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Bozin T, Berdyshev I, Chukhontseva K, Karaseva M, Konarev P, Varizhuk A, Lesovoy D, Arseniev A, Kostrov S, Bocharov E, Demidyuk I. NMR structure of emfourin, a novel protein metalloprotease inhibitor: insights into the mechanism of action. J Biol Chem 2023; 299:104585. [PMID: 36889586 PMCID: PMC10124921 DOI: 10.1016/j.jbc.2023.104585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 03/01/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
Emfourin (M4in) is a protein metalloprotease inhibitor recently discovered in the bacterium Serratia proteamaculans and the prototype of a new family of protein protease inhibitors with an unknown mechanism of action. Protealysin-like proteases (PLPs) of the thermolysin family are natural targets of emfourin-like inhibitors (ELIs) widespread in bacteria and known in archaea. The available data indicate the involvement of PLPs in interbacterial interaction as well as bacterial interaction with other organisms and likely in pathogenesis. Arguably, ELIs participate in the regulation of bacterial pathogenesis by controlling PLP activity. Here, we determined the 3D structure of M4in using solution NMR spectroscopy. The obtained structure demonstrated no significant similarity to known protein structures. This structure was used to model the M4in-enzyme complex, and the complex model was verified by small-angle X-ray scattering. Based on our analysis of the model, we propose a molecular mechanism for the inhibitor, which was confirmed by site-directed mutagenesis. We show that two spatially close flexible loop regions are critical for the inhibitor-protease interaction. One region includes aspartic acid forming a coordination bond with catalytic Zn2+ of the enzyme, and the second region carries hydrophobic amino acids interacting with protease substrate binding sites. Such an active site structure corresponds to the noncanonical inhibition mechanism. This is the first demonstration of such a mechanism for protein inhibitors of thermolysin family metalloproteases, which puts forward M4in as a new basis for the development of antibacterial agents relying on selective inhibition of prominent factors of bacterial pathogenesis belonging to this family.
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Affiliation(s)
- TimurN Bozin
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute," Moscow, Russia; National Research Centre "Kurchatov Institute," Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - IgorM Berdyshev
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute," Moscow, Russia
| | - KseniaN Chukhontseva
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute," Moscow, Russia
| | - MariaA Karaseva
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute," Moscow, Russia
| | - PetrV Konarev
- Shubnikov Institute of Crystallography of the Federal Scientific Research Centre "Crystallography and Photonics," Russian Academy of Sciences, Moscow, Russia
| | - AnnaM Varizhuk
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Russia
| | - DmitryM Lesovoy
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - AlexanderS Arseniev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - SergeyV Kostrov
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute," Moscow, Russia
| | - EduardV Bocharov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia; Moscow Institute of Physics and Technology (State University), Dolgoprudny, Russia
| | - IlyaV Demidyuk
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute," Moscow, Russia.
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Sokolova OS, Pichkur EB, Maslova ES, Kurochkina LP, Semenyuk PI, Konarev PV, Samygina VR, Stanishneva-Konovalova TB. Local Flexibility of a New Single-Ring Chaperonin Encoded by Bacteriophage AR9 Bacillus subtilis. Biomedicines 2022; 10:biomedicines10102347. [PMID: 36289609 PMCID: PMC9598537 DOI: 10.3390/biomedicines10102347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/13/2022] [Accepted: 09/19/2022] [Indexed: 11/25/2022] Open
Abstract
Chaperonins, a family of molecular chaperones, assist protein folding in all domains of life. They are classified into two groups: bacterial variants and those present in endosymbiotic organelles of eukaryotes belong to group I, while group II includes chaperonins from the cytosol of archaea and eukaryotes. Recently, chaperonins of a prospective new group were discovered in giant bacteriophages; however, structures have been determined for only two of them. Here, using cryo-EM, we resolved a structure of a new chaperonin encoded by gene 228 of phage AR9 B. subtilis. This structure has similarities and differences with members of both groups, as well as with other known phage chaperonins, which further proves their diversity.
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Affiliation(s)
- Olga S. Sokolova
- Faculty of Biology, MSU-BIT Shenzhen University, Shenzhen 518172, China
| | - Evgeny B. Pichkur
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123098 Moscow, Russia
| | | | - Lidia P. Kurochkina
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Pavel I. Semenyuk
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Petr V. Konarev
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123098 Moscow, Russia
- Shubnikov Institute of Crystallography of FSRC “Crystallography and Photonics”, RAS, 119333 Moscow, Russia
| | - Valeriya R. Samygina
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123098 Moscow, Russia
- Shubnikov Institute of Crystallography of FSRC “Crystallography and Photonics”, RAS, 119333 Moscow, Russia
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Wieland DCF, Schroer MA, Gruzinov AY, Blanchet CE, Jeffries CM, Svergun DI. ASAXS measurements on ferritin and apoferritin at the bioSAXS beamline P12 (PETRA III, DESY). J Appl Crystallogr 2021; 54:830-838. [PMID: 34188614 PMCID: PMC8202030 DOI: 10.1107/s1600576721003034] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 03/23/2021] [Indexed: 11/10/2022] Open
Abstract
Small-angle X-ray scattering is widely utilized to study biological macromol-ecules in solution. For samples containing specific (e.g. metal) atoms, additional information can be obtained using anomalous scattering. Here, measuring samples at different energies close to the absorption edges of relevant elements provides specific structural details. However, anomalous small-angle X-ray scattering (ASAXS) applications to dilute macromolecular solutions are challenging owing to the overall low anomalous scattering effect. Here, pilot ASAXS experiments from dilute solutions of ferritin and cobalt-loaded apoferritin are reported. These samples were investigated near the resonance X-ray K edges of Fe and Co, respectively, at the EMBL P12 bioSAXS beamline at PETRA III, DESY. Thanks to the high brilliance of the P12 beamline, ASAXS experiments are feasible on dilute protein solutions, allowing one to extract the Fe- or Co-specific anomalous dispersion terms from the ASAXS data. The data were subsequently used to determine the spatial distribution of either iron or cobalt atoms incorporated into the ferritin/apoferritin protein cages.
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Affiliation(s)
- D. C. F. Wieland
- Institute for Materials Research, Helmholtz-Zentrum Geesthacht, Max-Planck Strasse 1, Geesthacht, 21502, Germany
- European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, Hamburg, 22607, Germany
| | - M. A. Schroer
- European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, Hamburg, 22607, Germany
| | - A. Yu. Gruzinov
- European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, Hamburg, 22607, Germany
| | - C. E. Blanchet
- European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, Hamburg, 22607, Germany
| | - C. M. Jeffries
- European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, Hamburg, 22607, Germany
| | - D. I. Svergun
- European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, Hamburg, 22607, Germany
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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. JOURNAL OF SYNCHROTRON RADIATION 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] [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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Desjardins K, Pomorski M, Bizien T, Thureau A, Menneglier C, Pérez J. An active x-ray beamstop based on single crystal CVD diamond at beamline SWING. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2021; 92:043104. [PMID: 34243400 DOI: 10.1063/5.0048326] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 03/19/2021] [Indexed: 06/13/2023]
Abstract
A compact active x-ray beamstop has been developed for the SWING beamline at Synchrotron SOLEIL with two main functions, blocking the x-ray beam directly transmitted by the sample to protect the Dectris EigerX4M 2D detector and monitoring its intensity. The beamstop is composed of a sensor inserted in a well of tungsten carbide. The sensor is based on a piece of free-standing single crystal chemical vapor deposited diamond used in the ionization chamber mode. The beamstop has been installed on the beamline detector stage within the detection vacuum chamber, just upstream of the large 2D detector. The intensity monitoring performance (rms noise over signal) is shown to be better than 0.06% and the linearity is shown to be better than 2% for over more than five decades. The beamstop has been calibrated between 5 and 16 keV to provide the photon flux measurements in absolute units (ph/s). The specific design of the beamstop increases the small-angle x-ray scattering q-range by a factor of 1.5 in the low angle side, as compared to the previous active beamstop, based on a more standard commercial Si diode. The beamstop has been available for three years for SWING user operation (5-17 keV). It is fully compatible with the different beamline operating modes and fluxes, except in the microbeam mode, where the very divergent beam becomes too large at the beamstop position, and the previous, larger, beamstop is then more appropriate.
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Affiliation(s)
- K Desjardins
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin BP 48, Gif-sur-Yvette 91190, France
| | - M Pomorski
- Université Paris-Saclay, CEA, List, F-91120 Palaiseau, France
| | - T Bizien
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin BP 48, Gif-sur-Yvette 91190, France
| | - A Thureau
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin BP 48, Gif-sur-Yvette 91190, France
| | - C Menneglier
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin BP 48, Gif-sur-Yvette 91190, France
| | - J Pérez
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin BP 48, Gif-sur-Yvette 91190, France
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Konarev PV, Gruzinov AY, Mertens HDT, Svergun DI. Restoring structural parameters of lipid mixtures from small-angle X-ray scattering data. J Appl Crystallogr 2021; 54:169-179. [PMID: 33833646 PMCID: PMC7941313 DOI: 10.1107/s1600576720015368] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 11/19/2020] [Indexed: 11/26/2022] Open
Abstract
Small-angle X-ray scattering (SAXS) is widely utilized to study soluble macromolecules, including those embedded into lipid carriers and delivery systems such as surfactant micelles, phospho-lipid vesicles and bilayered nanodiscs. To adequately describe the scattering from such systems, one needs to account for both the form factor (overall structure) and long-range-order Bragg reflections emerging from the organization of bilayers, which is a non-trivial task. Presently existing methods separate the analysis of lipid mixtures into distinct procedures using form-factor fitting and the fitting of the Bragg peak regions. This article describes a general approach for the computation and analysis of SAXS data from lipid mixtures over the entire angular range of an experiment. The approach allows one to restore the electron density of a lipid bilayer and simultaneously recover the corresponding size distribution and multilamellar organization of the vesicles. The method is implemented in a computer program, LIPMIX, and its performance is demonstrated on an aqueous solution of layered lipid vesicles undergoing an extrusion process. The approach is expected to be useful for the analysis of various types of lipid-based systems, e.g. for the characterization of interactions between target drug molecules and potential carrier/delivery systems.
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Affiliation(s)
- 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
| | - Andrey Yu. Gruzinov
- Hamburg Outstation, European Molecular Biology Laboratory, Notkestrasse 85, Hamburg, 22607, Germany
| | - Haydyn D. T. Mertens
- Hamburg Outstation, European Molecular Biology Laboratory, Notkestrasse 85, Hamburg, 22607, Germany
| | - Dmitri I. Svergun
- Hamburg Outstation, European Molecular Biology Laboratory, Notkestrasse 85, Hamburg, 22607, Germany
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7
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Liu G, Li Y, Wu H, Wu X, Xu X, Wang W, Zhang R, Li N. Upgraded SSRF BL19U2 beamline for small-angle X-ray scattering of biological macromolecules in solution. J Appl Crystallogr 2018. [DOI: 10.1107/s160057671801316x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The biological small-angle X-ray scattering (BioSAXS) beamline (BL19U2) at the Shanghai Synchrotron Radiation Facility, China, is dedicated exclusively to small-angle scattering experiments for biological macromolecules in solution. With recent advances in data-analysis algorithms and X-ray detectors, SAXS becomes an ideal complementary technique to other structural and biophysical methods, but it can also be applied alone to obtain important structural information. Owing to the increasing interest in solution scattering studies from the biological community, the workload on BL19U2 has steadily risen. A major upgrade of BL19U2 was performed to improve the beamline data quality, to enrich the possible sample environments and to provide a user-friendly interface. These upgrades involved the major components of BL19U2, including the optical system (slits, beamstop), the electronics, the control and acquisition software, and the sample environments, which resulted in improvements to the collected angular range in BL19U2. These upgrades have significantly broadened the scope of macromolecule size (from kilodaltons to gigadaltons) analysed at the beamline. The dedicated BL19U2 BioSAXS beamline now offers fully automated data-collection and remote-control possibilities. These developments have paved the way for high-throughput studies that generate significant quantities of structure information over a short period of time.
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8
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Valencia-Sánchez MI, Rodríguez-Hernández A, Ferreira R, Santamaría-Suárez HA, Arciniega M, Dock-Bregeon AC, Moras D, Beinsteiner B, Mertens H, Svergun D, Brieba LG, Grøtli M, Torres-Larios A. Structural Insights into the Polyphyletic Origins of Glycyl tRNA Synthetases. J Biol Chem 2016; 291:14430-46. [PMID: 27226617 PMCID: PMC4938167 DOI: 10.1074/jbc.m116.730382] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 05/09/2016] [Indexed: 11/06/2022] Open
Abstract
Glycyl tRNA synthetase (GlyRS) provides a unique case among class II aminoacyl tRNA synthetases, with two clearly widespread types of enzymes: a dimeric (α2) species present in some bacteria, archaea, and eukaryotes; and a heterotetrameric form (α2β2) present in most bacteria. Although the differences between both types of GlyRS at the anticodon binding domain level are evident, the extent and implications of the variations in the catalytic domain have not been described, and it is unclear whether the mechanism of amino acid recognition is also dissimilar. Here, we show that the α-subunit of the α2β2 GlyRS from the bacterium Aquifex aeolicus is able to perform the first step of the aminoacylation reaction, which involves the activation of the amino acid with ATP. The crystal structure of the α-subunit in the complex with an analog of glycyl adenylate at 2.8 Å resolution presents a conformational arrangement that properly positions the cognate amino acid. This work shows that glycine is recognized by a subset of different residues in the two types of GlyRS. A structural and sequence analysis of class II catalytic domains shows that bacterial GlyRS is closely related to alanyl tRNA synthetase, which led us to define a new subclassification of these ancient enzymes and to propose an evolutionary path of α2β2 GlyRS, convergent with α2 GlyRS and divergent from AlaRS, thus providing a possible explanation for the puzzling existence of two proteins sharing the same fold and function but not a common ancestor.
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Affiliation(s)
- Marco Igor Valencia-Sánchez
- From the Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Apartado Postal 70-243, Mexico City 04510, México
| | - Annia Rodríguez-Hernández
- From the Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Apartado Postal 70-243, Mexico City 04510, México, the Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato 04510, México
| | - Ruben Ferreira
- the Department of Chemistry and Molecular Biology, University of Gothenburg, SE-412 96 Gothenburg, Sweden
| | - Hugo Aníbal Santamaría-Suárez
- From the Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Apartado Postal 70-243, Mexico City 04510, México
| | - Marcelino Arciniega
- From the Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Apartado Postal 70-243, Mexico City 04510, México
| | | | - Dino Moras
- the Centre for Integrative Biology, Department of Integrated Structural Biology, Institute of Genetics and of Molecular and Cellular Biology, CNRS UMR 7104, 1 Rue Laurent Fries, Illkirch, France, and
| | - Brice Beinsteiner
- the Centre for Integrative Biology, Department of Integrated Structural Biology, Institute of Genetics and of Molecular and Cellular Biology, CNRS UMR 7104, 1 Rue Laurent Fries, Illkirch, France, and
| | - Haydyn Mertens
- the European Molecular Biology Laboratory, Hamburg Outstation, c/o DESY, Notkestrasse 85, Hamburg 22603, Germany
| | - Dmitri Svergun
- the European Molecular Biology Laboratory, Hamburg Outstation, c/o DESY, Notkestrasse 85, Hamburg 22603, Germany
| | - Luis G Brieba
- the Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato 04510, México
| | - Morten Grøtli
- the Department of Chemistry and Molecular Biology, University of Gothenburg, SE-412 96 Gothenburg, Sweden
| | - Alfredo Torres-Larios
- From the Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Apartado Postal 70-243, Mexico City 04510, México,
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9
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Blanchet CE, Spilotros A, Schwemmer F, Graewert MA, Kikhney A, Jeffries CM, Franke D, Mark D, Zengerle R, Cipriani F, Fiedler S, Roessle M, Svergun DI. Versatile sample environments and automation for biological solution X-ray scattering experiments at the P12 beamline (PETRA III, DESY). J Appl Crystallogr 2015; 48:431-443. [PMID: 25844078 PMCID: PMC4379436 DOI: 10.1107/s160057671500254x] [Citation(s) in RCA: 394] [Impact Index Per Article: 43.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 02/06/2015] [Indexed: 11/12/2023] Open
Abstract
A high-brilliance synchrotron P12 beamline of the EMBL located at the PETRA III storage ring (DESY, Hamburg) is dedicated to biological small-angle X-ray scattering (SAXS) and has been designed and optimized for scattering experiments on macromolecular solutions. Scatterless slits reduce the parasitic scattering, a custom-designed miniature active beamstop ensures accurate data normalization and the photon-counting PILATUS 2M detector enables the background-free detection of weak scattering signals. The high flux and small beam size allow for rapid experiments with exposure time down to 30-50 ms covering the resolution range from about 300 to 0.5 nm. P12 possesses a versatile and flexible sample environment system that caters for the diverse experimental needs required to study macromolecular solutions. These include an in-vacuum capillary mode for standard batch sample analyses with robotic sample delivery and for continuous-flow in-line sample purification and characterization, as well as an in-air capillary time-resolved stopped-flow setup. A novel microfluidic centrifugal mixing device (SAXS disc) is developed for a high-throughput screening mode using sub-microlitre sample volumes. Automation is a key feature of P12; it is controlled by a beamline meta server, which coordinates and schedules experiments from either standard or nonstandard operational setups. The integrated SASFLOW pipeline automatically checks for consistency, and processes and analyses the data, providing near real-time assessments of overall parameters and the generation of low-resolution models within minutes of data collection. These advances, combined with a remote access option, allow for rapid high-throughput analysis, as well as time-resolved and screening experiments for novice and expert biological SAXS users.
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Affiliation(s)
- Clement E. Blanchet
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, Hamburg, 22603, Germany
| | - Alessandro Spilotros
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, Hamburg, 22603, Germany
| | - Frank Schwemmer
- Laboratory for MEMS Applications, IMTEK – Department of Microsystems Engineering, University of Freiburg, Georges-Koegler-Allee 103, Freiburg, 79110, Germany
| | - Melissa A. Graewert
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, Hamburg, 22603, Germany
| | - Alexey Kikhney
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, Hamburg, 22603, Germany
| | - Cy M. Jeffries
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, Hamburg, 22603, Germany
| | - Daniel Franke
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, Hamburg, 22603, Germany
| | - Daniel Mark
- Laboratory for MEMS Applications, IMTEK – Department of Microsystems Engineering, University of Freiburg, Georges-Koegler-Allee 103, Freiburg, 79110, Germany
| | - Roland Zengerle
- Laboratory for MEMS Applications, IMTEK – Department of Microsystems Engineering, University of Freiburg, Georges-Koegler-Allee 103, Freiburg, 79110, Germany
| | - Florent Cipriani
- European Molecular Biology Laboratory, Grenoble Outstation, 6 rue Jules Horowitz, BP 181, Grenoble, 38042, France
| | - Stefan Fiedler
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, Hamburg, 22603, Germany
| | - Manfred Roessle
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, Hamburg, 22603, Germany
| | - Dmitri I. Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, Hamburg, 22603, Germany
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