1
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Brookes E, Rocco M, Vachette P, Trewhella J. AlphaFold-predicted protein structures and small-angle X-ray scattering: insights from an extended examination of selected data in the Small-Angle Scattering Biological Data Bank. J Appl Crystallogr 2023; 56:910-926. [PMID: 37555230 PMCID: PMC10405597 DOI: 10.1107/s1600576723005344] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 06/15/2023] [Indexed: 08/10/2023] Open
Abstract
By providing predicted protein structures from nearly all known protein sequences, the artificial intelligence program AlphaFold (AF) is having a major impact on structural biology. While a stunning accuracy has been achieved for many folding units, predicted unstructured regions and the arrangement of potentially flexible linkers connecting structured domains present challenges. Focusing on single-chain structures without prosthetic groups, an earlier comparison of features derived from small-angle X-ray scattering (SAXS) data taken from the Small-Angle Scattering Biological Data Bank (SASBDB) is extended to those calculated using the corresponding AF-predicted structures. Selected SASBDB entries were carefully examined to ensure that they represented data from monodisperse protein solutions and had sufficient statistical precision and q resolution for reliable structural evaluation. Three examples were identified where there is clear evidence that the single AF-predicted structure cannot account for the experimental SAXS data. Instead, excellent agreement is found with ensemble models generated by allowing for flexible linkers between high-confidence predicted structured domains. A pool of representative structures was generated using a Monte Carlo method that adjusts backbone dihedral allowed angles along potentially flexible regions. A fast ensemble modelling method was employed that optimizes the fit of pair distance distribution functions [P(r) versus r] and intensity profiles [I(q) versus q] computed from the pool to their experimental counterparts. These results highlight the complementarity between AF prediction, solution SAXS and molecular dynamics/conformational sampling for structural modelling of proteins having both structured and flexible regions.
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Affiliation(s)
- Emre Brookes
- Department of Chemistry and Biochemistry, University of Montana, 32 Campus Drive, Missoula, MT 59812, USA
| | - Mattia Rocco
- Proteomica e Spettrometria di Massa, IRCCS Ospedale Policlinico San Martino, Largo R. Benzi 10, Genova 16132, Italy
| | - Patrice Vachette
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette 91198, France
| | - Jill Trewhella
- School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia
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2
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N-terminal phosphorylation regulates the activity of Glycogen Synthase Kinase 3 from Plasmodium falciparum. Biochem J 2022; 479:337-356. [PMID: 35023554 PMCID: PMC8883495 DOI: 10.1042/bcj20210829] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/09/2022] [Accepted: 01/12/2022] [Indexed: 11/17/2022]
Abstract
As the decline of malaria cases stalled over the last five years, novel targets in Plasmodium falciparum are necessary for the development of new drugs. Glycogen Synthase Kinase (PfGSK3) has been identified as a potential target, since its selective inhibitors were shown to disrupt the parasitès life cycle. In the uncanonical N-terminal region of the parasite enzyme, we identified several autophosphorylation sites and probed their role in activity regulation of PfGSK3. By combining molecular modeling with experimental small-angle X-ray scattering data, we show that increased PfGSK3 activity is promoted by conformational changes in the PfGSK3 N-terminus, triggered by N-terminal phosphorylation. Our work provides novel insights into the structure and regulation of the malarial PfGSK3.
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3
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Zhang F, Richter G, Bourgeois B, Spreitzer E, Moser A, Keilbach A, Kotnik P, Madl T. A General Small-Angle X-ray Scattering-Based Screening Protocol for Studying Physical Stability of Protein Formulations. Pharmaceutics 2021; 14:69. [PMID: 35056965 PMCID: PMC8778066 DOI: 10.3390/pharmaceutics14010069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 11/16/2022] Open
Abstract
A fundamental step in developing a protein drug is the selection of a stable storage formulation that ensures efficacy of the drug and inhibits physiochemical degradation or aggregation. Here, we designed and evaluated a general workflow for screening of protein formulations based on small-angle X-ray scattering (SAXS). Our SAXS pipeline combines automated sample handling, temperature control, and fast data analysis and provides protein particle interaction information. SAXS, together with different methods including turbidity analysis, dynamic light scattering (DLS), and SDS-PAGE measurements, were used to obtain different parameters to provide high throughput screenings. Using a set of model proteins and biopharmaceuticals, we show that SAXS is complementary to dynamic light scattering (DLS), which is widely used in biopharmaceutical research and industry. We found that, compared to DLS, SAXS can provide a more sensitive measure for protein particle interactions, such as protein aggregation and repulsion. Moreover, we show that SAXS is compatible with a broader range of buffers, excipients, and protein concentrations and that in situ SAXS provides a sensitive measure for long-term protein stability. This workflow can enable future high-throughput analysis of proteins and biopharmaceuticals and can be integrated with well-established complementary physicochemical analysis pipelines in (biopharmaceutical) research and industry.
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Affiliation(s)
- Fangrong Zhang
- Key Laboratory of Gastrointestinal Cancer, Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350122, China;
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, 8010 Graz, Austria; (G.R.); (B.B.); (E.S.)
| | - Gesa Richter
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, 8010 Graz, Austria; (G.R.); (B.B.); (E.S.)
| | - Benjamin Bourgeois
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, 8010 Graz, Austria; (G.R.); (B.B.); (E.S.)
| | - Emil Spreitzer
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, 8010 Graz, Austria; (G.R.); (B.B.); (E.S.)
| | - Armin Moser
- Anton Paar GmbH, 8054 Graz, Austria; (A.M.); (A.K.); (P.K.)
| | | | - Petra Kotnik
- Anton Paar GmbH, 8054 Graz, Austria; (A.M.); (A.K.); (P.K.)
| | - Tobias Madl
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, 8010 Graz, Austria; (G.R.); (B.B.); (E.S.)
- BioTechMed-Graz, 8010 Graz, Austria
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4
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Pohl C, Mahapatra S, Kulakova A, Streicher W, Peters GHJ, Nørgaard A, Harris P. Combination of high throughput and structural screening to assess protein stability - a screening perspective. Eur J Pharm Biopharm 2021; 171:1-10. [PMID: 34826593 DOI: 10.1016/j.ejpb.2021.08.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 08/23/2021] [Accepted: 08/27/2021] [Indexed: 11/04/2022]
Abstract
High throughput screening to measure the stability of industrially relevant proteins and their variants is necessary for quality assessment in the development process. Advances in automation, measurement time and sample consumption for many techniques allow rapid measurements with minimal amount of protein. However, many methods include automated data analysis, potentially neglecting important aspects of the proteińs behavior in certain conditions. In this study we implement small angle X-ray scattering (SAXS), typically not used to assess protein behavior in industrial screening, in a high throughput screening workflow to address problems of contradicting results and reproducibility among different high throughput methods. As a case study we use the lipases of Thermomyces lanuginosus and Rhizomucor miehei, widely used industrial biocatalysts. We show that even the initial analysis of the SAXS data without performing any time-consuming modelling provide valuable information on interparticle interactions. We conclude that recent advances in automation and data processing, have enabled SAXS to be used more widely as a tool to gain in-depth knowledge highly useful for protein formulation development. This is especially relevant in light of increasing accessibility to SAXS due to the commercial availability of benchtop instruments.
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Affiliation(s)
- Christin Pohl
- Novozymes A/S, Krogshoejvej 36, 2880, Bagsvaerd, Denmark; Technical University of Denmark, Department of Chemistry, Kemitorvet 207, 2800 Kongens Lyngby, Denmark.
| | - Sujata Mahapatra
- Novozymes A/S, Krogshoejvej 36, 2880, Bagsvaerd, Denmark; Technical University of Denmark, Department of Chemistry, Kemitorvet 207, 2800 Kongens Lyngby, Denmark
| | - Alina Kulakova
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen
| | | | - Günther H J Peters
- Technical University of Denmark, Department of Chemistry, Kemitorvet 207, 2800 Kongens Lyngby, Denmark
| | - Allan Nørgaard
- Novozymes A/S, Krogshoejvej 36, 2880, Bagsvaerd, Denmark
| | - Pernille Harris
- Technical University of Denmark, Department of Chemistry, Kemitorvet 207, 2800 Kongens Lyngby, Denmark.
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5
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Baudis S, Behl M. High-Throughput and Combinatorial Approaches for the Development of Multifunctional Polymers. Macromol Rapid Commun 2021; 43:e2100400. [PMID: 34460146 DOI: 10.1002/marc.202100400] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/18/2021] [Indexed: 01/22/2023]
Abstract
High-throughput (HT) development of new multifunctional polymers is accomplished by the combination of different HT tools established in polymer sciences in the last decade. Important advances are robotic/HT synthesis of polymer libraries, the HT characterization of polymers, and the application of spatially resolved polymer library formats, explicitly microarray and gradient libraries. HT polymer synthesis enables the generation of material libraries with combinatorial design motifs. Polymer composition, molecular weight, macromolecular architecture, etc. may be varied in a systematic, fine-graded manner to obtain libraries with high chemical diversity and sufficient compositional resolution as model systems for the screening of these materials for the functions aimed. HT characterization allows a fast assessment of complementary properties, which are employed to decipher quantitative structure-properties relationships. Moreover, these methods facilitate the HT determination of important surface parameters by spatially resolved characterization methods, including time-of-flight secondary ion mass spectrometry and X-ray photoelectron spectroscopy. Here current methods for the high-throughput robotic synthesis of multifunctional polymers as well as their characterization are presented and advantages as well as present limitations are discussed.
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Affiliation(s)
- Stefan Baudis
- Institute of Active Polymers, Helmholtz-Zentrum Hereon, 14513, Teltow, Germany
| | - Marc Behl
- Institute of Active Polymers, Helmholtz-Zentrum Hereon, 14513, Teltow, Germany
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6
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A Giant Extracellular Matrix Binding Protein of Staphylococcus epidermidis Binds Surface-Immobilized Fibronectin via a Novel Mechanism. mBio 2020; 11:mBio.01612-20. [PMID: 33082256 PMCID: PMC7587433 DOI: 10.1128/mbio.01612-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Although it is normally an innocuous part of the human skin microbiota, Staphylococcus epidermidis has emerged as a major nosocomial pathogen, and implanted foreign materials are an essential risk factor for the development of an infection. The extraordinary efficiency of S. epidermidis to colonize artificial surfaces is particularly related to the ability to form biofilms. Biofilm formation itself critically depends on stable pathogen binding to extracellular host matrix components, e.g. fibronectin (Fn), covering inserted devices in vast amounts. Extracellular matrix binding protein (Embp) and its subdomains referred to as the F-repeat and the FG-repeat are critical for adherence of S. epidermidis to surface-immobilized Fn. Embp-Fn interactions preferentially occur with surface-bound, but not folded, globular Fn via binding to the F3 domain. High-resolution structure analysis of F- and FG-repeats revealed that both repeats are composed of two tightly connected triple α-helix bundles, exhibiting an elongated but rather rigid structural organization in solution. Both F- and FG-repeat possess Fn-binding capacity via interactions with type III subdomain FN12, involving residues within the C and F β-sheet. FN12 essentially supports stability of the globular Fn state, and thus these findings reasonably explain why Embp-mediated interaction of S. epidermidis necessitates Fn surface immobilization. Thus, Embp employs an uncharacterized bacterial Fn-binding mechanism to promote staphylococcal adherence.IMPORTANCE Staphylococcus epidermidis is a leading pathogen in implant-associated hospital infections. The pathogenesis critically depends on bacterial binding to ECM components, specifically fibronectin (Fn). The cell surface-localized, 1-MDa extracellular matrix binding protein (Embp) is essentially characterized by 10 F- and 40 FG-repeats. These repetitive units, each characterized by two α-helical bundles, organize themselves in a rigid, elongated form. Embp binds preferentially to surface-localized but not soluble Fn, with both F- and FG-repeats being sufficient for Fn binding and resulting bacterial adherence. Binding preferentially involves Fn type III domain, specifically residues of FN12 β-sheets C and F. Both play key role in stabilizing the globular Fn conformation, explaining the necessity of Fn surface immobilization for a subsequent interaction with Embp. In comparison to many other bacterial Fn-binding proteins using the Fn N terminus, Embp employs a previously undescribed mechanism supporting the adhesion of S. epidermidis to surface-immobilized Fn.
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7
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Marchenkova MA, Konarev PV, Rakitina TV, Timofeev VI, Boikova AS, Dyakova YA, Ilina KB, Korzhenevskiy DA, Yu Nikolaeva A, Pisarevsky YV, Kovalchuk MV. Dodecamers derived from the crystal structure were found in the pre-crystallization solution of the transaminase from the thermophilic bacterium Thermobaculum terrenum by small-angle X-ray scattering. J Biomol Struct Dyn 2019; 38:2939-2944. [PMID: 31347457 DOI: 10.1080/07391102.2019.1649195] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The pre-crystallization solution of the transaminase from Thermobaculum terrenum (TaTT) has been studied by small-angle X-ray scattering (SAXS). Regular changes in the oligomeric composition of the protein were observed after the addition of the precipitant. Comparison of the observed oligomers with the crystal structure of TaTT (PDB ID 6GKR) shows that dodecamers may act as building blocks in the growth of transaminase single crystals. Correlating of these results to the similar X-ray studies of other proteins suggests that SAXS may be a valuable tool for searching optimum crystallization conditions. AbbreviationSAXSsmall-angle X-ray scatteringTatransaminaseTaTTtransaminase from Thermobaculum terrenumPLPpyridoxal-5'-phosphateR-PEAR-(þ)-1-phenylethylamineBCATbranched-chain amino acid aminotransferaseDAATD-aminoacid aminotransferaseR-TAR-amine:pyruvate transaminaseCommunicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Margarita A Marchenkova
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre 'Crystallography and Photonics' of Russian Academy of Sciences, Moscow, Russian Federation.,National Research Centre 'Kurchatov Institute', Moscow, Russian Federation
| | - Petr V Konarev
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre 'Crystallography and Photonics' of Russian Academy of Sciences, Moscow, Russian Federation.,National Research Centre 'Kurchatov Institute', Moscow, Russian Federation
| | - Tatiana V Rakitina
- National Research Centre 'Kurchatov Institute', Moscow, Russian Federation.,Shemyakin - Ovchinnikov Institute of Bioorganic Chemistry, Laboratory of Hormonal Regulation Proteins, Russian Academy of Sciences, Moscow, Russian Federation
| | - Vladimir I Timofeev
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre 'Crystallography and Photonics' of Russian Academy of Sciences, Moscow, Russian Federation.,National Research Centre 'Kurchatov Institute', Moscow, Russian Federation
| | - Anastasiia S Boikova
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre 'Crystallography and Photonics' of Russian Academy of Sciences, Moscow, Russian Federation.,National Research Centre 'Kurchatov Institute', Moscow, Russian Federation
| | - Yulia A Dyakova
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre 'Crystallography and Photonics' of Russian Academy of Sciences, Moscow, Russian Federation.,National Research Centre 'Kurchatov Institute', Moscow, Russian Federation
| | - Kseniia B Ilina
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre 'Crystallography and Photonics' of Russian Academy of Sciences, Moscow, Russian Federation.,National Research Centre 'Kurchatov Institute', Moscow, Russian Federation
| | | | - Alena Yu Nikolaeva
- National Research Centre 'Kurchatov Institute', Moscow, Russian Federation
| | - Yurii V Pisarevsky
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre 'Crystallography and Photonics' of Russian Academy of Sciences, Moscow, Russian Federation.,National Research Centre 'Kurchatov Institute', Moscow, Russian Federation
| | - Mikhail V Kovalchuk
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre 'Crystallography and Photonics' of Russian Academy of Sciences, Moscow, Russian Federation.,National Research Centre 'Kurchatov Institute', Moscow, Russian Federation.,St. Petersburg State University, St. Petersburg, Russian Federation
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8
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Kovalchuk MV, Alekseeva OA, Blagov AE, Ilyushin GD, Il’ina KB, Konarev PV, Lomonov VA, Pisarevsky YV, Peters GS. Investigation of the Structure of Crystal-Forming Solutions of Potassium Dihydrogen Phosphate K(H2PO4) (KDP type) on the Basis of Modeling Precursor Clusters and According to Small-Angle X-Ray Scattering Data. CRYSTALLOGR REP+ 2019. [DOI: 10.1134/s1063774519010140] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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9
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Sharma A, Berntsen P, Harimoorthy R, Appio R, Sjöhamn J, Järvå M, Björling A, Hammarin G, Westenhoff S, Brändén G, Neutze R. A simple adaptation to a protein crystallography station to facilitate difference X-ray scattering studies. J Appl Crystallogr 2019; 52:378-386. [PMID: 30996717 PMCID: PMC6448683 DOI: 10.1107/s1600576719001900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 02/01/2019] [Indexed: 11/10/2022] Open
Abstract
A setup is constructed to facilitate difference X-ray scattering studies at a synchrotron-based protein crystallography beamline. This setup provides a flexible platform for preparative studies of protein structural dynamics. The X-ray crystallography station I911-2 at MAXLab II (Lund, Sweden) has been adapted to enable difference small- and wide-angle X-ray scattering (SAXS/WAXS) data to be recorded. Modifications to the beamline included a customized flow cell, a motorized flow cell holder, a helium cone, a beam stop, a sample stage and a sample delivery system. This setup incorporated external devices such as infrared lasers, LEDs and reaction mixers to induce conformational changes in macromolecules. This platform was evaluated through proof-of-principle experiments capturing light-induced conformational changes in phytochromes. A difference WAXS signature of conformational changes in a plant aquaporin was also demonstrated using caged calcium.
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Affiliation(s)
- Amit Sharma
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden.,Multidisciplinary Centre for Advanced Research and Studies, Jamia Millia Islamia, New Delhi 110025, India
| | - Peter Berntsen
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden.,ARC Centre of Exellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Victoria 3086, Australia
| | - Rajiv Harimoorthy
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | | | - Jennie Sjöhamn
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Michael Järvå
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Alexander Björling
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden.,MAX IV Laboratory, Box 118, 221 00 Lund, Sweden
| | - Greger Hammarin
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Sebastian Westenhoff
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Gisela Brändén
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Richard Neutze
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
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10
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Sviridova E, Rezacova P, Bondar A, Veverka V, Novak P, Schenk G, Svergun DI, Kuta Smatanova I, Bumba L. Structural basis of the interaction between the putative adhesion-involved and iron-regulated FrpD and FrpC proteins of Neisseria meningitidis. Sci Rep 2017; 7:40408. [PMID: 28084396 PMCID: PMC5233953 DOI: 10.1038/srep40408] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 12/06/2016] [Indexed: 01/14/2023] Open
Abstract
The iron-regulated protein FrpD from Neisseria meningitidis is an outer membrane lipoprotein that interacts with very high affinity (Kd ~ 0.2 nM) with the N-terminal domain of FrpC, a Type I-secreted protein from the Repeat in ToXin (RTX) protein family. In the presence of Ca2+, FrpC undergoes Ca2+ -dependent protein trans-splicing that includes an autocatalytic cleavage of the Asp414-Pro415 peptide bond and formation of an Asp414-Lys isopeptide bond. Here, we report the high-resolution structure of FrpD and describe the structure-function relationships underlying the interaction between FrpD and FrpC1-414. We identified FrpD residues involved in FrpC1-414 binding, which enabled localization of FrpD within the low-resolution SAXS model of the FrpD-FrpC1-414 complex. Moreover, the trans-splicing activity of FrpC resulted in covalent linkage of the FrpC1-414 fragment to plasma membrane proteins of epithelial cells in vitro, suggesting that formation of the FrpD-FrpC1-414 complex may be involved in the interaction of meningococci with the host cell surface.
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Affiliation(s)
- Ekaterina Sviridova
- Faculty of Science, University of South Bohemia Ceske Budejovice, Branisovska 1760, 37005 Ceske Budejovice, Czech Republic.,Center for Nanobiology and Structural Biology, Institute of Microbiology, Czech Academy of Sciences, Zamek 136, 37333 Nove Hrady, Czech Republic
| | - Pavlina Rezacova
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16610 Prague, Czech Republic
| | - Alexey Bondar
- Center for Nanobiology and Structural Biology, Institute of Microbiology, Czech Academy of Sciences, Zamek 136, 37333 Nove Hrady, Czech Republic.,Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16610 Prague, Czech Republic
| | - Vaclav Veverka
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16610 Prague, Czech Republic
| | - Petr Novak
- Institute of Microbiology, Czech Academy of Sciences, Videnska 1083, 14220 Prague, Czech Republic
| | - Gundolf Schenk
- EMBL Hamburg Outstation, c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany
| | - Dmitri I Svergun
- EMBL Hamburg Outstation, c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany
| | - Ivana Kuta Smatanova
- Faculty of Science, University of South Bohemia Ceske Budejovice, Branisovska 1760, 37005 Ceske Budejovice, Czech Republic.,Center for Nanobiology and Structural Biology, Institute of Microbiology, Czech Academy of Sciences, Zamek 136, 37333 Nove Hrady, Czech Republic
| | - Ladislav Bumba
- Institute of Microbiology, Czech Academy of Sciences, Videnska 1083, 14220 Prague, Czech Republic
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11
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Hopkins JB, Thorne RE. Quantifying radiation damage in biomolecular small-angle X-ray scattering. J Appl Crystallogr 2016; 49:880-890. [PMID: 27275138 PMCID: PMC4886981 DOI: 10.1107/s1600576716005136] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 03/25/2016] [Indexed: 11/10/2022] Open
Abstract
Small-angle X-ray scattering (SAXS) is an increasingly popular technique that provides low-resolution structural information about biological macromolecules in solution. Many of the practical limitations of the technique, such as minimum required sample volume, and of experimental design, such as sample flow cells, are necessary because the biological samples are sensitive to damage from the X-rays. Radiation damage typically manifests as aggregation of the sample, which makes the collected data unreliable. However, there has been little systematic investigation of the most effective methods to reduce damage rates, and results from previous damage studies are not easily compared with results from other beamlines. Here a methodology is provided for quantifying radiation damage in SAXS to provide consistent results between different experiments, experimenters and beamlines. These methods are demonstrated on radiation damage data collected from lysozyme, glucose isomerase and xylanase, and it is found that no single metric is sufficient to describe radiation damage in SAXS for all samples. The radius of gyration, molecular weight and integrated SAXS profile intensity constitute a minimal set of parameters that capture all types of observed behavior. Radiation sensitivities derived from these parameters show a large protein dependence, varying by up to six orders of magnitude between the different proteins tested. This work should enable consistent reporting of radiation damage effects, allowing more systematic studies of the most effective minimization strategies.
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Affiliation(s)
| | - Robert E. Thorne
- Department of Physics, Cornell University, Ithaca, NY 14853, USA
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12
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Pevala V, Truban D, Bauer JA, Košťan J, Kunová N, Bellová J, Brandstetter M, Marini V, Krejčí L, Tomáška Ľ, Nosek J, Kutejová E. The structure and DNA-binding properties of Mgm101 from a yeast with a linear mitochondrial genome. Nucleic Acids Res 2016; 44:2227-39. [PMID: 26743001 PMCID: PMC4797282 DOI: 10.1093/nar/gkv1529] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 12/22/2015] [Indexed: 11/14/2022] Open
Abstract
To study the mechanisms involved in the maintenance of a linear mitochondrial genome we investigated the biochemical properties of the recombination protein Mgm101 from Candida parapsilosis. We show that CpMgm101 complements defects associated with the Saccharomyces cerevisiae mgm101-1(ts) mutation and that it is present in both the nucleus and mitochondrial nucleoids of C. parapsilosis. Unlike its S. cerevisiae counterpart, CpMgm101 is associated with the entire nucleoid population and is able to bind to a broad range of DNA substrates in a non-sequence specific manner. CpMgm101 is also able to catalyze strand annealing and D-loop formation. CpMgm101 forms a roughly C-shaped trimer in solution according to SAXS. Electron microscopy of a complex of CpMgm101 with a model mitochondrial telomere revealed homogeneous, ring-shaped structures at the telomeric single-stranded overhangs. The DNA-binding properties of CpMgm101, together with its DNA recombination properties, suggest that it can play a number of possible roles in the replication of the mitochondrial genome and the maintenance of its telomeres.
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Affiliation(s)
- Vladimír Pevala
- Department of Biochemistry and Structural Biology, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia
| | - Dominika Truban
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University, Mlynská dolina CH-1, Ilkovičova 6, 842 15 Bratislava, Slovakia
| | - Jacob A Bauer
- Department of Biochemistry and Structural Biology, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia
| | - Július Košťan
- Department for Structural and Computational Biology, Max F. Perutz Laboratories, Dr. Bohr-Gasse 9 (VBC 5), 1030 Vienna, Austria
| | - Nina Kunová
- Department of Biochemistry and Structural Biology, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia
| | - Jana Bellová
- Department of Biochemistry and Structural Biology, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia
| | - Marlene Brandstetter
- Electron Microscopy Facility of the Campus Science Support Facilities GmbH, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Victoria Marini
- Department of Biology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic National Centre for Biomolecular Research, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Lumír Krejčí
- Department of Biology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic National Centre for Biomolecular Research, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Ľubomír Tomáška
- Department of Genetics, Faculty of Natural Sciences, Comenius University, Mlynská dolina B-1, Ilkovičova 6, 842 15 Bratislava, Slovakia
| | - Jozef Nosek
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University, Mlynská dolina CH-1, Ilkovičova 6, 842 15 Bratislava, Slovakia
| | - Eva Kutejová
- Department of Biochemistry and Structural Biology, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia Institute of Microbiology of the CAS, v. v. i., 142 20 Prague, Czech Republic
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13
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Monoclonal Antibodies Follow Distinct Aggregation Pathways During Production-Relevant Acidic Incubation and Neutralization. Pharm Res 2015; 33:716-28. [DOI: 10.1007/s11095-015-1821-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 10/29/2015] [Indexed: 01/23/2023]
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14
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Structural analysis of Clostridium botulinum neurotoxin type D as a platform for the development of targeted secretion inhibitors. Sci Rep 2015; 5:13397. [PMID: 26324071 PMCID: PMC4555039 DOI: 10.1038/srep13397] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 07/27/2015] [Indexed: 12/02/2022] Open
Abstract
The botulinum neurotoxin type D is one of seven highly potent toxins produced by Clostridium botulinum which inhibit neurotransmission at cholinergic nerve terminals. A functional fragment derived from the toxin, LHn, consisting of the catalytic and translocation domains, has been heralded as a platform for the development of targeted secretion inhibitors. These secretion inhibitors are aimed at retargeting the toxin towards a specific cell type to inhibit vesicular secretion. Here we report crystal structures of LHn from serotype D at 2.3 Å, and that of SXN101959 at 3.1 Å resolution. SXN101959, a derivative that combines LHn from serotype D with a fragment of the growth hormone releasing hormone, has previously revealed promising results in inhibiting growth hormone release in pituitary somatotrophs. These structures offer for the first time insights into the translocation domain interaction with the catalytic domain in serotype D. Furthermore, structural information from small-angle X-ray scattering of LHn/D is compared among serotypes A, B, and D. Taken together, these results demonstrate the robustness of the ‘LHn fold’ across serotypes and its use in engineering additional polypeptide components with added functionality. Our study demonstrates the suitability of botulinum neurotoxin, and serotype D in particular, as a basis for engineering novel secretion inhibitors.
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15
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Karlsen ML, Thorsen TS, Johner N, Ammendrup-Johnsen I, Erlendsson S, Tian X, Simonsen JB, Høiberg-Nielsen R, Christensen NM, Khelashvili G, Streicher W, Teilum K, Vestergaard B, Weinstein H, Gether U, Arleth L, Madsen KL. Structure of Dimeric and Tetrameric Complexes of the BAR Domain Protein PICK1 Determined by Small-Angle X-Ray Scattering. Structure 2015; 23:1258-1270. [PMID: 26073603 DOI: 10.1016/j.str.2015.04.020] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 04/20/2015] [Accepted: 04/23/2015] [Indexed: 11/15/2022]
Abstract
PICK1 is a neuronal scaffolding protein containing a PDZ domain and an auto-inhibited BAR domain. BAR domains are membrane-sculpting protein modules generating membrane curvature and promoting membrane fission. Previous data suggest that BAR domains are organized in lattice-like arrangements when stabilizing membranes but little is known about structural organization of BAR domains in solution. Through a small-angle X-ray scattering (SAXS) analysis, we determine the structure of dimeric and tetrameric complexes of PICK1 in solution. SAXS and biochemical data reveal a strong propensity of PICK1 to form higher-order structures, and SAXS analysis suggests an offset, parallel mode of BAR-BAR oligomerization. Furthermore, unlike accessory domains in other BAR domain proteins, the positioning of the PDZ domains is flexible, enabling PICK1 to perform long-range, dynamic scaffolding of membrane-associated proteins. Together with functional data, these structural findings are compatible with a model in which oligomerization governs auto-inhibition of BAR domain function.
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Affiliation(s)
- Morten L Karlsen
- Molecular Neuropharmacology and Genetics Laboratory, Lundbeck Foundation Center for Biomembranes in Nanomedicine, Department of Neuroscience and Pharmacology, Faculty of Health and Medical Sciences, The Panum Institute 18.6, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Thor S Thorsen
- Molecular Neuropharmacology and Genetics Laboratory, Lundbeck Foundation Center for Biomembranes in Nanomedicine, Department of Neuroscience and Pharmacology, Faculty of Health and Medical Sciences, The Panum Institute 18.6, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Niklaus Johner
- Department of Physiology and Biophysics, Weill Cornell Medical College, Cornell University, Room E-509, 1300 York Avenue, 10065, New York City, NY, USA
| | - Ina Ammendrup-Johnsen
- Molecular Neuropharmacology and Genetics Laboratory, Lundbeck Foundation Center for Biomembranes in Nanomedicine, Department of Neuroscience and Pharmacology, Faculty of Health and Medical Sciences, The Panum Institute 18.6, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Simon Erlendsson
- Molecular Neuropharmacology and Genetics Laboratory, Lundbeck Foundation Center for Biomembranes in Nanomedicine, Department of Neuroscience and Pharmacology, Faculty of Health and Medical Sciences, The Panum Institute 18.6, University of Copenhagen, 2200 Copenhagen N, Denmark.,Structural Biology and NMR Laboratory, Department of Biology, Faculty of Science, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Xinsheng Tian
- Biostructural Research, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen Ø, Denmark
| | - Jens B Simonsen
- Structural Biophysics, Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen Ø, Denmark
| | - Rasmus Høiberg-Nielsen
- Structural Biophysics, Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen Ø, Denmark
| | - Nikolaj M Christensen
- Molecular Neuropharmacology and Genetics Laboratory, Lundbeck Foundation Center for Biomembranes in Nanomedicine, Department of Neuroscience and Pharmacology, Faculty of Health and Medical Sciences, The Panum Institute 18.6, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - George Khelashvili
- Department of Physiology and Biophysics, Weill Cornell Medical College, Cornell University, Room E-509, 1300 York Avenue, 10065, New York City, NY, USA
| | - Werner Streicher
- NNF Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen N, Denmark
| | - Kaare Teilum
- Structural Biology and NMR Laboratory, Department of Biology, Faculty of Science, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Bente Vestergaard
- Biostructural Research, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen Ø, Denmark
| | - Harel Weinstein
- Department of Physiology and Biophysics, Weill Cornell Medical College, Cornell University, Room E-509, 1300 York Avenue, 10065, New York City, NY, USA
| | - Ulrik Gether
- Molecular Neuropharmacology and Genetics Laboratory, Lundbeck Foundation Center for Biomembranes in Nanomedicine, Department of Neuroscience and Pharmacology, Faculty of Health and Medical Sciences, The Panum Institute 18.6, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Lise Arleth
- Structural Biophysics, Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen Ø, Denmark
| | - Kenneth L Madsen
- Molecular Neuropharmacology and Genetics Laboratory, Lundbeck Foundation Center for Biomembranes in Nanomedicine, Department of Neuroscience and Pharmacology, Faculty of Health and Medical Sciences, The Panum Institute 18.6, University of Copenhagen, 2200 Copenhagen N, Denmark
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16
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Malyutin AG, Cheng H, Sanchez-Felix OR, Carlson K, Stein BD, Konarev PV, Svergun DI, Dragnea B, Bronstein LM. Coat Protein-Dependent Behavior of Poly(ethylene glycol) Tails in Iron Oxide Core Virus-like Nanoparticles. ACS APPLIED MATERIALS & INTERFACES 2015; 7:12089-12098. [PMID: 25989427 DOI: 10.1021/acsami.5b02278] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Here we explore the formation of virus-like nanoparticles (VNPs) utilizing 22-24 nm iron oxide nanoparticles (NPs) as cores and proteins derived from viral capsids of brome mosaic virus (BMV) or hepatitis B virus (HBV) as shells. To accomplish that, hydrophobic FeO/Fe3O4 NPs prepared by thermal decomposition of iron oleate were coated with poly(maleic acid-alt-octadecene) modified with poly(ethylene glycol) (PEG) tails of different lengths and grafting densities. MRI studies show high r2/r1 relaxivity ratios of these NPs that are practically independent of the polymer coating type. The versatility and flexibility of the viral capsid protein are on display as they readily form shells that exceed their native size. The location of the long PEG tails upon shell formation was investigated by electron microscopy and small-angle X-ray scattering. PEG tails were located differently in the BMV and HBV VNPs, with the BMV VNPs preferentially entrapping the tails in the interior and the HBV VNPs allowing the tails to extend through the capsid, which highlights the differences between intersubunit interactions in these two icosahedral viruses. The robustness of the assembly reaction and the protruding PEG tails, potentially useful in modulating the immune response, make the systems introduced here a promising platform for biomedical applications.
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Affiliation(s)
- Andrey G Malyutin
- †Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Hu Cheng
- §Department of Psychological and Brain Sciences, Indiana University, 1101 East Tenth Street, Bloomington, Indiana 47403, United States
| | - Olivia R Sanchez-Felix
- †Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Kenneth Carlson
- †Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Barry D Stein
- ∥Department of Biology, Indiana University, 1001 East Third Street, Bloomington, Indiana 47405, United States
| | - Petr V Konarev
- ‡EMBL, Hamburg Outstation, Notkestraße 85, D-22603 Hamburg, Germany
| | - Dmitri I Svergun
- ‡EMBL, Hamburg Outstation, Notkestraße 85, D-22603 Hamburg, Germany
| | - Bogdan Dragnea
- †Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Lyudmila M Bronstein
- †Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
- #Department of Physics, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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17
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Konarev PV, Svergun DI. A posteriori determination of the useful data range for small-angle scattering experiments on dilute monodisperse systems. IUCRJ 2015; 2:352-360. [PMID: 25995844 PMCID: PMC4420545 DOI: 10.1107/s2052252515005163] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 03/13/2015] [Indexed: 05/29/2023]
Abstract
Small-angle X-ray and neutron scattering (SAXS and SANS) experiments on solutions provide rapidly decaying scattering curves, often with a poor signal-to-noise ratio, especially at higher angles. On modern instruments, the noise is partially compensated for by oversampling, thanks to the fact that the angular increment in the data is small compared with that needed to describe adequately the local behaviour and features of the scattering curve. Given a (noisy) experimental data set, an important question arises as to which part of the data still contains useful information and should be taken into account for the interpretation and model building. Here, it is demonstrated that, for monodisperse systems, the useful experimental data range is defined by the number of meaningful Shannon channels that can be determined from the data set. An algorithm to determine this number and thus the data range is developed, and it is tested on a number of simulated data sets with various noise levels and with different degrees of oversampling, corresponding to typical SAXS/SANS experiments. The method is implemented in a computer program and examples of its application to analyse the experimental data recorded under various conditions are presented. The program can be employed to discard experimental data containing no useful information in automated pipelines, in modelling procedures, and for data deposition or publication. The software is freely accessible to academic users.
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Affiliation(s)
- Petr V. Konarev
- Hamburg Outstation, European Molecular Biology Laboratory, Notkestrasse 85, Hamburg 22607, Germany
- Laboratory of Reflectometry and Small-angle Scattering, Institute of Crystallography of the Russian Academy of Sciences, Leninsky prospekt 59, Moscow 119333, Russian Federation
| | - Dmitri I. Svergun
- Hamburg Outstation, European Molecular Biology Laboratory, Notkestrasse 85, Hamburg 22607, Germany
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18
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Petoukhov MV, Svergun DI. Ambiguity assessment of small-angle scattering curves from monodisperse systems. ACTA ACUST UNITED AC 2015; 71:1051-8. [PMID: 25945570 DOI: 10.1107/s1399004715002576] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 02/06/2015] [Indexed: 01/09/2023]
Abstract
A novel approach is presented for an a priori assessment of the ambiguity associated with spherically averaged single-particle scattering. The approach is of broad interest to the structural biology community, allowing the rapid and model-independent assessment of the inherent non-uniqueness of three-dimensional shape reconstruction from scattering experiments on solutions of biological macromolecules. One-dimensional scattering curves recorded from monodisperse systems are nowadays routinely utilized to generate low-resolution particle shapes, but the potential ambiguity of such reconstructions remains a major issue. At present, the (non)uniqueness can only be assessed by a posteriori comparison and averaging of repetitive Monte Carlo-based shape-determination runs. The new a priori ambiguity measure is based on the number of distinct shape categories compatible with a given data set. For this purpose, a comprehensive library of over 14,000 shape topologies has been generated containing up to seven beads closely packed on a hexagonal grid. The computed scattering curves rescaled to keep only the shape topology rather than the overall size information provide a `scattering map' of this set of shapes. For a given scattering data set, one rapidly obtains the number of neighbours in the map and the associated shape topologies such that in addition to providing a quantitative ambiguity measure the algorithm may also serve as an alternative shape-analysis tool. The approach has been validated in model calculations on geometrical bodies and its usefulness is further demonstrated on a number of experimental X-ray scattering data sets from proteins in solution. A quantitative ambiguity score (a-score) is introduced to provide immediate and convenient guidance to the user on the uniqueness of the ab initio shape reconstruction from the given data set.
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Affiliation(s)
- Maxim V Petoukhov
- European Molecular Biology Laboratory, Hamburg Unit, EMBL c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany
| | - Dmitri I Svergun
- European Molecular Biology Laboratory, Hamburg Unit, EMBL c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany
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19
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Langkilde AE, Morris KL, Serpell LC, Svergun DI, Vestergaard B. The architecture of amyloid-like peptide fibrils revealed by X-ray scattering, diffraction and electron microscopy. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:882-95. [PMID: 25849399 PMCID: PMC4388266 DOI: 10.1107/s1399004715001674] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 01/25/2015] [Indexed: 11/12/2022]
Abstract
Structural analysis of protein fibrillation is inherently challenging. Given the crucial role of fibrils in amyloid diseases, method advancement is urgently needed. A hybrid modelling approach is presented enabling detailed analysis of a highly ordered and hierarchically organized fibril of the GNNQQNY peptide fragment of a yeast prion protein. Data from small-angle X-ray solution scattering, fibre diffraction and electron microscopy are combined with existing high-resolution X-ray crystallographic structures to investigate the fibrillation process and the hierarchical fibril structure of the peptide fragment. The elongation of these fibrils proceeds without the accumulation of any detectable amount of intermediate oligomeric species, as is otherwise reported for, for example, glucagon, insulin and α-synuclein. Ribbons constituted of linearly arranged protofilaments are formed. An additional hierarchical layer is generated via the pairing of ribbons during fibril maturation. Based on the complementary data, a quasi-atomic resolution model of the protofilament peptide arrangement is suggested. The peptide structure appears in a β-sheet arrangement reminiscent of the β-zipper structures evident from high-resolution crystal structures, with specific differences in the relative peptide orientation. The complexity of protein fibrillation and structure emphasizes the need to use multiple complementary methods.
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Affiliation(s)
- Annette E. Langkilde
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Kyle L. Morris
- School of Life Sciences, University of Sussex, Falmer, Brighton, England
| | - Louise C. Serpell
- School of Life Sciences, University of Sussex, Falmer, Brighton, England
| | - Dmitri I. Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, 22607 Hamburg, Germany
| | - Bente Vestergaard
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
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20
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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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21
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Jeffries CM, Graewert MA, Svergun DI, Blanchet CE. Limiting radiation damage for high-brilliance biological solution scattering: practical experience at the EMBL P12 beamline PETRAIII. JOURNAL OF SYNCHROTRON RADIATION 2015; 22:273-279. [PMID: 25723929 DOI: 10.1107/s1600577515000375] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Accepted: 01/08/2015] [Indexed: 06/04/2023]
Abstract
Radiation damage is the general curse of structural biologists who use synchrotron small-angle X-ray scattering (SAXS) to investigate biological macromolecules in solution. The EMBL-P12 biological SAXS beamline located at the PETRAIII storage ring (DESY, Hamburg, Germany) caters to an extensive user community who integrate SAXS into their diverse structural biology programs. The high brilliance of the beamline [5.1 × 10(12) photons s(-1), 10 keV, 500 (H) µm × 250 (V) µm beam size at the sample position], combined with automated sample handling and data acquisition protocols, enable the high-throughput structural characterization of macromolecules in solution. However, considering the often-significant resources users invest to prepare samples, it is crucial that simple and effective protocols are in place to limit the effects of radiation damage once it has been detected. Here various practical approaches are evaluated that users can implement to limit radiation damage at the P12 beamline to maximize the chances of collecting quality data from radiation sensitive samples.
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Affiliation(s)
- Cy M Jeffries
- European Molecular Biology Laboratory Hamburg Outstation, c/o Deutsches Elektronen-Synchrotron, Notkestrasse 85, Hamburg 22603, Germany
| | - Melissa A Graewert
- European Molecular Biology Laboratory Hamburg Outstation, c/o Deutsches Elektronen-Synchrotron, Notkestrasse 85, Hamburg 22603, Germany
| | - Dmitri I Svergun
- European Molecular Biology Laboratory Hamburg Outstation, c/o Deutsches Elektronen-Synchrotron, Notkestrasse 85, Hamburg 22603, Germany
| | - Clément E Blanchet
- European Molecular Biology Laboratory Hamburg Outstation, c/o Deutsches Elektronen-Synchrotron, Notkestrasse 85, Hamburg 22603, Germany
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22
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Grant TD, Luft JR, Carter LG, Matsui T, Weiss TM, Martel A, Snell EH. The accurate assessment of small-angle X-ray scattering data. ACTA ACUST UNITED AC 2015; 71:45-56. [PMID: 25615859 PMCID: PMC4304685 DOI: 10.1107/s1399004714010876] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 05/12/2014] [Indexed: 12/05/2022]
Abstract
A set of quantitative techniques is suggested for assessing SAXS data quality. These are applied in the form of a script, SAXStats, to a test set of 27 proteins, showing that these techniques are more sensitive than manual assessment of data quality. Small-angle X-ray scattering (SAXS) has grown in popularity in recent times with the advent of bright synchrotron X-ray sources, powerful computational resources and algorithms enabling the calculation of increasingly complex models. However, the lack of standardized data-quality metrics presents difficulties for the growing user community in accurately assessing the quality of experimental SAXS data. Here, a series of metrics to quantitatively describe SAXS data in an objective manner using statistical evaluations are defined. These metrics are applied to identify the effects of radiation damage, concentration dependence and interparticle interactions on SAXS data from a set of 27 previously described targets for which high-resolution structures have been determined via X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. The studies show that these metrics are sufficient to characterize SAXS data quality on a small sample set with statistical rigor and sensitivity similar to or better than manual analysis. The development of data-quality analysis strategies such as these initial efforts is needed to enable the accurate and unbiased assessment of SAXS data quality.
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Affiliation(s)
- Thomas D Grant
- Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA
| | - Joseph R Luft
- Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA
| | - Lester G Carter
- Stanford Synchrotron Radiation Lightsource, 2575 Sand Hill Road, MS69, Menlo Park, CA 94025, USA
| | - Tsutomu Matsui
- Stanford Synchrotron Radiation Lightsource, 2575 Sand Hill Road, MS69, Menlo Park, CA 94025, USA
| | - Thomas M Weiss
- Stanford Synchrotron Radiation Lightsource, 2575 Sand Hill Road, MS69, Menlo Park, CA 94025, USA
| | - Anne Martel
- Stanford Synchrotron Radiation Lightsource, 2575 Sand Hill Road, MS69, Menlo Park, CA 94025, USA
| | - Edward H Snell
- Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA
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23
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Jeffries CM, Svergun DI. High-throughput studies of protein shapes and interactions by synchrotron small-angle X-ray scattering. Methods Mol Biol 2015; 1261:277-301. [PMID: 25502205 DOI: 10.1007/978-1-4939-2230-7_15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Solution-based small angle X-ray scattering (SAXS) affords the opportunity to extract accurate structural parameters and global shape information from diverse biological macromolecular systems. SAXS is an ideal complementary technique to other structural and biophysical methods but it can also be applied alone to access structural information that is otherwise unobtainable using high-resolution methods. Macromolecular structures ranging from kilodaltons to gigadaltons can be analyzed, which encompasses the size of most proteins and functional cellular complexes. The SAXS analysis is performed using only a few microliters of solution containing microgram quantities of purified material in sample environments that can be tailored to mimic physiological conditions or altered to suit a particular question. High-brilliance synchrotron X-ray sources and parallel advances in hardware and computing have reduced data acquisition times to the millisecond range and the application of automated methods have allowed data processing and low resolution shape modelling to be completed within minutes. These developments have paved the way for high-throughput studies that generate significant quantities of structural information over a short period of time. Here, we briefly consider the basics of SAXS and describe major methods and protocols employed in high-throughput SAXS studies.
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Affiliation(s)
- Cy M Jeffries
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o DESY, Notkestraße 85, 22603, Hamburg, Germany
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24
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Angelova A, Angelov B, Mutafchieva R, Lesieur S. Biocompatible Mesoporous and Soft Nanoarchitectures. J Inorg Organomet Polym Mater 2014. [DOI: 10.1007/s10904-014-0143-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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25
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Ribeiro EDA, Pinotsis N, Ghisleni A, Salmazo A, Konarev PV, Kostan J, Sjöblom B, Schreiner C, Polyansky AA, Gkougkoulia EA, Holt MR, Aachmann FL, Zagrović B, Bordignon E, Pirker KF, Svergun DI, Gautel M, Djinović-Carugo K. The structure and regulation of human muscle α-actinin. Cell 2014; 159:1447-60. [PMID: 25433700 PMCID: PMC4259493 DOI: 10.1016/j.cell.2014.10.056] [Citation(s) in RCA: 142] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 10/01/2014] [Accepted: 10/24/2014] [Indexed: 11/29/2022]
Abstract
The spectrin superfamily of proteins plays key roles in assembling the actin cytoskeleton in various cell types, crosslinks actin filaments, and acts as scaffolds for the assembly of large protein complexes involved in structural integrity and mechanosensation, as well as cell signaling. α-actinins in particular are the major actin crosslinkers in muscle Z-disks, focal adhesions, and actin stress fibers. We report a complete high-resolution structure of the 200 kDa α-actinin-2 dimer from striated muscle and explore its functional implications on the biochemical and cellular level. The structure provides insight into the phosphoinositide-based mechanism controlling its interaction with sarcomeric proteins such as titin, lays a foundation for studying the impact of pathogenic mutations at molecular resolution, and is likely to be broadly relevant for the regulation of spectrin-like proteins. Structure of human α-actinin-2 in an autoinhibited closed conformation Facilitation of PIP2-induced allosteric modulation for opening and titin binding Essentiality of structural flexibility for crosslinking antiparallel F-actin Relevance for the intramolecular pseudoligand regulation mechanism of the spectrin family
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Affiliation(s)
- Euripedes de Almeida Ribeiro
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, 1030 Vienna, Austria
| | - Nikos Pinotsis
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, 1030 Vienna, Austria
| | - Andrea Ghisleni
- British Heart Foundation Centre of Research Excellence, Randall Division for Cell and Molecular Biophysics and Cardiovascular Division, King's College London, London SE1 1UL, UK
| | - Anita Salmazo
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, 1030 Vienna, Austria
| | - Petr V Konarev
- European Molecular Biology Laboratory, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22603 Hamburg, Germany
| | - Julius Kostan
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, 1030 Vienna, Austria
| | - Björn Sjöblom
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, 1030 Vienna, Austria
| | - Claudia Schreiner
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, 1030 Vienna, Austria
| | - Anton A Polyansky
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, 1030 Vienna, Austria; M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Eirini A Gkougkoulia
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, 1030 Vienna, Austria
| | - Mark R Holt
- British Heart Foundation Centre of Research Excellence, Randall Division for Cell and Molecular Biophysics and Cardiovascular Division, King's College London, London SE1 1UL, UK
| | - Finn L Aachmann
- Department of Biotechnology, Norwegian University of Science and Technology, Sem Sælands vei 6/8, 7491 Trondheim, Norway
| | - Bojan Zagrović
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, 1030 Vienna, Austria
| | - Enrica Bordignon
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland; Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Katharina F Pirker
- Division of Biochemistry, Department of Chemistry, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Dmitri I Svergun
- European Molecular Biology Laboratory, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22603 Hamburg, Germany
| | - Mathias Gautel
- British Heart Foundation Centre of Research Excellence, Randall Division for Cell and Molecular Biophysics and Cardiovascular Division, King's College London, London SE1 1UL, UK.
| | - Kristina Djinović-Carugo
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, 1030 Vienna, Austria; Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5, 1000 Ljubljana, Slovenia.
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26
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Cantara WA, Olson ED, Musier-Forsyth K. Progress and outlook in structural biology of large viral RNAs. Virus Res 2014; 193:24-38. [PMID: 24956407 PMCID: PMC4252365 DOI: 10.1016/j.virusres.2014.06.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 06/11/2014] [Accepted: 06/12/2014] [Indexed: 02/05/2023]
Abstract
The field of viral molecular biology has reached a precipice for which pioneering studies on the structure of viral RNAs are beginning to bridge the gap. It has become clear that viral genomic RNAs are not simply carriers of hereditary information, but rather are active players in many critical stages during replication. Indeed, functions such as cap-independent translation initiation mechanisms are, in some cases, primarily driven by RNA structural determinants. Other stages including reverse transcription initiation in retroviruses, nuclear export and viral packaging are specifically dependent on the proper 3-dimensional folding of multiple RNA domains to recruit necessary viral and host factors required for activity. Furthermore, a large-scale conformational change within the 5'-untranslated region of HIV-1 has been proposed to regulate the temporal switch between viral protein synthesis and packaging. These RNA-dependent functions are necessary for replication of many human disease-causing viruses such as severe acute respiratory syndrome (SARS)-associated coronavirus, West Nile virus, and HIV-1. The potential for antiviral development is currently hindered by a poor understanding of RNA-driven molecular mechanisms, resulting from a lack of structural information on large RNAs and ribonucleoprotein complexes. Herein, we describe the recent progress that has been made on characterizing these large RNAs and provide brief descriptions of the techniques that will be at the forefront of future advances. Ongoing and future work will contribute to a more complete understanding of the lifecycles of retroviruses and RNA viruses and potentially lead to novel antiviral strategies.
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Affiliation(s)
| | | | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, Center for Retrovirus Research, Center for RNA Biology, The Ohio State University, Columbus, OH 43210, United States
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27
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Sibillano T, De Caro L, Altamura D, Siliqi D, Ramella M, Boccafoschi F, Ciasca G, Campi G, Tirinato L, Di Fabrizio E, Giannini C. An optimized table-top small-angle X-ray scattering set-up for the nanoscale structural analysis of soft matter. Sci Rep 2014; 4:6985. [PMID: 25382272 PMCID: PMC4225548 DOI: 10.1038/srep06985] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 10/23/2014] [Indexed: 01/30/2023] Open
Abstract
The paper shows how a table top superbright microfocus laboratory X-ray source and an innovative restoring-data algorithm, used in combination, allow to analyze the super molecular structure of soft matter by means of Small Angle X-ray Scattering ex-situ experiments. The proposed theoretical approach is aimed to restore diffraction features from SAXS profiles collected from low scattering biomaterials or soft tissues, and therefore to deal with extremely noisy diffraction SAXS profiles/maps. As biological test cases we inspected: i) residues of exosomes' drops from healthy epithelial colon cell line and colorectal cancer cells; ii) collagen/human elastin artificial scaffolds developed for vascular tissue engineering applications; iii) apoferritin protein in solution. Our results show how this combination can provide morphological/structural nanoscale information to characterize new artificial biomaterials and/or to get insight into the transition between healthy and pathological tissues during the progression of a disease, or to morphologically characterize nanoscale proteins, based on SAXS data collected in a room-sized laboratory.
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Affiliation(s)
- T. Sibillano
- Istituto di Cristallografia (IC-CNR), via Amendola 122/O, I-70126 Bari, Italy
| | - L. De Caro
- Istituto di Cristallografia (IC-CNR), via Amendola 122/O, I-70126 Bari, Italy
| | - D. Altamura
- Istituto di Cristallografia (IC-CNR), via Amendola 122/O, I-70126 Bari, Italy
| | - D. Siliqi
- Istituto di Cristallografia (IC-CNR), via Amendola 122/O, I-70126 Bari, Italy
| | - M. Ramella
- Department of Health Sciences, University of Piemonte Orientale “A. Avogadro”, 28100 Novara, Italy
| | - F. Boccafoschi
- Department of Health Sciences, University of Piemonte Orientale “A. Avogadro”, 28100 Novara, Italy
| | - G. Ciasca
- Istituto di Fisica, Universitá Cattolica S. Cuore, L.go Francesco Vito 1 I-00168, Roma, Italy
| | - G. Campi
- Istituto di Cristallografia (IC-CNR), Via Salaria Km 29.300, 00015 Monterotondo, Roma, Italy
| | - L. Tirinato
- King Abdullah University of Science and Technology, PSE and BESE Divisions, Thuwal. 23955 -6900, Kingdom of Saudi Arabia
- BIONEMlab University Magna Graecia, Department of Clinical and Experimental Medicine, Viale Europa, 88100 Catanzaro, Italy
| | - E. Di Fabrizio
- King Abdullah University of Science and Technology, PSE and BESE Divisions, Thuwal. 23955 -6900, Kingdom of Saudi Arabia
- BIONEMlab University Magna Graecia, Department of Clinical and Experimental Medicine, Viale Europa, 88100 Catanzaro, Italy
| | - C. Giannini
- Istituto di Cristallografia (IC-CNR), via Amendola 122/O, I-70126 Bari, Italy
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28
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Bras W, Koizumi S, Terrill NJ. Beyond simple small-angle X-ray scattering: developments in online complementary techniques and sample environments. IUCRJ 2014; 1:478-91. [PMID: 25485128 PMCID: PMC4224466 DOI: 10.1107/s2052252514019198] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2014] [Accepted: 08/25/2014] [Indexed: 05/20/2023]
Abstract
Small- and wide-angle X-ray scattering (SAXS, WAXS) are standard tools in materials research. The simultaneous measurement of SAXS and WAXS data in time-resolved studies has gained popularity due to the complementary information obtained. Furthermore, the combination of these data with non X-ray based techniques, via either simultaneous or independent measurements, has advanced understanding of the driving forces that lead to the structures and morphologies of materials, which in turn give rise to their properties. The simultaneous measurement of different data regimes and types, using either X-rays or neutrons, and the desire to control parameters that initiate and control structural changes have led to greater demands on sample environments. Examples of developments in technique combinations and sample environment design are discussed, together with a brief speculation about promising future developments.
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Affiliation(s)
- Wim Bras
- Netherlands Organization for Scientific Research (NWO), DUBBLE@ESRF, BP 220, 6 Rue Jules Horowitz, Grenoble 38043, France
| | - Satoshi Koizumi
- College of Engineering, Ibaraki University, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
| | - Nicholas J Terrill
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
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29
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Nilsson OB, Neimert-Andersson T, Bronge M, Grundström J, Sarma R, Uchtenhagen H, Kikhney A, Sandalova T, Holmgren E, Svergun D, Achour A, van Hage M, Grönlund H. Designing a multimer allergen for diagnosis and immunotherapy of dog allergic patients. PLoS One 2014; 9:e111041. [PMID: 25353166 PMCID: PMC4212987 DOI: 10.1371/journal.pone.0111041] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 09/19/2014] [Indexed: 12/04/2022] Open
Abstract
Background Dog dander extract used for diagnosis and allergen-specific immunotherapy is often of variable and of poor quality. Objective To assemble four well-established dog allergen components into one recombinant folded protein for improved diagnosis and vaccination of allergy to dog. Methods A linked molecule, comprising the four dog lipocalin allergens Can f 1, Can f 2, Can f 4 and Can f 6 was constructed. The tetrameric protein was structurally characterized by small angle X-ray scattering, and compared with each single recombinant lipocalin allergen or an equimolar mix of the four allergens by analytical size exclusion chromatography, circular dichroism, allergen-specific IgE in serum by ELISA and allergen-dependent capacity to activate basophils. The immunogenicity of the fusion protein was evaluated in immunized mice by assessing splenocyte proliferation and antibody production. Results The linked tetrameric construct was produced as a soluble fusion protein, with the specific folds of the four individual allergens conserved. This multi-allergen molecule was significantly more efficient (p<0.001) than each single recombinant allergen in binding to dog-specific IgE, and the epitope spectrum was unaffected compared to an equimolar mix of the four allergens. Basophil degranulation revealed that the biologic activity of the linked molecule was retained. Immunization of mice with the linked construct induced comparable allergen-specific IgG responses with blocking capacity towards all included allergens and generated comparably low T-cell responses. Conclusion We provide the first evidence for a linked recombinant molecule covering the major dog allergens for potential use in diagnostics and allergy vaccination of dog allergic patients.
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Affiliation(s)
- Ola B. Nilsson
- Department of Medicine, Clinical Immunology and Allergy Unit, Karolinska Institutet, Stockholm, Sweden
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Theresa Neimert-Andersson
- Department of Clinical Neuroscience, Therapeutic Immune Design Unit, Center for molecular Medicine (CMM), Karolinska Institutet, Stockholm, Sweden
| | - Mattias Bronge
- Department of Clinical Neuroscience, Therapeutic Immune Design Unit, Center for molecular Medicine (CMM), Karolinska Institutet, Stockholm, Sweden
| | - Jeanette Grundström
- Department of Medicine, Clinical Immunology and Allergy Unit, Karolinska Institutet, Stockholm, Sweden
| | - Ranjana Sarma
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Hannes Uchtenhagen
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Alexey Kikhney
- European Molecular Biology Laboratory (EMBL) - Hamburg Outstation, c/o DESY, Hamburg, Germany
| | - Tatyana Sandalova
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Erik Holmgren
- Department of Medicine, Clinical Immunology and Allergy Unit, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Neuroscience, Therapeutic Immune Design Unit, Center for molecular Medicine (CMM), Karolinska Institutet, Stockholm, Sweden
| | - Dmitri Svergun
- European Molecular Biology Laboratory (EMBL) - Hamburg Outstation, c/o DESY, Hamburg, Germany
| | - Adnane Achour
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Marianne van Hage
- Department of Medicine, Clinical Immunology and Allergy Unit, Karolinska Institutet, Stockholm, Sweden
| | - Hans Grönlund
- Department of Clinical Neuroscience, Therapeutic Immune Design Unit, Center for molecular Medicine (CMM), Karolinska Institutet, Stockholm, Sweden
- * E-mail:
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30
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Why are the 2-oxoacid dehydrogenase complexes so large? Generation of an active trimeric complex. Biochem J 2014; 463:405-12. [DOI: 10.1042/bj20140359] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A trimeric core of the 42-mer 2-oxoacid dehydrogenase complex of the thermophilic archaeon Thermoplasma has been generated and its structure determined. This trimeric core binds both E1 and E3 component enzymes to form for the first time a catalytically active mini-complex.
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31
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Bezerra GA, Viertlmayr R, Moura TR, Delatorre P, Rocha BAM, do Nascimento KS, Figueiredo JG, Bezerra IG, Teixeira CS, Simões RC, Nagano CS, de Alencar NMN, Gruber K, Cavada BS. Structural studies of an anti-inflammatory lectin from Canavalia boliviana seeds in complex with dimannosides. PLoS One 2014; 9:e97015. [PMID: 24865454 PMCID: PMC4035259 DOI: 10.1371/journal.pone.0097015] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 04/15/2014] [Indexed: 11/19/2022] Open
Abstract
Plant lectins, especially those purified from species of the Leguminosae family, represent the best-studied group of carbohydrate-binding proteins. Lectins purified from seeds of the Diocleinae subtribe exhibit a high degree of sequence identity notwithstanding that they show very distinct biological activities. Two main factors have been related to this feature: variance in key residues influencing the carbohydrate-binding site geometry and differences in the pH-dependent oligomeric state profile. In this work, we have isolated a lectin from Canavalia boliviana (Cbol) and solved its x-ray crystal structure in the unbound form and in complex with the carbohydrates Man(α1-3)Man(α1-O)Me, Man(α1-4)Man(α1-O)Me and 5-bromo-4-chloro-3-indolyl-α-D-mannose. We evaluated its oligomerization profile at different pH values using Small Angle X-ray Scattering and compared it to that of Concanavalin A. Based on predicted pKa-shifts of amino acids in the subunit interfaces we devised a model for the dimer-tetramer equilibrium phenomena of these proteins. Additionally, we demonstrated Cbol anti-inflammatory properties and further characterized them using in vivo and in vitro models.
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Affiliation(s)
- Gustavo Arruda Bezerra
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- * E-mail: (BSC); (GAB)
| | - Roland Viertlmayr
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Tales Rocha Moura
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Brazil
| | - Plínio Delatorre
- Department of Molecular Biology, Federal University of Paraíba, João Pessoa, Brazil
| | | | | | - Jozi Godoy Figueiredo
- Department of Physiology and Pharmacology, Federal University of Ceará, Fortaleza, Brazil
| | | | - Cicero Silvano Teixeira
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Brazil
| | - Rafael Conceição Simões
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Brazil
| | - Celso Shiniti Nagano
- Department of Fishing Engineering, Federal University of Ceará, Fortaleza, Brazil
| | | | - Karl Gruber
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Benildo Sousa Cavada
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Brazil
- * E-mail: (BSC); (GAB)
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32
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Syson K, Stevenson CEM, Rashid AM, Saalbach G, Tang M, Tuukkanen A, Svergun DI, Withers SG, Lawson DM, Bornemann S. Structural insight into how Streptomyces coelicolor maltosyl transferase GlgE binds α-maltose 1-phosphate and forms a maltosyl-enzyme intermediate. Biochemistry 2014; 53:2494-504. [PMID: 24689960 PMCID: PMC4048318 DOI: 10.1021/bi500183c] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
![]()
GlgE (EC 2.4.99.16) is an α-maltose
1-phosphate:(1→4)-α-d-glucan 4-α-d-maltosyltransferase of the CAZy
glycoside hydrolase 13_3 family. It is the defining enzyme of a bacterial
α-glucan biosynthetic pathway and is a genetically validated
anti-tuberculosis target. It catalyzes the α-retaining transfer
of maltosyl units from α-maltose 1-phosphate to maltooligosaccharides
and is predicted to use a double-displacement mechanism. Evidence
of this mechanism was obtained using a combination of site-directed
mutagenesis of Streptomyces coelicolor GlgE isoform
I, substrate analogues, protein crystallography, and mass spectrometry.
The X-ray structures of α-maltose 1-phosphate bound to a D394A
mutein and a β-2-deoxy-2-fluoromaltosyl-enzyme intermediate
with a E423A mutein were determined. There are few examples of CAZy
glycoside hydrolase family 13 members that have had their glycosyl-enzyme
intermediate structures determined, and none before now have been
obtained with a 2-deoxy-2-fluoro substrate analogue. The covalent
modification of Asp394 was confirmed using mass spectrometry. A similar
modification of wild-type GlgE proteins from S. coelicolor and Mycobacterium tuberculosis was also observed.
Small-angle X-ray scattering of the M. tuberculosis enzyme revealed a homodimeric assembly similar to that of the S. coelicolor enzyme but with slightly differently oriented
monomers. The deeper understanding of the structure–function
relationships of S. coelicolor GlgE will aid the
development of inhibitors of the M. tuberculosis enzyme.
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Affiliation(s)
- Karl Syson
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park , Norwich NR4 7UH, United Kingdom
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Tian X, Langkilde AE, Thorolfsson M, Rasmussen HB, Vestergaard B. Small-angle x-ray scattering screening complements conventional biophysical analysis: comparative structural and biophysical analysis of monoclonal antibodies IgG1, IgG2, and IgG4. J Pharm Sci 2014; 103:1701-10. [PMID: 24700358 PMCID: PMC4298811 DOI: 10.1002/jps.23964] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 02/25/2014] [Accepted: 03/13/2014] [Indexed: 12/21/2022]
Abstract
A crucial step in the development of therapeutic monoclonal antibodies is the selection of robust pharmaceutical candidates and screening of efficacious protein formulations to increase the resistance toward physicochemical degradation and aggregation during processing and storage. Here, we introduce small-angle X-ray scattering (SAXS) to characterize antibody solution behavior, which strongly complements conventional biophysical analysis. First, we apply a variety of conventional biophysical techniques for the evaluation of structural, conformational, and colloidal stability and report a systematic comparison between designed humanized IgG1, IgG2, and IgG4 with identical variable regions. Then, the high information content of SAXS data enables sensitive detection of structural differences between three IgG subclasses at neutral pH and rapid formation of dimers of IgG2 and IgG4 at low pH. We reveal subclass-specific variation in intermolecular repulsion already at low and medium protein concentrations, which explains the observed improved stability of IgG1 with respect to aggregation. We show how excipients dramatically influence such repulsive effects, hence demonstrating the potential application of extensive SAXS screening in antibody selection, eventual engineering, and formulation development.
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Affiliation(s)
- Xinsheng Tian
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
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34
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Malecki PH, Vorgias CE, Petoukhov MV, Svergun DI, Rypniewski W. Crystal structures of substrate-bound chitinase from the psychrophilic bacterium Moritella marina and its structure in solution. ACTA ACUST UNITED AC 2014; 70:676-84. [PMID: 24598737 DOI: 10.1107/s1399004713032264] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 11/26/2013] [Indexed: 11/11/2022]
Abstract
The four-domain structure of chitinase 60 from Moritella marina (MmChi60) is outstanding in its complexity. Many glycoside hydrolases, such as chitinases and cellulases, have multi-domain structures, but only a few have been solved. The flexibility of the hinge regions between the domains apparently makes these proteins difficult to crystallize. The analysis of an active-site mutant of MmChi60 in an unliganded form and in complex with the substrates NAG4 and NAG5 revealed significant differences in the substrate-binding site compared with the previously determined complexes of most studied chitinases. A SAXS experiment demonstrated that in addition to the elongated state found in the crystal, the protein can adapt other conformations in solution ranging from fully extended to compact.
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Affiliation(s)
- Piotr H Malecki
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Constantinos E Vorgias
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Zografou Campus, 157 01 Athens, Greece
| | - Maxim V Petoukhov
- Hamburg Unit, EMBL c/o DESY, European Molecular Biology Laboratory, Notkestrasse 85, 22607 Hamburg, Germany
| | - Dmitri I Svergun
- Hamburg Unit, EMBL c/o DESY, European Molecular Biology Laboratory, Notkestrasse 85, 22607 Hamburg, Germany
| | - Wojciech Rypniewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
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35
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Structural and functional insights into peptidoglycan access for the lytic amidase LytA of Streptococcus pneumoniae. mBio 2014; 5:e01120-13. [PMID: 24520066 PMCID: PMC3950521 DOI: 10.1128/mbio.01120-13] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The cytosolic N-acetylmuramoyl-l-alanine amidase LytA protein of Streptococcus pneumoniae, which is released by bacterial lysis, associates with the cell wall via its choline-binding motif. During exponential growth, LytA accesses its peptidoglycan substrate to cause lysis only when nascent peptidoglycan synthesis is stalled by nutrient starvation or β-lactam antibiotics. Here we present three-dimensional structures of LytA and establish the requirements for substrate binding and catalytic activity. The solution structure of the full-length LytA dimer reveals a peculiar fold, with the choline-binding domains forming a rigid V-shaped scaffold and the relatively more flexible amidase domains attached in a trans position. The 1.05-Å crystal structure of the amidase domain reveals a prominent Y-shaped binding crevice composed of three contiguous subregions, with a zinc-containing active site localized at the bottom of the branch point. Site-directed mutagenesis was employed to identify catalytic residues and to investigate the relative impact of potential substrate-interacting residues lining the binding crevice for the lytic activity of LytA. In vitro activity assays using defined muropeptide substrates reveal that LytA utilizes a large substrate recognition interface and requires large muropeptide substrates with several connected saccharides that interact with all subregions of the binding crevice for catalysis. We hypothesize that the substrate requirements restrict LytA to the sites on the cell wall where nascent peptidoglycan synthesis occurs. IMPORTANCE Streptococcus pneumoniae is a human respiratory tract pathogen responsible for millions of deaths annually. Its major pneumococcal autolysin, LytA, is required for autolysis and fratricidal lysis and functions as a virulence factor that facilitates the spread of toxins and factors involved in immune evasion. LytA is also activated by penicillin and vancomycin and is responsible for the lysis induced by these antibiotics. The factors that regulate the lytic activity of LytA are unclear, but it was recently demonstrated that control is at the level of substrate recognition and that LytA required access to the nascent peptidoglycan. The present study was undertaken to structurally and functionally investigate LytA and its substrate-interacting interface and to determine the requirements for substrate recognition and catalysis. Our results reveal that the amidase domain comprises a complex substrate-binding crevice and needs to interact with a large-motif epitope of peptidoglycan for catalysis.
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Structural data on the periplasmic aldehyde oxidoreductase PaoABC from Escherichia coli: SAXS and preliminary X-ray crystallography analysis. Int J Mol Sci 2014; 15:2223-36. [PMID: 24492481 PMCID: PMC3958847 DOI: 10.3390/ijms15022223] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2013] [Revised: 01/21/2014] [Accepted: 01/22/2014] [Indexed: 11/17/2022] Open
Abstract
The periplasmic aldehyde oxidoreductase PaoABC from Escherichia coli is a molybdenum enzyme involved in detoxification of aldehydes in the cell. It is an example of an αβγ heterotrimeric enzyme of the xanthine oxidase family of enzymes which does not dimerize via its molybdenum cofactor binding domain. In order to structurally characterize PaoABC, X-ray crystallography and small angle X-ray scattering (SAXS) have been carried out. The protein crystallizes in the presence of 20% (w/v) polyethylene glycol 3350 using the hanging-drop vapour diffusion method. Although crystals were initially twinned, several experiments were done to overcome twinning and lowering the crystallization temperature (293 K to 277 K) was the solution to the problem. The non-twinned crystals used to solve the structure diffract X-rays to beyond 1.80 Å and belong to the C2 space group, with cell parameters a = 109.42 Å, b = 78.08 Å, c = 151.77 Å, β = 99.77°, and one molecule in the asymmetric unit. A molecular replacement solution was found for each subunit separately, using several proteins as search models. SAXS data of PaoABC were also collected showing that, in solution, the protein is also an αβγ heterotrimer.
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Inhibition of master transcription factors in pluripotent cells induces early stage differentiation. Proc Natl Acad Sci U S A 2014; 111:1778-83. [PMID: 24434556 DOI: 10.1073/pnas.1323386111] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The potential for pluripotent cells to differentiate into diverse specialized cell types has given much hope to the field of regenerative medicine. Nevertheless, the low efficiency of cell commitment has been a major bottleneck in this field. Here we provide a strategy to enhance the efficiency of early differentiation of pluripotent cells. We hypothesized that the initial phase of differentiation can be enhanced if the transcriptional activity of master regulators of stemness is suppressed, blocking the formation of functional transcriptomes. However, an obstacle is the lack of an efficient strategy to block protein-protein interactions. In this work, we take advantage of the biochemical property of seventeen kilodalton protein (Skp), a bacterial molecular chaperone that binds directly to sex determining region Y-box 2 (Sox2). The small angle X-ray scattering analyses provided a low resolution model of the complex and suggested that the transactivation domain of Sox2 is probably wrapped in a cleft on Skp trimer. Upon the transduction of Skp into pluripotent cells, the transcriptional activity of Sox2 was inhibited and the expression of Sox2 and octamer-binding transcription factor 4 was reduced, which resulted in the expression of early differentiation markers and appearance of early neuronal and cardiac progenitors. These results suggest that the initial stage of differentiation can be accelerated by inhibiting master transcription factors of stemness. This strategy can possibly be applied to increase the efficiency of stem cell differentiation into various cell types and also provides a clue to understanding the mechanism of early differentiation.
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38
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Schulte T, Löfling J, Mikaelsson C, Kikhney A, Hentrich K, Diamante A, Ebel C, Normark S, Svergun D, Henriques-Normark B, Achour A. The basic keratin 10-binding domain of the virulence-associated pneumococcal serine-rich protein PsrP adopts a novel MSCRAMM fold. Open Biol 2014; 4:130090. [PMID: 24430336 PMCID: PMC3909270 DOI: 10.1098/rsob.130090] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Streptococcus pneumoniae is a major human pathogen, and a leading cause of disease and death worldwide. Pneumococcal invasive disease is triggered by initial asymptomatic colonization of the human upper respiratory tract. The pneumococcal serine-rich repeat protein (PsrP) is a lung-specific virulence factor whose functional binding region (BR) binds to keratin-10 (KRT10) and promotes pneumococcal biofilm formation through self-oligomerization. We present the crystal structure of the KRT10-binding domain of PsrP (BR187–385) determined to 2.0 Å resolution. BR187–385 adopts a novel variant of the DEv-IgG fold, typical for microbial surface components recognizing adhesive matrix molecules adhesins, despite very low sequence identity. An extended β-sheet on one side of the compressed, two-sided barrel presents a basic groove that possibly binds to the acidic helical rod domain of KRT10. Our study also demonstrates the importance of the other side of the barrel, formed by extensive well-ordered loops and stabilized by short β-strands, for interaction with KRT10.
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Affiliation(s)
- Tim Schulte
- Science for Life Laboratory, Center for Infectious Medicine (CIM), Department of Medicine, Karolinska University Hospital Huddinge, Karolinska Institutet Science Park, Tomtebodavägen 23A Solna, Stockholm 17165, Sweden
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39
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Sergeeva O, Vlasov PS, Domnina NS, Bogomolova A, Konarev PV, Svergun DI, Walterova Z, Horsky J, Stepanek P, Filippov SK. Novel thermosensitive telechelic PEGs with antioxidant activity: synthesis, molecular properties and conformational behaviour. RSC Adv 2014. [DOI: 10.1039/c4ra06978a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
We report on the tailor-made polymer conjugates, which are highly compelling for biomedical applications due to their antioxidant activity and the adjustable thermosensitive properties.
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Affiliation(s)
- Olga Sergeeva
- Institute of Chemistry
- Saint-Petersburg State University
- Russia
| | - Petr S. Vlasov
- Institute of Chemistry
- Saint-Petersburg State University
- Russia
| | - Nina S. Domnina
- Institute of Chemistry
- Saint-Petersburg State University
- Russia
| | | | | | | | | | - Jiri Horsky
- Institute of Macromolecular Chemistry
- Prague, Czech Republic
| | - Petr Stepanek
- Institute of Macromolecular Chemistry
- Prague, Czech Republic
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40
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Begum A, Drebes J, Kikhney A, Müller IB, Perbandt M, Svergun D, Wrenger C, Betzel C. Staphylococcus aureus thiaminase II: oligomerization warrants proteolytic protection against serine proteases. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:2320-9. [PMID: 24311574 DOI: 10.1107/s0907444913021550] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Accepted: 08/01/2013] [Indexed: 11/10/2022]
Abstract
Staphylococcus aureus TenA (SaTenA) is a thiaminase type II enzyme that catalyzes the deamination of aminopyrimidine, as well as the cleavage of thiamine into 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP) and 5-(2-hydroxyethyl)-4-methylthiazole (THZ), within thiamine (vitamin B1) metabolism. Further, by analogy with studies of Bacillus subtilis TenA, SaTenA may act as a regulator controlling the secretion of extracellular proteases such as the subtilisin type of enzymes in bacteria. Thiamine biosynthesis has been identified as a potential drug target of the multi-resistant pathogen S. aureus and therefore all enzymes involved in the S. aureus thiamine pathway are presently being investigated in detail. Here, the structure of SaTenA, determined by molecular replacement and refined at 2.7 Å resolution to an R factor of 21.6% with one homotetramer in the asymmetric unit in the orthorhombic space group P212121, is presented. The tetrameric state of wild-type (WT) SaTenA was postulated to be the functional biological unit and was confirmed by small-angle X-ray scattering (SAXS) experiments in solution. To obtain insights into structural and functional features of the oligomeric SaTenA, comparative kinetic investigations as well as experiments analyzing the structural stability of the WT SaTenA tetramer versus a monomeric SaTenA mutant were performed.
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Affiliation(s)
- Afshan Begum
- Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY, Notkestrasse 85, Building 22A, 22603 Hamburg, Germany
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41
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Stuart DI, Abrescia NGA. From lows to highs: using low-resolution models to phase X-ray data. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:2257-65. [PMID: 24189238 PMCID: PMC3817700 DOI: 10.1107/s0907444913022336] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Accepted: 08/08/2013] [Indexed: 11/11/2022]
Abstract
The study of virus structures has contributed to methodological advances in structural biology that are generally applicable (molecular replacement and noncrystallographic symmetry are just two of the best known examples). Moreover, structural virology has been instrumental in forging the more general concept of exploiting phase information derived from multiple structural techniques. This hybridization of structural methods, primarily electron microscopy (EM) and X-ray crystallography, but also small-angle X-ray scattering (SAXS) and nuclear magnetic resonance (NMR) spectroscopy, is central to integrative structural biology. Here, the interplay of X-ray crystallography and EM is illustrated through the example of the structural determination of the marine lipid-containing bacteriophage PM2. Molecular replacement starting from an ~13 Å cryo-EM reconstruction, followed by cycling density averaging, phase extension and solvent flattening, gave the X-ray structure of the intact virus at 7 Å resolution This in turn served as a bridge to phase, to 2.5 Å resolution, data from twinned crystals of the major coat protein (P2), ultimately yielding a quasi-atomic model of the particle, which provided significant insights into virus evolution and viral membrane biogenesis.
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Affiliation(s)
- David I. Stuart
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Headington, Oxford OX3 7BN, England
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot, England
| | - Nicola G. A. Abrescia
- Structural Biology Unit, CIC bioGUNE, CIBERehd, Bizkaia Technology Park, Bld 800, 48160 Derio, Spain
- IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain
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42
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Filippov SK, Franklin JM, Konarev PV, Chytil P, Etrych T, Bogomolova A, Dyakonova M, Papadakis CM, Radulescu A, Ulbrich K, Stepanek P, Svergun DI. Hydrolytically Degradable Polymer Micelles for Drug Delivery: A SAXS/SANS Kinetic Study. Biomacromolecules 2013; 14:4061-70. [DOI: 10.1021/bm401186z] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Sergey K. Filippov
- Institute of Macromolecular Chemistry, AS CR, Heyrovsky Sq.
2, Prague, Prague 6, 162
06, Czech Republic
| | - John M. Franklin
- European Molecular
Biology Laboratory, EMBL c/o DESY, Notkestrasse 85, Hamburg, D-22603, Germany
| | - Petr V. Konarev
- European Molecular
Biology Laboratory, EMBL c/o DESY, Notkestrasse 85, Hamburg, D-22603, Germany
| | - Petr Chytil
- Institute of Macromolecular Chemistry, AS CR, Heyrovsky Sq.
2, Prague, Prague 6, 162
06, Czech Republic
| | - Tomas Etrych
- Institute of Macromolecular Chemistry, AS CR, Heyrovsky Sq.
2, Prague, Prague 6, 162
06, Czech Republic
| | - Anna Bogomolova
- Institute of Macromolecular Chemistry, AS CR, Heyrovsky Sq.
2, Prague, Prague 6, 162
06, Czech Republic
| | - Margarita Dyakonova
- Technische Universität München, Physik-Department, Fachgebiet Physik weicher Materie, James-Franck-Str. 1, 85748 Garching, Germany
| | - Christine M. Papadakis
- Technische Universität München, Physik-Department, Fachgebiet Physik weicher Materie, James-Franck-Str. 1, 85748 Garching, Germany
| | - Aurel Radulescu
- Forschungszentrum Jülich GmbH, Jülich Centre for Neutron Science JCNS, Lichtenbergstraße 1, 85748 Garching, Germany
| | - Karel Ulbrich
- Institute of Macromolecular Chemistry, AS CR, Heyrovsky Sq.
2, Prague, Prague 6, 162
06, Czech Republic
| | - Petr Stepanek
- Institute of Macromolecular Chemistry, AS CR, Heyrovsky Sq.
2, Prague, Prague 6, 162
06, Czech Republic
| | - Dmitri I. Svergun
- European Molecular
Biology Laboratory, EMBL c/o DESY, Notkestrasse 85, Hamburg, D-22603, Germany
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43
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Sander B, Tria G, Shkumatov AV, Kim EY, Grossmann JG, Tessmer I, Svergun DI, Schindelin H. Structural characterization of gephyrin by AFM and SAXS reveals a mixture of compact and extended states. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:2050-60. [DOI: 10.1107/s0907444913018714] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Accepted: 07/05/2013] [Indexed: 11/10/2022]
Abstract
Gephyrin is a trimeric protein involved in the final steps of molybdenum-cofactor (Moco) biosynthesis and in the clustering of inhibitory glycine and GABAAreceptors at postsynaptic specializations. Each protomer consists of stably folded domains (referred to as the G and E domains) located at either terminus and connected by a proteolytically sensitive linker of ∼150 residues. Both terminal domains can oligomerize in their isolated forms; however, in the context of the full-length protein only the G-domain trimer is permanently present, whereas E-domain dimerization is prevented. Atomic force microscopy (AFM) and small-angle X-ray scattering (SAXS) reveal a high degree of flexibility in the structure of gephyrin. The results imply an equilibrium between compact and extended conformational states in solution, with a preference for compact states. CD spectroscopy suggests that a partial compaction is achieved by interactions of the linker with the G and E domains. Taken together, the data provide a rationale for the role of the linker in the overall structure and the conformational dynamics of gephyrin.
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44
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Dölker N, Blanchet CE, Voß B, Haselbach D, Kappel C, Monecke T, Svergun DI, Stark H, Ficner R, Zachariae U, Grubmüller H, Dickmanns A. Structural determinants and mechanism of mammalian CRM1 allostery. Structure 2013; 21:1350-60. [PMID: 23850451 DOI: 10.1016/j.str.2013.05.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Revised: 05/07/2013] [Accepted: 05/26/2013] [Indexed: 10/26/2022]
Abstract
Proteins carrying nuclear export signals cooperatively assemble with the export factor CRM1 and the effector protein RanGTP. In lower eukaryotes, this cooperativity is coupled to CRM1 conformational changes; however, it is unknown if mammalian CRM1 maintains its compact conformation or shows similar structural flexibility. Here, combinations of small-angle X-ray solution scattering and electron microscopy experiments with molecular dynamics simulations reveal pronounced conformational flexibility in mammalian CRM1 and demonstrate that RanGTP binding induces association of its N- and C-terminal regions to form a toroid structure. The CRM1 toroid is stabilized mainly by local interactions between the terminal regions, rather than by global strain. The CRM1 acidic loop is key in transmitting the effect of this RanGTP-induced global conformational change to the NES-binding cleft by shifting its population to the open state, which displays enhanced cargo affinity. Cooperative CRM1 export complex assembly thus constitutes a highly dynamic process, encompassing an intricate interplay of global and local structural changes.
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Affiliation(s)
- Nicole Dölker
- Abteilung für Theoretische und Computergestützte Biophysik, Max-Planck-Institut für Biophysikalische Chemie, Am Faßberg 11, 37077 Göttingen, Germany
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45
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Purushothaman S, Gauthé BLLE, Brooks NJ, Templer RH, Ces O. Automated laboratory based X-ray beamline with multi-capillary sample chamber. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2013; 84:085104. [PMID: 24007104 DOI: 10.1063/1.4816825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
An automated laboratory based X-ray beamline with a multi-capillary sample chamber capable of undertaking small angle X-ray scattering measurements on a maximum of 104 samples at a time as a function of temperature between 5 and 85 °C has been developed. The modular format of the system enables the user to simultaneously equilibrate samples at eight different temperatures with an accuracy of ±0.005 °C. This system couples a rotating anode generator and 2D optoelectronic detector with Franks X-ray optics, leading to typical exposure times of less than 5 min for lyotropic liquid crystalline samples. Beamline control including sample exchange and data acquisition has been fully automated via a custom designed LabVIEW framework.
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Affiliation(s)
- S Purushothaman
- Department of Chemistry, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
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46
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Graewert MA, Svergun DI. Impact and progress in small and wide angle X-ray scattering (SAXS and WAXS). Curr Opin Struct Biol 2013; 23:748-54. [PMID: 23835228 DOI: 10.1016/j.sbi.2013.06.007] [Citation(s) in RCA: 118] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 06/12/2013] [Indexed: 10/26/2022]
Abstract
The advances made in small and wide angle X-ray scattering over the past decades have had a large impact on structural biology. Many new insights into challenging biological probes including large and transient complexes, flexible macromolecules as well as other exciting objects of various sizes were gained with this low resolution technique. Here, we review the recent developments in the experimental setups and in software for data collection and analysis, specifically for hybrid approaches. These progresses have allowed scientists to address a number of intriguing questions which could not be answered with other structural methods alone.
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Affiliation(s)
- Melissa A Graewert
- European Molecular Biology Laboratory, Hamburg Unit, EMBL c/o DESY, Notkestraße 85, Hamburg 22603, Germany
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47
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Groothuizen FS, Fish A, Petoukhov MV, Reumer A, Manelyte L, Winterwerp HHK, Marinus MG, Lebbink JHG, Svergun DI, Friedhoff P, Sixma TK. Using stable MutS dimers and tetramers to quantitatively analyze DNA mismatch recognition and sliding clamp formation. Nucleic Acids Res 2013; 41:8166-81. [PMID: 23821665 PMCID: PMC3783165 DOI: 10.1093/nar/gkt582] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The process of DNA mismatch repair is initiated when MutS recognizes mismatched DNA bases and starts the repair cascade. The Escherichia coli MutS protein exists in an equilibrium between dimers and tetramers, which has compromised biophysical analysis. To uncouple these states, we have generated stable dimers and tetramers, respectively. These proteins allowed kinetic analysis of DNA recognition and structural analysis of the full-length protein by X-ray crystallography and small angle X-ray scattering. Our structural data reveal that the tetramerization domains are flexible with respect to the body of the protein, resulting in mostly extended structures. Tetrameric MutS has a slow dissociation from DNA, which can be due to occasional bending over and binding DNA in its two binding sites. In contrast, the dimer dissociation is faster, primarily dependent on a combination of the type of mismatch and the flanking sequence. In the presence of ATP, we could distinguish two kinetic groups: DNA sequences where MutS forms sliding clamps and those where sliding clamps are not formed efficiently. Interestingly, this inability to undergo a conformational change rather than mismatch affinity is correlated with mismatch repair.
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Affiliation(s)
- Flora S Groothuizen
- Division of Biochemistry and CancerGenomiCs.nl, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands, European Molecular Biology Laboratory, Hamburg Outstation, EMBL c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany, Institute for Biochemistry, Justus Liebig University, Heinrich-Buff Ring 58, D-35392, Giessen, Germany, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA, Department of Cell Biology and Genetics, Cancer Genomics Center, Erasmus Medical Center, PO Box 2040, 3000 CA Rotterdam, the Netherlands and Department of Radiation Oncology, Erasmus Medical Center, PO Box 2040, 3000 CA Rotterdam, the Netherlands
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48
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Nowak E, Potrzebowski W, Konarev PV, Rausch JW, Bona MK, Svergun DI, Bujnicki JM, Le Grice SFJ, Nowotny M. Structural analysis of monomeric retroviral reverse transcriptase in complex with an RNA/DNA hybrid. Nucleic Acids Res 2013; 41:3874-87. [PMID: 23382176 PMCID: PMC3616737 DOI: 10.1093/nar/gkt053] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Revised: 01/11/2013] [Accepted: 01/11/2013] [Indexed: 11/19/2022] Open
Abstract
A key step in proliferation of retroviruses is the conversion of their RNA genome to double-stranded DNA, a process catalysed by multifunctional reverse transcriptases (RTs). Dimeric and monomeric RTs have been described, the latter exemplified by the enzyme of Moloney murine leukaemia virus. However, structural information is lacking that describes the substrate binding mechanism for a monomeric RT. We report here the first crystal structure of a complex between an RNA/DNA hybrid substrate and polymerase-connection fragment of the single-subunit RT from xenotropic murine leukaemia virus-related virus, a close relative of Moloney murine leukaemia virus. A comparison with p66/p51 human immunodeficiency virus-1 RT shows that substrate binding around the polymerase active site is conserved but differs in the thumb and connection subdomains. Small-angle X-ray scattering was used to model full-length xenotropic murine leukaemia virus-related virus RT, demonstrating that its mobile RNase H domain becomes ordered in the presence of a substrate-a key difference between monomeric and dimeric RTs.
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Affiliation(s)
- Elżbieta Nowak
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, European Molecular Biology Laboratory, Hamburg Outstation c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany, RT Biochemistry Section, HIV Drug Resistance Program, Frederick National Laboratory, Frederick, MD 21702, USA and Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Wojciech Potrzebowski
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, European Molecular Biology Laboratory, Hamburg Outstation c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany, RT Biochemistry Section, HIV Drug Resistance Program, Frederick National Laboratory, Frederick, MD 21702, USA and Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Petr V. Konarev
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, European Molecular Biology Laboratory, Hamburg Outstation c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany, RT Biochemistry Section, HIV Drug Resistance Program, Frederick National Laboratory, Frederick, MD 21702, USA and Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Jason W. Rausch
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, European Molecular Biology Laboratory, Hamburg Outstation c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany, RT Biochemistry Section, HIV Drug Resistance Program, Frederick National Laboratory, Frederick, MD 21702, USA and Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Marion K. Bona
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, European Molecular Biology Laboratory, Hamburg Outstation c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany, RT Biochemistry Section, HIV Drug Resistance Program, Frederick National Laboratory, Frederick, MD 21702, USA and Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Dmitri I. Svergun
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, European Molecular Biology Laboratory, Hamburg Outstation c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany, RT Biochemistry Section, HIV Drug Resistance Program, Frederick National Laboratory, Frederick, MD 21702, USA and Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Janusz M. Bujnicki
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, European Molecular Biology Laboratory, Hamburg Outstation c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany, RT Biochemistry Section, HIV Drug Resistance Program, Frederick National Laboratory, Frederick, MD 21702, USA and Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Stuart F. J. Le Grice
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, European Molecular Biology Laboratory, Hamburg Outstation c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany, RT Biochemistry Section, HIV Drug Resistance Program, Frederick National Laboratory, Frederick, MD 21702, USA and Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Marcin Nowotny
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, European Molecular Biology Laboratory, Hamburg Outstation c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany, RT Biochemistry Section, HIV Drug Resistance Program, Frederick National Laboratory, Frederick, MD 21702, USA and Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
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Blanchet CE, Svergun DI. Small-Angle X-Ray Scattering on Biological Macromolecules and Nanocomposites in Solution. Annu Rev Phys Chem 2013; 64:37-54. [DOI: 10.1146/annurev-physchem-040412-110132] [Citation(s) in RCA: 152] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Clement E. Blanchet
- European Molecular Biology Laboratory (EMBL) Hamburg, 22603 Hamburg, Germany;
| | - Dmitri I. Svergun
- European Molecular Biology Laboratory (EMBL) Hamburg, 22603 Hamburg, Germany;
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Söderberg CAG, Rajan S, Shkumatov AV, Gakh O, Schaefer S, Ahlgren EC, Svergun DI, Isaya G, Al-Karadaghi S. The molecular basis of iron-induced oligomerization of frataxin and the role of the ferroxidation reaction in oligomerization. J Biol Chem 2013; 288:8156-8167. [PMID: 23344952 PMCID: PMC3605634 DOI: 10.1074/jbc.m112.442285] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Revised: 01/22/2013] [Indexed: 11/06/2022] Open
Abstract
The role of the mitochondrial protein frataxin in iron storage and detoxification, iron delivery to iron-sulfur cluster biosynthesis, heme biosynthesis, and aconitase repair has been extensively studied during the last decade. However, still no general consensus exists on the details of the mechanism of frataxin function and oligomerization. Here, using small-angle x-ray scattering and x-ray crystallography, we describe the solution structure of the oligomers formed during the iron-dependent assembly of yeast (Yfh1) and Escherichia coli (CyaY) frataxin. At an iron-to-protein ratio of 2, the initially monomeric Yfh1 is converted to a trimeric form in solution. The trimer in turn serves as the assembly unit for higher order oligomers induced at higher iron-to-protein ratios. The x-ray crystallographic structure obtained from iron-soaked crystals demonstrates that iron binds at the trimer-trimer interaction sites, presumably contributing to oligomer stabilization. For the ferroxidation-deficient D79A/D82A variant of Yfh1, iron-dependent oligomerization may still take place, although >50% of the protein is found in the monomeric state at the highest iron-to-protein ratio used. This demonstrates that the ferroxidation reaction controls frataxin assembly and presumably the iron chaperone function of frataxin and its interactions with target proteins. For E. coli CyaY, the assembly unit of higher order oligomers is a tetramer, which could be an effect of the much shorter N-terminal region of this protein. The results show that understanding of the mechanistic features of frataxin function requires detailed knowledge of the interplay between the ferroxidation reaction, iron-induced oligomerization, and the structure of oligomers formed during assembly.
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Affiliation(s)
- Christopher A G Söderberg
- Center for Molecular Protein Science, Institute for Chemistry and Chemical Engineering, Lund University, P. O. Box 124, SE-221 00 Lund, Sweden
| | - Sreekanth Rajan
- Center for Molecular Protein Science, Institute for Chemistry and Chemical Engineering, Lund University, P. O. Box 124, SE-221 00 Lund, Sweden
| | - Alexander V Shkumatov
- European Molecular Biology Laboratory (EMBL), Hamburg Unit c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany
| | - Oleksandr Gakh
- Departments of Pediatric and Adolescent Medicine and Biochemistry and Molecular Biology, Mayo Clinic, College of Medicine, Rochester, Minnesota 55905
| | - Susanne Schaefer
- Center for Molecular Protein Science, Institute for Chemistry and Chemical Engineering, Lund University, P. O. Box 124, SE-221 00 Lund, Sweden
| | - Eva-Christina Ahlgren
- Center for Molecular Protein Science, Institute for Chemistry and Chemical Engineering, Lund University, P. O. Box 124, SE-221 00 Lund, Sweden
| | - Dmitri I Svergun
- European Molecular Biology Laboratory (EMBL), Hamburg Unit c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany
| | - Grazia Isaya
- Departments of Pediatric and Adolescent Medicine and Biochemistry and Molecular Biology, Mayo Clinic, College of Medicine, Rochester, Minnesota 55905.
| | - Salam Al-Karadaghi
- Center for Molecular Protein Science, Institute for Chemistry and Chemical Engineering, Lund University, P. O. Box 124, SE-221 00 Lund, Sweden.
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