biological macromolecules or nanoparticles are described. ATSAS is a comprehensive software suite for the analysis of small-angle scattering data from dilute solutions of biological macromolecules or nanoparticles. It contains applications for primary data processing and assessment, ab initio bead modelling, and model validation, as well as methods for the analysis of flexibility and mixtures. In addition, approaches are supported that utilize information from X-ray crystallography, nuclear magnetic resonance spectroscopy or atomistic homology modelling to construct hybrid models based on the scattering data. This article summarizes the progress made during the 2.5–2.8 ATSAS release series and highlights the latest developments. These include AMBIMETER, an assessment of the reconstruction ambiguity of experimental data; DATCLASS, a multiclass shape classification based on experimental data; SASRES, for estimating the resolution of ab initio model reconstructions; CHROMIXS, a convenient interface to analyse in-line size exclusion chromatography data; SHANUM, to evaluate the useful angular range in measured data; SREFLEX, to refine available high-resolution models using normal mode analysis; SUPALM for a rapid superposition of low- and high-resolution models; and SASPy, the ATSAS plugin for interactive modelling in PyMOL. All these features and other improvements are included in the ATSAS release 2.8, freely available for academic users from https://www.embl-hamburg.de/biosaxs/software.html.
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Affiliation(s)
- D Franke
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, D-22607 Hamburg, Germany
| | - M V Petoukhov
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, D-22607 Hamburg, Germany.,Federal Scientific Research Centre 'Crystallography and Photonics' of Russian Academy of Sciences, Leninsky prospect 59, 119333 Moscow, Russian Federation.,A. N. Frumkin Institute of Physical Chemistry and Electrochemistry RAS, Leninsky prospect 31, 119071 Moscow, and N.N. Semenov Institute of Chemical Physics of Russian Academy of Sciences, Kosygina street 4, 119991 Moscow, Russian Federation
| | - P V Konarev
- Federal Scientific Research Centre 'Crystallography and Photonics' of Russian Academy of Sciences, Leninsky prospect 59, 119333 Moscow, Russian Federation.,National Research Centre 'Kurchatov Institute', ploshchad Kurchatova 1, 123182 Moscow, Russian Federation
| | - A Panjkovich
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, D-22607 Hamburg, Germany
| | - A Tuukkanen
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, D-22607 Hamburg, Germany
| | - H D T Mertens
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, D-22607 Hamburg, Germany
| | - A G Kikhney
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, D-22607 Hamburg, Germany
| | - N R Hajizadeh
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, D-22607 Hamburg, Germany
| | - J M Franklin
- Department of Chemical Engineering, Stanford University, Stanford, California, USA
| | - C M Jeffries
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, D-22607 Hamburg, Germany
| | - D I Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, D-22607 Hamburg, Germany
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7
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Berneking L, Schnapp M, Rumm A, Trasak C, Ruckdeschel K, Alawi M, Grundhoff A, Kikhney AG, Koch-Nolte F, Buck F, Perbandt M, Betzel C, Svergun DI, Hentschke M, Aepfelbacher M. Immunosuppressive Yersinia Effector YopM Binds DEAD Box Helicase DDX3 to Control Ribosomal S6 Kinase in the Nucleus of Host Cells. PLoS Pathog 2016; 12:e1005660. [PMID: 27300509 PMCID: PMC4907486 DOI: 10.1371/journal.ppat.1005660] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 05/05/2016] [Indexed: 02/07/2023] Open
Abstract
Yersinia outer protein M (YopM) is a crucial immunosuppressive effector of the plaque agent Yersinia pestis and other pathogenic Yersinia species. YopM enters the nucleus of host cells but neither the mechanisms governing its nucleocytoplasmic shuttling nor its intranuclear activities are known. Here we identify the DEAD-box helicase 3 (DDX3) as a novel interaction partner of Y. enterocolitica YopM and present the three-dimensional structure of a YopM:DDX3 complex. Knockdown of DDX3 or inhibition of the exportin chromosomal maintenance 1 (CRM1) increased the nuclear level of YopM suggesting that YopM exploits DDX3 to exit the nucleus via the CRM1 export pathway. Increased nuclear YopM levels caused enhanced phosphorylation of Ribosomal S6 Kinase 1 (RSK1) in the nucleus. In Y. enterocolitica infected primary human macrophages YopM increased the level of Interleukin-10 (IL-10) mRNA and this effect required interaction of YopM with RSK and was enhanced by blocking YopM's nuclear export. We propose that the DDX3/CRM1 mediated nucleocytoplasmic shuttling of YopM determines the extent of phosphorylation of RSK in the nucleus to control transcription of immunosuppressive cytokines.
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Affiliation(s)
- Laura Berneking
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Marie Schnapp
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Andreas Rumm
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Claudia Trasak
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Klaus Ruckdeschel
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Malik Alawi
- Bioinformatics Core, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Heinrich-Pette-Institute (HPI), Leibniz Institute for Experimental Virology, Research Group Virus Genomics, Hamburg, Germany
| | - Adam Grundhoff
- Heinrich-Pette-Institute (HPI), Leibniz Institute for Experimental Virology, Research Group Virus Genomics, Hamburg, Germany
| | - Alexey G. Kikhney
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Hamburg, Germany
| | | | - Friedrich Buck
- Institute of Clinical Chemistry, University Medical Center, Hamburg, Germany
| | - Markus Perbandt
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Laboratory of Structural Biology of Infection and Inflammation, Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Hamburg, Germany
| | - Christian Betzel
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Laboratory of Structural Biology of Infection and Inflammation, Hamburg, Germany
| | - Dmitri I. Svergun
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Hamburg, Germany
| | - Moritz Hentschke
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Martin Aepfelbacher
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
- * E-mail:
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8
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Kikhney AG, Panjkovich A, Sokolova AV, Svergun DI. DARA: a web server for rapid search of structural neighbours using solution small angle X-ray scattering data. Bioinformatics 2015; 32:616-8. [PMID: 26504146 PMCID: PMC4743626 DOI: 10.1093/bioinformatics/btv611] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [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: 05/26/2015] [Accepted: 10/17/2015] [Indexed: 11/14/2022] Open
Abstract
Motivation: Small angle X-ray scattering (SAXS) is an established method for studying biological macromolecules in solution, whereby the experimental scattering patterns relate to the quaternary and tertiary structure of the macromolecule. Here we present DARA, a web-server, that queries over 150 000 scattering profiles pre-computed from the high resolution models of macromolecules and biological assemblies in the Protein Data Bank, to rapidly find nearest neighbours of a given experimental or theoretical SAXS pattern. Identification of the best scattering equivalents provides a straightforward and automated way of structural assessment of macromolecules based on a SAXS profile. DARA results are useful e.g. for fold recognition and finding of biologically active oligomers. Availability and implementation:http://dara.embl-hamburg.de/ Contact:svergun@embl-hamburg.de
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Affiliation(s)
- Alexey G Kikhney
- European Molecular Biology Laboratory, Hamburg Outstation, EMBL c/o DESY, 22607 Hamburg, Germany and
| | - Alejandro Panjkovich
- European Molecular Biology Laboratory, Hamburg Outstation, EMBL c/o DESY, 22607 Hamburg, Germany and
| | | | - Dmitri I Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, EMBL c/o DESY, 22607 Hamburg, Germany and
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9
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Kikhney AG, Svergun DI. A practical guide to small angle X-ray scattering (SAXS) of flexible and intrinsically disordered proteins. FEBS Lett 2015; 589:2570-7. [PMID: 26320411 DOI: 10.1016/j.febslet.2015.08.027] [Citation(s) in RCA: 370] [Impact Index Per Article: 41.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2015] [Revised: 08/14/2015] [Accepted: 08/15/2015] [Indexed: 12/17/2022]
Abstract
Small-angle X-ray scattering (SAXS) is a biophysical method to study the overall shape and structural transitions of biological macromolecules in solution. SAXS provides low resolution information on the shape, conformation and assembly state of proteins, nucleic acids and various macromolecular complexes. The technique also offers powerful means for the quantitative analysis of flexible systems, including intrinsically disordered proteins (IDPs). Here, the basic principles of SAXS are presented, and profits and pitfalls of the characterization of multidomain flexible proteins and IDPs using SAXS are discussed from the practical point of view. Examples of the synergistic use of SAXS with high resolution methods like X-ray crystallography and nuclear magnetic resonance (NMR), as well as other experimental and in silico techniques to characterize completely, or partially unstructured proteins, are presented.
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Affiliation(s)
- Alexey G Kikhney
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestr. 85, Geb. 25a, 22607 Hamburg, Germany
| | - Dmitri I Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestr. 85, Geb. 25a, 22607 Hamburg, Germany.
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10
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Abstract
Small-angle X-ray and neutron scattering (SAXS and SANS) are fundamental tools used to study the global shapes of proteins, nucleic acids, macromolecular complexes and assemblies in solution. Due to recent advances in instrumentation and computational methods, the quantity of experimental scattering data and subsequent publications is increasing dramatically. The need for a global repository allowing investigators to locate and access experimental scattering data and associated models was recently emphasized by the wwPDB small-angle scattering task force (SAStf). The small-angle scattering biological data bank (SASBDB) www.sasbdb.org has been designed in accordance with the plans of the SAStf as part of a future federated system of databases for biological SAXS and SANS. SASBDB is a comprehensive repository of freely accessible and fully searchable SAS experimental data and models that are deposited together with the relevant experimental conditions, sample details and instrument characteristics. At present the quality of deposited experimental data and the accuracy of models are manually curated, with future plans to integrate automated systems as the database expands.
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Affiliation(s)
- Erica Valentini
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestr. 85, Geb. 25a, 22603 Hamburg, Germany
| | - Alexey G Kikhney
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestr. 85, Geb. 25a, 22603 Hamburg, Germany
| | - Gianpietro Previtali
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestr. 85, Geb. 25a, 22603 Hamburg, Germany
| | - Cy M Jeffries
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestr. 85, Geb. 25a, 22603 Hamburg, Germany
| | - Dmitri I Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestr. 85, Geb. 25a, 22603 Hamburg, Germany
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11
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Sayers Z, Aydin M, Bal E, Yesilirmak F, Konarev PV, Petoukhov MV, Roessle M, Kikhney AG, Shang W, Svergun DI. Comparative Characterization of Apo-, Reconstituted- and In Vivo-Folded forms of a Durum Wheat Metallothionein. Biophys J 2013. [DOI: 10.1016/j.bpj.2012.11.2209] [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: 11/29/2022] Open
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12
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Blanchet CE, Zozulya AV, Kikhney AG, Franke D, Konarev PV, Shang W, Klaering R, Robrahn B, Hermes C, Cipriani F, Svergun DI, Roessle M. Instrumental setup for high-throughput small- and wide-angle solution scattering at the X33 beamline of EMBL Hamburg. J Appl Crystallogr 2012. [DOI: 10.1107/s0021889812013490] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
A setup is presented for automated high-throughput measurements of small-angle X-ray scattering (SAXS) from macromolecular solutions on the bending-magnet beamline X33 of EMBL at the storage ring DORIS-III (DESY, Hamburg). A new multi-cell compartment allows for rapid switching between in-vacuum and in-air operation, for digital camera assisted control of cell filling and for colour sample illumination. The beamline is equipped with a Pilatus 1 M-W pixel detector for SAXS and a Pilatus 300 k-W for wide-angle scattering (WAXS), and results from the use of the Pilatus detectors for scattering studies are reported. The setup provides a broad resolution range from 100 to 0.36 nm without the necessity of changing the sample-to-detector distance. A new optimized robotic sample changer is installed, permitting rapid and reliable automated sample loading and cell cleaning with a required sample volume of 40 µl. All the devices are fully integrated into the beamline control software system, ensuring fully automated and user-friendly operation (attended, unattended and remote) with a throughput of up to 15 measurements per hour.
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Petoukhov MV, Franke D, Shkumatov AV, Tria G, Kikhney AG, Gajda M, Gorba C, Mertens HDT, Konarev PV, Svergun DI. New developments in the ATSAS program package for small-angle scattering data analysis. J Appl Crystallogr 2012; 45:342-350. [PMID: 25484842 PMCID: PMC4233345 DOI: 10.1107/s0021889812007662] [Citation(s) in RCA: 1350] [Impact Index Per Article: 112.5] [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: 01/05/2012] [Accepted: 02/20/2012] [Indexed: 11/26/2022] Open
Abstract
New developments in the program package ATSAS (version 2.4) for the processing and analysis of isotropic small-angle X-ray and neutron scattering data are described. They include (i) multiplatform data manipulation and display tools, (ii) programs for automated data processing and calculation of overall parameters, (iii) improved usage of high- and low-resolution models from other structural methods, (iv) new algorithms to build three-dimensional models from weakly interacting oligomeric systems and complexes, and (v) enhanced tools to analyse data from mixtures and flexible systems. The new ATSAS release includes installers for current major platforms (Windows, Linux and Mac OSX) and provides improved indexed user documentation. The web-related developments, including a user discussion forum and a widened online access to run ATSAS programs, are also presented.
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Affiliation(s)
- Maxim V. Petoukhov
- European Molecular Biology Laboratory, Hamburg Unit, EMBL c/o DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Daniel Franke
- European Molecular Biology Laboratory, Hamburg Unit, EMBL c/o DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Alexander V. Shkumatov
- European Molecular Biology Laboratory, Hamburg Unit, EMBL c/o DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Giancarlo Tria
- European Molecular Biology Laboratory, Hamburg Unit, EMBL c/o DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Alexey G. Kikhney
- European Molecular Biology Laboratory, Hamburg Unit, EMBL c/o DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Michal Gajda
- European Molecular Biology Laboratory, Hamburg Unit, EMBL c/o DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Christian Gorba
- European Molecular Biology Laboratory, Hamburg Unit, EMBL c/o DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Haydyn D. T. Mertens
- European Molecular Biology Laboratory, Hamburg Unit, EMBL c/o DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Petr V. Konarev
- European Molecular Biology Laboratory, Hamburg Unit, EMBL c/o DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Dmitri I. Svergun
- European Molecular Biology Laboratory, Hamburg Unit, EMBL c/o DESY, Notkestrasse 85, Hamburg 22607, Germany
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Kikhney AG. Small-angle X-ray scattering from biological macromolecules. Acta Crystallogr A 2010. [DOI: 10.1107/s0108767310099630] [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: 11/10/2022] Open
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Petoukhov MV, Konarev PV, Kikhney AG, Svergun DI. ATSAS 2.1 – towards automated and web-supported small-angle scattering data analysis. J Appl Crystallogr 2007. [DOI: 10.1107/s0021889807002853] [Citation(s) in RCA: 372] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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