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Vorovitch MF, Samygina VR, Pichkur E, Konarev PV, Peters G, Khvatov EV, Ivanova AL, Tuchynskaya KK, Konyushko OI, Fedotov AY, Armeev G, Shaytan KV, Kovalchuk MV, Osolodkin DI, Egorov AM, Ishmukhametov AA. Preparation and characterization of inactivated tick-borne encephalitis virus samples for single-particle imaging at the European XFEL. Acta Crystallogr D Struct Biol 2024; 80:44-59. [PMID: 38164954 DOI: 10.1107/s2059798323010562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 12/10/2023] [Indexed: 01/03/2024] Open
Abstract
X-ray imaging of virus particles at the European XFEL could eventually allow their complete structures to be solved, potentially approaching the resolution of other structural virology methods. To achieve this ambitious goal with today's technologies, about 1 ml of purified virus suspension containing at least 1012 particles per millilitre is required. Such large amounts of concentrated suspension have never before been obtained for enveloped viruses. Tick-borne encephalitis virus (TBEV) represents an attractive model system for the development of enveloped virus purification and concentration protocols, given the availability of large amounts of inactivated virus material provided by vaccine-manufacturing facilities. Here, the development of a TBEV vaccine purification and concentration scheme is presented combined with a quality-control protocol that allows substantial amounts of highly concentrated non-aggregated suspension to be obtained. Preliminary single-particle imaging experiments were performed for this sample at the European XFEL, showing distinct diffraction patterns.
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Affiliation(s)
- Mikhail F Vorovitch
- Institute of Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, Moscow 119991, Russian Federation
| | | | - Evgeny Pichkur
- NRC `Kurchatov Insitute', Moscow 123182, Russian Federation
| | | | - Georgy Peters
- NRC `Kurchatov Insitute', Moscow 123182, Russian Federation
| | - Evgeny V Khvatov
- FSASI `Chumakov FSC R&D IBP RAS' (Institute of Poliomyelitis), Moscow 108819, Russian Federation
| | - Alla L Ivanova
- FSASI `Chumakov FSC R&D IBP RAS' (Institute of Poliomyelitis), Moscow 108819, Russian Federation
| | - Ksenia K Tuchynskaya
- FSASI `Chumakov FSC R&D IBP RAS' (Institute of Poliomyelitis), Moscow 108819, Russian Federation
| | - Olga I Konyushko
- FSASI `Chumakov FSC R&D IBP RAS' (Institute of Poliomyelitis), Moscow 108819, Russian Federation
| | - Anton Y Fedotov
- FSASI `Chumakov FSC R&D IBP RAS' (Institute of Poliomyelitis), Moscow 108819, Russian Federation
| | - Grigory Armeev
- Department of Biology, Lomonosov Moscow State University, Moscow 119991, Russian Federation
| | - Konstantin V Shaytan
- Department of Biology, Lomonosov Moscow State University, Moscow 119991, Russian Federation
| | | | - Dmitry I Osolodkin
- FSASI `Chumakov FSC R&D IBP RAS' (Institute of Poliomyelitis), Moscow 108819, Russian Federation
| | - Alexey M Egorov
- FSASI `Chumakov FSC R&D IBP RAS' (Institute of Poliomyelitis), Moscow 108819, Russian Federation
| | - Aydar A Ishmukhametov
- FSASI `Chumakov FSC R&D IBP RAS' (Institute of Poliomyelitis), Moscow 108819, Russian Federation
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Chukhovskii FN, Konarev PV, Volkov VV. X-Ray Diffraction Tomography Recovery of the 3D Displacement-Field Function of the Coulomb-Type Point Defect in a Crystal. Sci Rep 2019; 9:14216. [PMID: 31578401 PMCID: PMC6775144 DOI: 10.1038/s41598-019-50833-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [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: 05/08/2019] [Accepted: 09/18/2019] [Indexed: 12/03/2022] Open
Abstract
A successive approach to the solution of the inverse problem of the X-ray diffraction tomography (XRDT) is proposed. It is based on the semi-kinematical solution of the dynamical Takagi–Taupin equations for the σ-polarized diffracted wave amplitude. Theoretically, the case of the Coulomb-type point defect in a single crystal Si(111) under the exact conditions of the symmetric Laue diffraction for a set of the tilted X-ray topography 2D-images (2D projections) is considered provided that the plane-parallel sample is rotated around the diffraction vector [\documentclass[12pt]{minimal}
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\begin{document}$$\bar{{\bf{2}}}$$\end{document}2¯20]. The iterative simulated annealing (SA) and quasi-Newton gradient descent (qNGD) algorithm codes are used for a recovery of the 3D displacement-field function of the Coulomb-type point defect. The computer recovery data of the 3D displacement-field function related to the one XRDT 2D projection are presented. It is proved that the semi-kinematical approach to the solution of the dynamical Takagi–Taupin equations is effective for recovering the 3D displacement-field function even for the one XRDT 2D projection.
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Affiliation(s)
- F N Chukhovskii
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre "Crystallography and Photonics", Russian Academy of Sciences, Moscow, 119333, Russia.
| | - P V Konarev
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre "Crystallography and Photonics", Russian Academy of Sciences, Moscow, 119333, Russia. .,National Research Centre "Kurchatov Institute", Moscow, 123182, Russia.
| | - V V Volkov
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre "Crystallography and Photonics", Russian Academy of Sciences, Moscow, 119333, Russia.
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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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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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Wong E, Vaaje-Kolstad G, Ghosh A, Hurtado-Guerrero R, Konarev PV, Ibrahim AFM, Svergun DI, Eijsink VGH, Chatterjee NS, van Aalten DMF. The Vibrio cholerae colonization factor GbpA possesses a modular structure that governs binding to different host surfaces. PLoS Pathog 2012; 8:e1002373. [PMID: 22253590 PMCID: PMC3257281 DOI: 10.1371/journal.ppat.1002373] [Citation(s) in RCA: 114] [Impact Index Per Article: 9.5] [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: 08/26/2011] [Accepted: 09/27/2011] [Indexed: 02/06/2023] Open
Abstract
Vibrio cholerae is a bacterial pathogen that colonizes the chitinous exoskeleton of zooplankton as well as the human gastrointestinal tract. Colonization of these different niches involves an N-acetylglucosamine binding protein (GbpA) that has been reported to mediate bacterial attachment to both marine chitin and mammalian intestinal mucin through an unknown molecular mechanism. We report structural studies that reveal that GbpA possesses an unusual, elongated, four-domain structure, with domains 1 and 4 showing structural homology to chitin binding domains. A glycan screen revealed that GbpA binds to GlcNAc oligosaccharides. Structure-guided GbpA truncation mutants show that domains 1 and 4 of GbpA interact with chitin in vitro, whereas in vivo complementation studies reveal that domain 1 is also crucial for mucin binding and intestinal colonization. Bacterial binding studies show that domains 2 and 3 bind to the V. cholerae surface. Finally, mouse virulence assays show that only the first three domains of GbpA are required for colonization. These results explain how GbpA provides structural/functional modular interactions between V. cholerae, intestinal epithelium and chitinous exoskeletons. Vibrio cholerae is the bacterium that causes cholera, a disease endemic in developing countries with poor sanitation. The bacterium colonizes aquatic organisms that serve as a reservoir of transmission to humans. Our work has focused on GbpA, a protein that is secreted by V. cholerae and appears to facilitate growth of the bacteria both in the human intestine and on the exoskeletons of marine organisms. We show that the protein possesses an unusual three-dimensional structure consisting of four separate domains. Two of the domains are similar to proteins that are known to bind chitin, an exoskeleton biopolymer, and our data show that these domains indeed harbour the chitin binding properties of GbpA. One of these domains is also capable of binding intestinal mucus. The two remaining domains are required for interacting with the bacterium itself, creating a stable interface between the bacterium and the human/marine host, facilitating colonization. Finally, work with a cholera mouse model shows that only the first three domains of GbpA are required for colonization. These results show how GbpA provides structural/functional modular interactions between V. cholerae, the intestinal epithelium and chitinous exoskeletons.
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Affiliation(s)
- Edmond Wong
- Division of Molecular Microbiology, College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Gustav Vaaje-Kolstad
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Avishek Ghosh
- Division of Biochemistry, National Institute of Cholera and Enteric Diseases, Scheme XM, Beliaghata, Kolkata, India
| | - Ramon Hurtado-Guerrero
- Division of Molecular Microbiology, College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Peter V. Konarev
- European Molecular Biology Laboratory (EMBL), Outstation Hamburg at DESY, Hamburg, Germany
| | - Adel F. M. Ibrahim
- Division of Molecular Microbiology, College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Dmitri I. Svergun
- European Molecular Biology Laboratory (EMBL), Outstation Hamburg at DESY, Hamburg, Germany
| | - Vincent G. H. Eijsink
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Nabendu S. Chatterjee
- Division of Biochemistry, National Institute of Cholera and Enteric Diseases, Scheme XM, Beliaghata, Kolkata, India
| | - Daan M. F. van Aalten
- Division of Molecular Microbiology, College of Life Sciences, University of Dundee, Dundee, United Kingdom
- * E-mail:
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Gráczer É, Konarev PV, Szimler T, Bacsó A, Bodonyi A, Svergun DI, Závodszky P, Vas M. Essential role of the metal-ion in the IPM-assisted domain closure of 3-isopropylmalate dehydrogenase. FEBS Lett 2011; 585:3297-302. [DOI: 10.1016/j.febslet.2011.09.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Revised: 09/06/2011] [Accepted: 09/08/2011] [Indexed: 11/27/2022]
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Bronstein LM, Shtykova EV, Malyutin A, Dyke JC, Gunn E, Gao X, Stein B, Konarev PV, Dragnea B, Svergun DI. Hydrophilization of Magnetic Nanoparticles with Modified Alternating Copolymers. Part 1: The Influence of the Grafting. J Phys Chem C Nanomater Interfaces 2010; 114:21900-21907. [PMID: 21221425 PMCID: PMC3017398 DOI: 10.1021/jp107283w] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Iron oxide nanoparticles (NPs) with a diameter 21.6 nm were coated with poly(maleic acid-alt-1-octadecene) (PMAcOD) modified with grafted 5,000 Da poly(ethyelene glycol) (PEG) or short ethylene glycol (EG) tails. The coating procedure utilizes hydrophobic interactions of octadecene and oleic acid tails, while the hydrolysis of maleic anhydride moieties as well as the presence of hydrophilic PEG (EG) tails allows the NP hydrophilicity. The success of the NP coating was found to be independent of the degree of grafting which was varied between 20 and 80% of the -MacOD-units, but depended on the length of the grafted tail. The NP coating and hydrophilization did not occur when the modified copolymer contained 750 Da PEG tails independently of the grafting degree. To explain this phenomenon the micellization of the modified PMAcOD copolymers in water was analyzed by small angle x-ray scattering (SAXS). The PMAcOD molecules with the grafted 750 Da PEG tails form compact non-interacting disk-like micelles, whose stability apparently allows for no interactions with the NP hydrophobic shells. The PMAcOD containing the 5,000 Da PEG and EG tails form much larger aggregates capable of an efficient coating of the NPs. The coated NPs were characterized using transmission electron microscopy, dynamic light scattering, ζ-potential measurements, and thermal gravimetry analysis. The latter method demonstrated that the presence of long PEG tails in modified PMAcOD allows the attachment of fewer macromolecules (by a factor of ~20) compared to the case of non-modified or EG modified PMAcOD, emphasizing the importance of PEG tails in NP hydrophilization. The NPs coated with PMAcOD modified with 60% (towards all -MAcOD- units) of the 5,000 PEG tails bear a significant negative charge and display good stability in buffers. Such NPs can be useful as magnetic cores for virus-like particle formation.
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Affiliation(s)
- Lyudmila M. Bronstein
- Indiana University, Department of Chemistry, 800 E. Kirkwood Av., Bloomington, IN 47405, USA
| | - Eleonora V. Shtykova
- Institute of Crystallography, Russian Academy of Sciences, Leninsky pr. 59, 117333 Moscow, Russia
| | - Andrey Malyutin
- Indiana University, Department of Chemistry, 800 E. Kirkwood Av., Bloomington, IN 47405, USA
| | - Jason C. Dyke
- Indiana University, Department of Chemistry, 800 E. Kirkwood Av., Bloomington, IN 47405, USA
| | - Emily Gunn
- Indiana University, Department of Chemistry, 800 E. Kirkwood Av., Bloomington, IN 47405, USA
| | - Xinfeng Gao
- Indiana University, Department of Chemistry, 800 E. Kirkwood Av., Bloomington, IN 47405, USA
| | - Barry Stein
- Indiana University, Department of Biology, 1001 East Third Street, Bloomington, IN 47405, USA
| | - Peter V. Konarev
- EMBL, Hamburg Outstation, Notkestraße 85, D-22603 Hamburg, Germany
| | - Bogdan Dragnea
- Indiana University, Department of Chemistry, 800 E. Kirkwood Av., Bloomington, IN 47405, USA
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Shtykova EV, Malyutin A, Dyke J, Stein B, Konarev PV, Dragnea B, Svergun DI, Bronstein LM. Hydrophilization of Magnetic Nanoparticles with Modified Alternating Copolymers. Part 2: Behavior in solution. J Phys Chem C Nanomater Interfaces 2010; 114:21908-21913. [PMID: 21243096 PMCID: PMC3018835 DOI: 10.1021/jp1072846] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Aqueous solutions of iron oxide nanoparticles (NPs) stabilized by poly(maleic acid-alt-1-octadecene) (PMAcOD) modified with the 5,000 Da poly(ethylene glycol) (PEG) or the short ethylene glycol (EG) tails were analyzed by small-angle X-ray scattering (SAXS). Advanced SAXS data analysis methods were employed to systematically characterize the structure and interactions between the NPs. Depending on the type of the grafted tail and the grafting density all NPs can be separated into three groups. All the samples contain mixtures of individual nanoparticles, their dynamic clusters and aggregates, and the fractions of these species are different in the different groups. The first group consists of NPs coated with PMAcOD modified with the long PEG tails with the maximal grafting density, and the content of dynamic clusters and aggregates in the samples of this group does not exceed 4%. The samples from the second group with less dense coatings demonstrate a larger amount (5-7%) of the aggregates and dynamic clusters. The samples from the third group consisting of the NPs protected by EG modified PMAcOD contain mostly individual NPs and some amount of dumbbell dimers without noticeable aggregation. Importantly, the solution behavior of the NPs is independent on the iron oxide core size. Our results therefore provide means of predicting stabilization and avoiding aggregation of NPs based on the type of a protective shell.
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Affiliation(s)
- Eleonora V. Shtykova
- Institute of Crystallography, Russian Academy of Sciences, Leninsky pr. 59, 117333 Moscow, Russia
| | - Andrey Malyutin
- Indiana University, Department of Chemistry, 800 East Kirkwood Av., Bloomington, IN 47405, USA
| | - Jason Dyke
- Indiana University, Department of Chemistry, 800 East Kirkwood Av., Bloomington, IN 47405, USA
| | - Barry Stein
- Indiana University, Department of Biology, 1001 East Third Street, Bloomington, IN 47405, USA
| | - Peter V. Konarev
- EMBL, Hamburg Outstation, Notkestraße 85, D-22603 Hamburg, Germany
| | - Bogdan Dragnea
- Indiana University, Department of Chemistry, 800 East Kirkwood Av., Bloomington, IN 47405, USA
| | | | - Lyudmila M. Bronstein
- Indiana University, Department of Chemistry, 800 East Kirkwood Av., Bloomington, IN 47405, USA
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Galantini L, Leggio C, Konarev PV, Pavel NV. Human serum albumin binding ibuprofen: A 3D description of the unfolding pathway in urea. Biophys Chem 2010; 147:111-22. [DOI: 10.1016/j.bpc.2010.01.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2009] [Revised: 01/08/2010] [Accepted: 01/10/2010] [Indexed: 11/28/2022]
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Leggio C, Galantini L, Konarev PV, Pavel NV. Urea-Induced Denaturation Process on Defatted Human Serum Albumin and in the Presence of Palmitic Acid. J Phys Chem B 2009; 113:12590-602. [DOI: 10.1021/jp904330v] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Claudia Leggio
- Dipartimento di Chimica, Sapienza Università di Roma, P.O. Box 34-Roma 62, Piazzale A. Moro 5, I-00185 Roma, Italy, INFM CRS-SOFT, c/o Sapienza Università di Roma, Roma, Italy, and Hamburg Outstation, European Molecular Biology Laboratory, D-22603 Hamburg, Germany
| | - Luciano Galantini
- Dipartimento di Chimica, Sapienza Università di Roma, P.O. Box 34-Roma 62, Piazzale A. Moro 5, I-00185 Roma, Italy, INFM CRS-SOFT, c/o Sapienza Università di Roma, Roma, Italy, and Hamburg Outstation, European Molecular Biology Laboratory, D-22603 Hamburg, Germany
| | - Peter V. Konarev
- Dipartimento di Chimica, Sapienza Università di Roma, P.O. Box 34-Roma 62, Piazzale A. Moro 5, I-00185 Roma, Italy, INFM CRS-SOFT, c/o Sapienza Università di Roma, Roma, Italy, and Hamburg Outstation, European Molecular Biology Laboratory, D-22603 Hamburg, Germany
| | - Nicolae V. Pavel
- Dipartimento di Chimica, Sapienza Università di Roma, P.O. Box 34-Roma 62, Piazzale A. Moro 5, I-00185 Roma, Italy, INFM CRS-SOFT, c/o Sapienza Università di Roma, Roma, Italy, and Hamburg Outstation, European Molecular Biology Laboratory, D-22603 Hamburg, Germany
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Heikkinen OK, Ruskamo S, Konarev PV, Svergun DI, Iivanainen T, Heikkinen SM, Permi P, Koskela H, Kilpeläinen I, Ylänne J. Atomic structures of two novel immunoglobulin-like domain pairs in the actin cross-linking protein filamin. J Biol Chem 2009; 284:25450-8. [PMID: 19622754 DOI: 10.1074/jbc.m109.019661] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Filamins are actin filament cross-linking proteins composed of an N-terminal actin-binding domain and 24 immunoglobulin-like domains (IgFLNs). Filamins interact with numerous proteins, including the cytoplasmic domains of plasma membrane signaling and cell adhesion receptors. Thereby filamins mechanically and functionally link the cell membrane to the cytoskeleton. Most of the interactions have been mapped to the C-terminal IgFLNs 16-24. Similarly, as with the previously known compact domain pair of IgFLNa20-21, the two-domain fragments IgFLNa16-17 and IgFLNa18-19 were more compact in small angle x-ray scattering analysis than would be expected for two independent domains. Solution state NMR structures revealed that the domain packing in IgFLNa18-19 resembles the structure of IgFLNa20-21. In both domain pairs the integrin-binding site is masked, although the details of the domain-domain interaction are partly distinct. The structure of IgFLNa16-17 revealed a new domain packing mode where the adhesion receptor binding site of domain 17 is not masked. Sequence comparison suggests that similar packing of three tandem filamin domain pairs is present throughout the animal kingdom, and we propose that this packing is involved in the regulation of filamin interactions through a mechanosensor mechanism.
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Affiliation(s)
- Outi K Heikkinen
- Department of Chemistry, University of Helsinki, FI-00014 Helsinki, Finland
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Paoletti F, Covaceuszach S, Konarev PV, Gonfloni S, Malerba F, Schwarz E, Svergun DI, Cattaneo A, Lamba D. Intrinsic structural disorder of mouse proNGF. Proteins 2009; 75:990-1009. [PMID: 19089979 DOI: 10.1002/prot.22311] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The unprocessed precursor of the Nerve Growth Factor (NGF), proNGF, has additional functions, besides its initially described role as a chaperone for NGF folding. The precursor protein endows apoptotic and/or neurotrophic properties, in contrast to the mature part. The structural and molecular basis for such distinct activities are presently unknown. Aiming to gain insights into the specific molecular interactions that govern rm-proNGF biological activities versus those of its mature counterpart, a structural study by synchrotron small angle X-ray scattering (SAXS) in solution was carried out. The different binding properties of the two proteins were investigated by surface plasmon resonance (SPR) using, as structural probes, a panel of anti-NGF antibodies and the soluble forms of TrkA and p75(NTR) receptors. SAXS measurements revealed the rm-proNGF to be dimeric and anisometric, with the propeptide domain being intrinsically unstructured. Ab initio reconstructions assuming twofold symmetry generated two types of structural models, a globular "crab-like" and an elongated shape that resulted in equally good fits of the scattering data. A novel method accounting for possible coexistence of different conformations contributing to the experimental scattering pattern, with no symmetry constraints, suggests the "crab-like" to be a more likely proNGF conformation. To exploit the potential of chemical stabilizers affecting the existing conformational protein populations, SAXS data were also collected in the presence of ammonium sulphate. An increase of the proNGF compactness was observed. SPR data pinpoints that the propeptide of proNGF may act as an intrinsically unstructured protein domain, characterized by a molecular promiscuity in the interaction/binding to multiple partners (TrkA and p75(NTR) receptors and a panel of neutralizing anti-NGF antibodies) depending on the physiological conditions of the cell. These data provide a first insight into the structural basis for the selectivity of mouse short proNGF, versus NGF, towards its binding partners.
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Affiliation(s)
- Francesca Paoletti
- SISSA-ISAS, Building Q1, Area Science Park - Basovizza, S.S 14 Km 163.5, 34012 Trieste, Italy.
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13
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Maveyraud L, Niwa H, Guillet V, Svergun DI, Konarev PV, Palmer RA, Peumans WJ, Rougé P, Van Damme EJM, Reynolds CD, Mourey L. Structural basis for sugar recognition, including the Tn carcinoma antigen, by the lectin SNA-II from Sambucus nigra. Proteins 2009; 75:89-103. [PMID: 18798567 DOI: 10.1002/prot.22222] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Bark of elderberry (Sambucus nigra) contains a galactose (Gal)/N-acetylgalactosamine (GalNAc)-specific lectin (SNA-II) corresponding to slightly truncated B-chains of a genuine Type-II ribosome-inactivating protein (Type-II RIPs, SNA-V), found in the same species. The three-dimensional X-ray structure of SNA-II has been determined in two distinct crystal forms, hexagonal and tetragonal, at 1.90 A and 1.35 A, respectively. In both crystal forms, the SNA-II molecule folds into two linked beta-trefoil domains, with an overall conformation similar to that of the B-chains of ricin and other Type-II RIPs. Glycosylation is observed at four sites along the polypeptide chain, accounting for 14 saccharide units. The high-resolution structures of SNA-II in complex with Gal and five Gal-related saccharides (GalNAc, lactose, alpha1-methylgalactose, fucose, and the carcinoma-specific Tn antigen) were determined at 1.55 A resolution or better. Binding is observed in two saccharide-binding sites for most of the sugars: a conserved aspartate residue interacts simultaneously with the O3 and O4 atoms of saccharides. In one of the binding sites, additional interactions with the protein involve the O6 atom. Analytical gel filtration, small angle X-ray scattering studies and crystal packing analysis indicate that, although some oligomeric species are present, the monomeric species predominate in solution.
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Affiliation(s)
- Laurent Maveyraud
- Institut de Pharmacologie et de Biologie Structurale (IPBS), UMR 5089, Université Paul Sabatier Toulouse III/CNRS, Toulouse, France.
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14
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Paravisi S, Fumagalli G, Riva M, Morandi P, Morosi R, Konarev PV, Petoukhov MV, Bernier S, Chênevert R, Svergun DI, Curti B, Vanoni MA. Kinetic and mechanistic characterization of Mycobacterium tuberculosis glutamyl-tRNA synthetase and determination of its oligomeric structure in solution. FEBS J 2009; 276:1398-417. [PMID: 19187240 DOI: 10.1111/j.1742-4658.2009.06880.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Mycobacterium tuberculosis glutamyl-tRNA synthetase (Mt-GluRS), encoded by Rv2992c, was overproduced in Escherichia coli cells, and purified to homogeneity. It was found to be similar to the other well-characterized GluRS, especially the E. coli enzyme, with respect to the requirement for bound tRNA(Glu) to produce the glutamyl-AMP intermediate, and the steady-state kinetic parameters k(cat) (130 min(-1)) and K(M) for tRNA (0.7 microm) and ATP (78 microm), but to differ by a one order of magnitude higher K(M) value for L-Glu (2.7 mm). At variance with the E. coli enzyme, among the several compounds tested as inhibitors, only pyrophosphate and the glutamyl-AMP analog glutamol-AMP were effective, with K(i) values in the mum range. The observed inhibition patterns are consistent with a random binding of ATP and L-Glu to the enzyme-tRNA complex. Mt-GluRS, which is predicted by genome analysis to be of the non-discriminating type, was not toxic when overproduced in E. coli cells indicating that it does not catalyse the mischarging of E. coli tRNA(Gln) with L-Glu and that GluRS/tRNA(Gln) recognition is species specific. Mt-GluRS was significantly more sensitive than the E. coli form to tryptic and chymotryptic limited proteolysis. For both enzymes chymotrypsin-sensitive sites were found in the predicted tRNA stem contact domain next to the ATP binding site. Mt-GluRS, but not Ec-GluRS, was fully protected from proteolysis by ATP and glutamol-AMP. Small-angle X-ray scattering showed that, at variance with the E. coli enzyme that is strictly monomeric, the Mt-GluRS monomer is present in solution in equilibrium with the homodimer. The monomer prevails at low protein concentrations and is stabilized by ATP but not by glutamol-AMP. Inspection of small-angle X-ray scattering-based models of Mt-GluRS reveals that both the monomer and the dimer are catalytically active. By using affinity chromatography and His(6)-tagged forms of either GluRS or glutamyl-tRNA reductase as the bait it was shown that the M. tuberculosis proteins can form a complex, which may control the flux of Glu-tRNA(Glu) toward protein or tetrapyrrole biosynthesis.
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Affiliation(s)
- Stefano Paravisi
- Dipartimento di Scienze Biomolecolari e Biotecnologie, Università degli Studi di Milano, Milan, Italy
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Weghofer M, Dall'Antonia Y, Grote M, Stöcklinger A, Kneidinger M, Balic N, Krauth MT, Fernández-Caldas E, Thomas WR, van Hage M, Vieths S, Spitzauer S, Horak F, Svergun DI, Konarev PV, Valent P, Thalhamer J, Keller W, Valenta R, Vrtala S. Characterization of Der p 21, a new important allergen derived from the gut of house dust mites. Allergy 2008; 63:758-67. [PMID: 18445190 DOI: 10.1111/j.1398-9995.2008.01647.x] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BACKGROUND The house dust mite (HDM) Dermatophagoides pteronyssinus is a major allergen source eliciting allergic asthma. The aim of the study was to identify new important HDM allergens associated with allergic asthma. METHODS A cDNA coding for a new mite allergen, designated Der p 21, was isolated using immunoglobulin E (IgE) antibodies from patients with allergic asthma out of a D. pteronyssinus expression cDNA library and expressed in Escherichia coli. RESULTS Circular dichroism analysis of the purified allergen showed that rDer p 21 (14 726 Da) is one of the few mite allergens with an alpha-helical secondary structure. The protein exhibited high thermal stability and refolding capacity, and, as determined by small angle X-ray scattering, formed a dimer consisting of two flat triangles. rDer p 21 bound high levels of patients' IgE antibodies and showed high allergenic activity in basophil activation experiments. Rabbit anti-Der p 21 IgG antibodies inhibited mite-allergic patients' IgE binding and allowed the ultrastructural localization of the allergen in the midgut (epithelium, lumen and faeces) of D. pteronyssinus by immunogold electron microscopy. Der p 21 revealed sequence homology with group 5 mite allergens, but IgE and IgG reactivity data and cross-inhibition studies identified it as a new mite allergen. CONCLUSIONS Der p 21 is a new important mite allergen which is liberated into the environment via faecal particles and hence may be associated with allergic asthma.
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Affiliation(s)
- M Weghofer
- Division of Immunopathology, Department of Pathophysiology, Center for Physiology and Pathophysiology, Medical University of Vienna, Vienna, Austria
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16
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Xu X, Reinle W, Hannemann F, Konarev PV, Svergun DI, Bernhardt R, Ubbink M. Dynamics in a Pure Encounter Complex of Two Proteins Studied by Solution Scattering and Paramagnetic NMR Spectroscopy. J Am Chem Soc 2008; 130:6395-403. [DOI: 10.1021/ja7101357] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xingfu Xu
- Institute of Chemistry, Leiden University, P.O. Box 9502, NL-2300RA Leiden, The Netherlands, Naturwissenschaftlich-Technische Fakultat III, Institut für Biochemie, Universität des Saarlandes, P.O. Box 151150, D-66041, Saarbrucken, Germany, EMBL Hamburg, Notkestrasse 85, D-22603 Hamburg, Germany, and Institute of Crystallography, Russian Academy of Sciences, Leninsky pr. 59, 117333, Moscow, Russia
| | - Wolfgang Reinle
- Institute of Chemistry, Leiden University, P.O. Box 9502, NL-2300RA Leiden, The Netherlands, Naturwissenschaftlich-Technische Fakultat III, Institut für Biochemie, Universität des Saarlandes, P.O. Box 151150, D-66041, Saarbrucken, Germany, EMBL Hamburg, Notkestrasse 85, D-22603 Hamburg, Germany, and Institute of Crystallography, Russian Academy of Sciences, Leninsky pr. 59, 117333, Moscow, Russia
| | - Frank Hannemann
- Institute of Chemistry, Leiden University, P.O. Box 9502, NL-2300RA Leiden, The Netherlands, Naturwissenschaftlich-Technische Fakultat III, Institut für Biochemie, Universität des Saarlandes, P.O. Box 151150, D-66041, Saarbrucken, Germany, EMBL Hamburg, Notkestrasse 85, D-22603 Hamburg, Germany, and Institute of Crystallography, Russian Academy of Sciences, Leninsky pr. 59, 117333, Moscow, Russia
| | - Peter V. Konarev
- Institute of Chemistry, Leiden University, P.O. Box 9502, NL-2300RA Leiden, The Netherlands, Naturwissenschaftlich-Technische Fakultat III, Institut für Biochemie, Universität des Saarlandes, P.O. Box 151150, D-66041, Saarbrucken, Germany, EMBL Hamburg, Notkestrasse 85, D-22603 Hamburg, Germany, and Institute of Crystallography, Russian Academy of Sciences, Leninsky pr. 59, 117333, Moscow, Russia
| | - Dmitri I. Svergun
- Institute of Chemistry, Leiden University, P.O. Box 9502, NL-2300RA Leiden, The Netherlands, Naturwissenschaftlich-Technische Fakultat III, Institut für Biochemie, Universität des Saarlandes, P.O. Box 151150, D-66041, Saarbrucken, Germany, EMBL Hamburg, Notkestrasse 85, D-22603 Hamburg, Germany, and Institute of Crystallography, Russian Academy of Sciences, Leninsky pr. 59, 117333, Moscow, Russia
| | - Rita Bernhardt
- Institute of Chemistry, Leiden University, P.O. Box 9502, NL-2300RA Leiden, The Netherlands, Naturwissenschaftlich-Technische Fakultat III, Institut für Biochemie, Universität des Saarlandes, P.O. Box 151150, D-66041, Saarbrucken, Germany, EMBL Hamburg, Notkestrasse 85, D-22603 Hamburg, Germany, and Institute of Crystallography, Russian Academy of Sciences, Leninsky pr. 59, 117333, Moscow, Russia
| | - Marcellus Ubbink
- Institute of Chemistry, Leiden University, P.O. Box 9502, NL-2300RA Leiden, The Netherlands, Naturwissenschaftlich-Technische Fakultat III, Institut für Biochemie, Universität des Saarlandes, P.O. Box 151150, D-66041, Saarbrucken, Germany, EMBL Hamburg, Notkestrasse 85, D-22603 Hamburg, Germany, and Institute of Crystallography, Russian Academy of Sciences, Leninsky pr. 59, 117333, Moscow, Russia
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Szabó J, Varga A, Flachner B, Konarev PV, Svergun DI, Závodszky P, Vas M. Role of side-chains in the operation of the main molecular hinge of 3-phosphoglycerate kinase. FEBS Lett 2008; 582:1335-40. [DOI: 10.1016/j.febslet.2008.03.016] [Citation(s) in RCA: 8] [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: 01/30/2008] [Revised: 02/14/2008] [Accepted: 03/12/2008] [Indexed: 11/16/2022]
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Shtykova EV, Huang X, Gao X, Dyke JC, Schmucker AL, Dragnea B, Remmes N, Baxter DV, Stein B, Konarev PV, Svergun DI, Bronstein LM. Hydrophilic Monodisperse Magnetic Nanoparticles Protected by an Amphiphilic Alternating Copolymer. J Phys Chem C Nanomater Interfaces 2008; 112:16809-16817. [PMID: 19194520 PMCID: PMC2633929 DOI: 10.1021/jp8053636] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Iron oxide nanoparticles (NPs) with diameters of 16.1, 20.5, and 20.8 nm prepared from iron oleate precursors were coated with poly(maleic acid-alt-1-octadecene) (PMAcOD). The coating procedure exploited hydrophobic interactions of octadecene and oleic acid tails while hydrolysis of maleic anhydride moieties allowed the NP hydrophilicity. The PMAcOD nanostructure in water and the PMAcOD-coated NPs were studied using transmission electron microscopy, zeta-potential measurements, small-angle X-ray scattering, and fluorescence measurements. The combination of several techniques suggests that independently of the iron oxide core and oleic acid shell structures, PMAcOD encapsulates NPs, forming stable hydrophilic shells which withstand absorption of hydrophobic molecules, such as pyrene, without shell disintegration. Moreover, the PMAcOD molecules are predominantly attached to a single NP instead of self-assembling into the PMAcOD disklike nanostructures or attachment to several NPs. This leads to highly monodisperse aqueous samples with only a small fraction of NPs forming large aggregates due to cross-linking by the copolymer macromolecules.
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Affiliation(s)
- Eleonora V Shtykova
- Institute of Crystallography, Russian Academy of Sciences, Leninsky pr. 59, 117333 Moscow, Russia
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Mumtsidu E, Makhov AM, Konarev PV, Svergun DI, Griffith JD, Tucker PA. Structural features of the single-stranded DNA-binding protein of Epstein-Barr virus. J Struct Biol 2007; 161:172-87. [PMID: 18068378 DOI: 10.1016/j.jsb.2007.10.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2007] [Revised: 10/16/2007] [Accepted: 10/17/2007] [Indexed: 01/19/2023]
Abstract
We report the structural features of a C-terminal deletion construct of the Epstein-Barr virus single-stranded DNA-binding protein, Balf2 (Balf2DeltaC), which like the herpes simplex virus I encoded protein, infected cell protein 8 (ICP8), binds non-sequence specifically to single-stranded DNA (ssDNA). ICP8, in the absence of ssDNA, assembles into long filamentous structures. Removal of the 60 C-terminal amino acids of ICP8 (ICP8DeltaC) prevents the formation of such filaments, whereas addition of circular ssDNA to ICP8DeltaC induces formation of "super helical" filaments. Balf2DeltaC, which we show is a zinc-binding protein, does not form these filaments under the same conditions but does bind ssDNA in a weakly cooperative manner. Further structural comparison of both proteins in solution by small-angle X-ray scattering shows proteins with similar molecular envelopes. One major difference is the tendency of Balf2DeltaC to dimerize on different surfaces to that used for oligomerization when binding to ssDNA, and this may have implications for the mechanism of replication initiation.
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Affiliation(s)
- E Mumtsidu
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, D-22603 Hamburg, Germany
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20
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Mastrangelo E, Milani M, Bollati M, Selisko B, Peyrane F, Pandini V, Sorrentino G, Canard B, Konarev PV, Svergun DI, de Lamballerie X, Coutard B, Khromykh AA, Bolognesi M. Crystal structure and activity of Kunjin virus NS3 helicase; protease and helicase domain assembly in the full length NS3 protein. J Mol Biol 2007; 372:444-55. [PMID: 17658551 DOI: 10.1016/j.jmb.2007.06.055] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2007] [Revised: 06/08/2007] [Accepted: 06/19/2007] [Indexed: 11/23/2022]
Abstract
Flaviviral NS3 is a multifunctional protein displaying N-terminal protease activity in addition to C-terminal helicase, nucleoside 5'-triphosphatase (NTPase), and 5'-terminal RNA triphosphatase (RTPase) activities. NS3 is held to support the separation of RNA daughter and template strands during viral replication. In addition, NS3 assists the initiation of replication by unwinding the RNA secondary structure in the 3' non-translated region (NTR). We report here the three-dimensional structure (at 3.1 A resolution) of the NS3 helicase domain (residues 186-619; NS3:186-619) from Kunjin virus, an Australian variant of the West Nile virus. As for homologous helicases, NS3:186-619 is composed of three domains, two of which are structurally related and held to host the NTPase and RTPase active sites. The third domain (C-terminal) is involved in RNA binding/recognition. The NS3:186-619 construct occurs as a dimer in solution and in the crystals. We show that NS3:186-619 displays both ATPase and RTPase activities, that it can unwind a double-stranded RNA substrate, being however inactive on a double-stranded DNA substrate. Analysis of different constructs shows that full length NS3 displays increased helicase activity, suggesting that the protease domain plays an assisting role in the RNA unwinding process. The structural interaction between the helicase and protease domain has been assessed using small angle X-ray scattering on full length NS3, disclosing that the protease and helicase domains build a rather elongated molecular assembly differing from that observed in the NS3 protein from hepatitis C virus.
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Affiliation(s)
- Eloise Mastrangelo
- Department of Biomolecular Sciences and Biotechnology, CNR-INFM, University of Milano, Via Celoria 26, 20133, Milano, Italy
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21
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Alazard R, Mourey L, Ebel C, Konarev PV, Petoukhov MV, Svergun DI, Erard M. Fine-tuning of intrinsic N-Oct-3 POU domain allostery by regulatory DNA targets. Nucleic Acids Res 2007; 35:4420-32. [PMID: 17576670 PMCID: PMC1935007 DOI: 10.1093/nar/gkm453] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The 'POU' (acronym of Pit-1, Oct-1, Unc-86) family of transcription factors share a common DNA-binding domain of approximately 160 residues, comprising so-called 'POUs' and 'POUh' sub-domains connected by a flexible linker. The importance of POU proteins as developmental regulators and tumor-promoting agents is due to linker flexibility, which allows them to adapt to a considerable variety of DNA targets. However, because of this flexibility, it has not been possible to determine the Oct-1/Pit-1 linker structure in crystallographic POU/DNA complexes. We have previously shown that the neuronal POU protein N-Oct-3 linker contains a structured region. Here, we have used a combination of hydrodynamic methods, DNA footprinting experiments, molecular modeling and small angle X-ray scattering to (i) structurally interpret the N-Oct-3-binding site within the HLA DRalpha gene promoter and deduce from this a novel POU domain allosteric conformation and (ii) analyze the molecular mechanisms involved in conformational transitions. We conclude that there might exist a continuum running from free to 'pre-bound' N-Oct-3 POU conformations and that regulatory DNA regions likely select pre-existing conformers, in addition to molding the appropriate DBD structure. Finally, we suggest that a specific pair of glycine residues in the linker might act as a major conformational switch.
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Affiliation(s)
- Robert Alazard
- Institut de Pharmacologie et de Biologie Structurale, 205 Route de Narbonne, 31077 Toulouse, Institut de Biologie Structurale, UMR 5075 CEA-CNRS-UJF, 41 rue Jules Horowitz, 38027 Grenoble, France and European Molecular Biology Laboratory, Hamburg Outstation, EMBL c/o DESY, D-22603 Hamburg, Germany and Institute of Crystallography, Russian Academy of Sciences, Leninsky pr. 59, 117333 Moscow, Russia
| | - Lionel Mourey
- Institut de Pharmacologie et de Biologie Structurale, 205 Route de Narbonne, 31077 Toulouse, Institut de Biologie Structurale, UMR 5075 CEA-CNRS-UJF, 41 rue Jules Horowitz, 38027 Grenoble, France and European Molecular Biology Laboratory, Hamburg Outstation, EMBL c/o DESY, D-22603 Hamburg, Germany and Institute of Crystallography, Russian Academy of Sciences, Leninsky pr. 59, 117333 Moscow, Russia
| | - Christine Ebel
- Institut de Pharmacologie et de Biologie Structurale, 205 Route de Narbonne, 31077 Toulouse, Institut de Biologie Structurale, UMR 5075 CEA-CNRS-UJF, 41 rue Jules Horowitz, 38027 Grenoble, France and European Molecular Biology Laboratory, Hamburg Outstation, EMBL c/o DESY, D-22603 Hamburg, Germany and Institute of Crystallography, Russian Academy of Sciences, Leninsky pr. 59, 117333 Moscow, Russia
| | - Peter V. Konarev
- Institut de Pharmacologie et de Biologie Structurale, 205 Route de Narbonne, 31077 Toulouse, Institut de Biologie Structurale, UMR 5075 CEA-CNRS-UJF, 41 rue Jules Horowitz, 38027 Grenoble, France and European Molecular Biology Laboratory, Hamburg Outstation, EMBL c/o DESY, D-22603 Hamburg, Germany and Institute of Crystallography, Russian Academy of Sciences, Leninsky pr. 59, 117333 Moscow, Russia
| | - Maxim V. Petoukhov
- Institut de Pharmacologie et de Biologie Structurale, 205 Route de Narbonne, 31077 Toulouse, Institut de Biologie Structurale, UMR 5075 CEA-CNRS-UJF, 41 rue Jules Horowitz, 38027 Grenoble, France and European Molecular Biology Laboratory, Hamburg Outstation, EMBL c/o DESY, D-22603 Hamburg, Germany and Institute of Crystallography, Russian Academy of Sciences, Leninsky pr. 59, 117333 Moscow, Russia
| | - Dmitri I. Svergun
- Institut de Pharmacologie et de Biologie Structurale, 205 Route de Narbonne, 31077 Toulouse, Institut de Biologie Structurale, UMR 5075 CEA-CNRS-UJF, 41 rue Jules Horowitz, 38027 Grenoble, France and European Molecular Biology Laboratory, Hamburg Outstation, EMBL c/o DESY, D-22603 Hamburg, Germany and Institute of Crystallography, Russian Academy of Sciences, Leninsky pr. 59, 117333 Moscow, Russia
| | - Monique Erard
- Institut de Pharmacologie et de Biologie Structurale, 205 Route de Narbonne, 31077 Toulouse, Institut de Biologie Structurale, UMR 5075 CEA-CNRS-UJF, 41 rue Jules Horowitz, 38027 Grenoble, France and European Molecular Biology Laboratory, Hamburg Outstation, EMBL c/o DESY, D-22603 Hamburg, Germany and Institute of Crystallography, Russian Academy of Sciences, Leninsky pr. 59, 117333 Moscow, Russia
- *To whom correspondence should be addressed. +33 (0) 562175496+33 (0) 562175994
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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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Redecke L, von Bergen M, Clos J, Konarev PV, Svergun DI, Fittschen UEA, Broekaert JAC, Bruns O, Georgieva D, Mandelkow E, Genov N, Betzel C. Structural characterization of β-sheeted oligomers formed on the pathway of oxidative prion protein aggregation in vitro. J Struct Biol 2007; 157:308-20. [PMID: 17023178 DOI: 10.1016/j.jsb.2006.06.013] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2006] [Revised: 06/16/2006] [Accepted: 06/19/2006] [Indexed: 11/26/2022]
Abstract
The pathology of transmissible spongiform encephalopathies (TSEs) is strongly associated with the structural conversion of the cellular prion protein (PrPC) into a misfolded isoform (PrPSc) that assembles into amyloid fibrils. Since increased levels of oxidative stress have been linked to prion diseases, we investigated the metal-induced oxidation of human PrP (90-231). A novel in vitro conversion assay based on aerobic incubation of PrP in the presence of elemental copper pellets at pH 5 was established, resulting in aggregation of highly beta-sheeted prion proteins. We show for the first time that two discrete oligomeric species of elongated shape, approx. 25 mers and 100 mers, are formed on the pathway of oxidative PrP aggregation in vitro, which are well characterized regarding shape and size using small-angle X-ray scattering (SAXS), dynamic light scattering (DLS), and electron microscopy (EM). Considering that small oligomers of highly similar size have recently been reported to show the highest specific infectivity within TSE-infected brain tissues of hamsters, the novel oligomers observed in this study are interesting candidates as agent causing neurodegenerative and/or self-propagating effects. Moreover, our results significantly strengthen the theory that oxidative stress might be an influence that leads to substantial structural conversions of PrP in vivo.
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Affiliation(s)
- Lars Redecke
- Center of Experimental Medicine, Institute of Biochemistry and Molecular Biology I, University Hospital Hamburg-Eppendorf, c/o DESY, 22603 Hamburg, Germany
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Zoldák G, Redecke L, Svergun DI, Konarev PV, Voertler CS, Dobbek H, Sedlák E, Sprinzl M. Release factors 2 from Escherichia coli and Thermus thermophilus: structural, spectroscopic and microcalorimetric studies. Nucleic Acids Res 2007; 35:1343-53. [PMID: 17272297 PMCID: PMC1849895 DOI: 10.1093/nar/gkl696] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Prokaryotic class I release factors (RFs) respond to mRNA stop codons and terminate protein synthesis. They interact with the ribosomal decoding site and the peptidyl-transferase centre bridging these 75 Å distant ribosomal centres. For this an elongated RF conformation, with partially unfolded core domains II·III·IV is required, which contrasts the known compact RF crystal structures. The crystal structure of Thermus thermophilus RF2 was determined and compared with solution structure of T. thermophilus and Escherichia coli RF2 by microcalorimetry, circular dichroism spectroscopy and small angle X-ray scattering. The structure of T. thermophilus RF2 in solution at 20°C is predominantly compact like the crystal structure. Thermodynamic analysis point to an initial melting of domain I, which is independent from the melting of the core. The core domains II·III·IV melt cooperatively at the respective physiological temperatures for T. thermophilus and E. coli. Thermodynamic analyses and the X-ray scattering results for T. thermophilus RF2 in solution suggest that the compact conformation of RF2 resembles a physiological state in absence of the ribosome.
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Affiliation(s)
| | - Lars Redecke
- Center of Experimental Medicine, Institute of Biochemistry and Molecular Biology I, University Hospital Hamburg-Eppendorfc/o DESY, Hamburg, Germany
| | - Dmitri I. Svergun
- European Molecular Biology Laboratory (EMBL), Outstation Hamburg at DESYHamburg, Germany
- Institute of Crystallography, Russian Academy of SciencesMoscow, Russia
| | - Peter V. Konarev
- European Molecular Biology Laboratory (EMBL), Outstation Hamburg at DESYHamburg, Germany
- Institute of Crystallography, Russian Academy of SciencesMoscow, Russia
| | - C. Stefan Voertler
- Laboratorium of Biochemistry, University of BayreuthUniversitätsstrasse 30, D-95440 Bayreuth, Germany
| | - Holger Dobbek
- Laboratorium of Biochemistry, University of BayreuthUniversitätsstrasse 30, D-95440 Bayreuth, Germany
| | | | - Mathias Sprinzl
- Laboratorium of Biochemistry, University of BayreuthUniversitätsstrasse 30, D-95440 Bayreuth, Germany
- To whom correspondence should be addressed. Tel: +49 921 55 2420; Fax: +49 921 55 2432;
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25
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Marino M, Svergun DI, Kreplak L, Konarev PV, Maco B, Labeit D, Mayans O. Poly-Ig tandems from I-band titin share extended domain arrangements irrespective of the distinct features of their modular constituents. J Muscle Res Cell Motil 2007; 26:355-65. [PMID: 16341830 DOI: 10.1007/s10974-005-9017-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The cellular function of the giant protein titin in striated muscle is a major focus of scientific attention. Particularly, its role in passive mechanics has been extensively investigated. In strong contrast, the structural details of this filament are very poorly understood. To date, only a handful of atomic models from single domain components have become available and data on poly-constructs are limited to scarce SAXS analyses. In this study, we examine the molecular parameters of poly-Ig tandems from I-band titin relevant to muscle elasticity. We revisit conservation patterns in domain and linker sequences of I-band modules and interpret these in the light of available atomic structures of Ig domains from muscle proteins. The emphasis is placed on features expected to affect inter-domain arrangements. We examine the overall conformation of a 6Ig fragment, I65-I70, from the skeletal I-band of soleus titin using SAXS and electron microscopy approaches. The possible effect of highly conserved glutamate groups at the linkers as well as the ionic strength of the medium on the overall molecular parameters of this sample is investigated. Our findings indicate that poly-Ig tandems from I-band titin tend to adopt extended arrangements with low or moderate intrinsic flexibility, independently of the specific features of linkers or component Ig domains across constitutively- and differentially-expressed tandems. Linkers do not appear to operate as free hinges so that lateral association of Ig domains must occur infrequently in samples in solution, even that inter-domain sequences of 4-5 residues length would well accommodate such geometry. It can be expected that this principle is generally applicable to all Ig-tandems from I-band titin.
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Affiliation(s)
- Marco Marino
- Division of Structural Biology, Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056, Basel, Switzerland
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26
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Abstract
The unprocessed pro-form of the NGF (nerve growth factor), proNGF (NGF precursor, without signal peptide), has been suggested to have additional functions distinct from its role as a promoter of protein folding, i.e. apoptosis and/or neurotrophic activity. Aiming to gain insights into the specific molecular interactions that mediate proNGF biological activity and into the structural determinants stabilizing its pro-region, rm-proNGF (recombinant mouse proNGF) was expressed in Escherichia coli, refolded in vitro and characterized by physicochemical methods. X-ray solution scattering measurements (small angle X-ray scattering) revealed that rm-proNGF is dimeric in solution and appears to be anisometric when compared with the compact structure of the NGF dimer. Two structural models, a globular crab-like shape and an elongated rod-like shape, equally fit to the experimental results, pointing to an intrinsically structural disordered pro-region of NGF. The models obtained allowed the interpretation of TrkA (tropomyosin receptor kinase A) binding and activation assays in cell cultures, shedding new light on the key role of proNGF in neuronal survival and neurodegeneration.
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Affiliation(s)
- F Paoletti
- SISSA/ISAS (Scuola Internazionale Superiore di Studi Avanzati/International School of Advanced Studies), Trieste, Italy.
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27
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Nardini M, Svergun D, Konarev PV, Spanò S, Fasano M, Bracco C, Pesce A, Donadini A, Cericola C, Secundo F, Luini A, Corda D, Bolognesi M. The C-terminal domain of the transcriptional corepressor CtBP is intrinsically unstructured. Protein Sci 2006; 15:1042-50. [PMID: 16597837 PMCID: PMC2242513 DOI: 10.1110/ps.062115406] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
C-terminal binding proteins (CtBPs) are moonlighting proteins involved in nuclear transcriptional corepression and in Golgi membrane tubule fission. Structural information on CtBPs is available for their substrate-binding domain, responsible for transcriptional repressor recognition/binding, and for the nucleotide-binding domain, involved in NAD(H)-binding and dimerization. On the contrary, little is known about the structure of CtBP C-terminal region ( approximately 90 residues), hosting sites for post-translational modifications. In the present communication we apply a combined approach based on bioinformatics, nuclear magnetic resonance, circular dichroism spectroscopy, and small-angle X-ray scattering, and we show that the CtBP C-terminal region is intrinsically unstructured in the full-length CtBP and in constructs lacking the substrate- and/or the nucleotide-binding domains. The flexible nature of this protein region, and its structural transitions, may be instrumental for CtBP recognition and binding to diverse molecular partners.
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Affiliation(s)
- Marco Nardini
- Department of Biomolecular Sciences and Biotechnology, and CNR-INFM, University of Milano, I-20131 Milano, Italy
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28
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Goettig P, Brandstetter H, Groll M, Göhring W, Konarev PV, Svergun DI, Huber R, Kim JS. X-ray Snapshots of Peptide Processing in Mutants of Tricorn-interacting Factor F1 from Thermoplasma acidophilum. J Biol Chem 2005; 280:33387-96. [PMID: 15994304 DOI: 10.1074/jbc.m505030200] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The tricorn-interacting factor F1 of the archaeon Thermoplasma acidophilum cleaves small hydrophobic peptide products of the proteasome and tricorn protease. F1 mutants of the active site residues that are involved in substrate recognition and catalysis displayed distinct activity patterns toward fluorogenic test substrates. Crystal structures of the mutant proteins complexed with peptides Phe-Leu, Pro-Pro, or Pro-Leu-Gly-Gly showed interaction of glutamates 213 and 245 with the N termini of the peptides and defined the S1 and S1' sites and the role of the catalytic residues. Evidence was found for processive peptide cleavage in the N-to-C direction, whereby the P1' product is translocated into the S1 site. A functional interaction of F1 with the tricorn protease was observed with the inactive F1 mutant G37A. Moreover, small angle x-ray scattering measurements for tricorn and inhibited F1 have been interpreted as formation of transient and substrate-induced complexes.
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Affiliation(s)
- Peter Goettig
- Max-Planck-Institut für Biochemie, Abteilung Strukturforschung, Am Klopferspitz 18, D-82152 Martinsried, Germany.
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29
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Simpson PJ, Monie TP, Szendröi A, Davydova N, Tyzack JK, Conte MR, Read CM, Cary PD, Svergun DI, Konarev PV, Curry S, Matthews S. Structure and RNA Interactions of the N-Terminal RRM Domains of PTB. Structure 2004; 12:1631-43. [PMID: 15341728 DOI: 10.1016/j.str.2004.07.008] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2004] [Revised: 05/28/2004] [Accepted: 07/06/2004] [Indexed: 11/25/2022]
Abstract
The polypyrimidine tract binding protein (PTB) is an important regulator of alternative splicing that also affects mRNA localization, stabilization, polyadenylation, and translation. NMR structural analysis of the N-terminal half of PTB (residues 55-301) shows a canonical structure for RRM1 but reveals novel extensions to the beta strands and C terminus of RRM2 that significantly modify the beta sheet RNA binding surface. Although PTB contains four RNA recognition motifs (RRMs), it is widely held that only RRMs 3 and 4 are involved in RNA binding and that RRM2 mediates homodimerization. However, we show here not only that the RRMs 1 and 2 contribute substantially to RNA binding but also that full-length PTB is monomeric, with an elongated structure determined by X-ray solution scattering that is consistent with a linear arrangement of the constituent RRMs. These new insights into the structure and RNA binding properties of PTB suggest revised models of its mechanism of action.
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Affiliation(s)
- Peter J Simpson
- Department of Biological Sciences, Imperial College, South Kensington Campus, Exhibition Road, London SW7 2AZ, UK
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30
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Petoukhov MV, Svergun DI, Konarev PV, Ravasio S, van den Heuvel RHH, Curti B, Vanoni MA. Quaternary structure of Azospirillum brasilense NADPH-dependent glutamate synthase in solution as revealed by synchrotron radiation x-ray scattering. J Biol Chem 2003; 278:29933-9. [PMID: 12777402 DOI: 10.1074/jbc.m304147200] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Azospirillum brasilense glutamate synthase (GltS) is the prototype of bacterial NADPH-dependent enzymes, a class of complex iron-sulfur flavoproteins essential in ammonia assimilation processes. The catalytically active GltS alpha beta holoenzyme and its isolated alpha and beta subunits (162 and 52 kDa, respectively) were analyzed using synchrotron radiation x-ray solution scattering. The GltS alpha subunit and alpha beta holoenzyme were found to be tetrameric in solution, whereas the beta subunit was a mixture of monomers and dimers. Ab initio low resolution shapes restored from the scattering data suggested that the arrangement of alpha subunits in the (alpha beta)4 holoenzyme is similar to that in the tetrameric alpha 4 complex and that beta subunits occupy the periphery of the holoenzyme. The structure of alpha 4 was further modeled using the available crystallographic coordinates of the monomeric alpha subunit assuming P222 symmetry. To model the entire alpha beta holoenzyme, a putative alpha beta protomer was constructed from the coordinates of the alpha subunit and those of the N-terminal region of porcine dihydropyrimidine dehydrogenase, which is similar to the beta subunit. Rigid body refinement yielded a model of GltS with an arrangement of alpha subunits similar to that in alpha 4, but displaying contacts also between beta subunits belonging to adjacent protomers. The holoenzyme model allows for independent catalytic activity of the alpha beta protomers, which is consistent with the available biochemical evidence.
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Affiliation(s)
- Maxim V Petoukhov
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, D-22603 Hamburg, Germany
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31
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Menushenkov AP, Konarev PV, Tsvyashchenko AV, Meyer-Klaucke W, Cortes R. Structural properties of Y1-xYbxNi2B2C synthesized at high pressure: EXAFS data analysis. J Synchrotron Radiat 2001; 8:910-912. [PMID: 11512975 DOI: 10.1107/s0909049500016733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2000] [Accepted: 11/08/2000] [Indexed: 05/23/2023]
Abstract
Local structure of Y(1-x)Yb(x)Ni2B2C series synthesized at high pressure 8 GPa has been studied using EXAFS. Measurements were performed at the Ni K-edge in temperature range 5-300 K. The results show that the Debye-Waller factor for Ni-Ni bond in the parent YNi2B2C compound is characterized by the Einstein temperature O(E) = 350 K, while a minimum value O(E) = 300 K is reached for the compound with = 0.025, which has the highest critical temperature T(c) = 12.5K of the superconductive transition. This correlates with the further suppressing of superconductivity and with the appearance of the local magnetic moments in the investigated Y(1-x)Yb(x)Ni2B2C series for x > or = 0.05 compounds. Observed changes in the local electronic and the local crystal structure of this system as a function of Yb concentration and of temperature were explained in the frame of the band filling effect.
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