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News Article | December 16, 2016
Site: www.eurekalert.org

Biological small-angle X-ray scattering (SAXS) is an experimental technique that provides low-resolution structural information on macromolecules. The surge of popularity of the technique is a result of recent improvements in both software and hardware, allowing for high-throughput data collection and analysis, reflected in the increasing number of dedicated SAXS beamlines such as BM29 at the ESRF, P12 at EMBL Hamburg and B21 at Diamond Light Source. However, as for most other macromolecular structural techniques, radiation damage is still a major factor hindering the success of experiments. The high solvent proportion of biological SAXS samples means that hydroxyl, hydroperoxyl radicals and hydrated electrons are produced in abundance by the radiolysis of water when it is irradiated with X-rays. These radicals can then interact with the protein molecules, ultimately leading to protein aggregation, fragmentation or unfolding. Furthermore, molecular repulsion due to protein charging can also decrease the scattering at low angles. Common methods used to reduce radiation damage to biological SAXS samples are generally concerned with limiting the X-ray exposure to any given volume of sample. In an analogous manner, cryo-cooling samples down to 100 K for SAXS (cryoSAXS) has been reported to increase the dose tolerance of SAXS samples by at least two orders of magnitude. Applications of the above radiation damage mitigation approaches are unable to completely circumvent its detrimental effects, in particular the change of the scattering profile throughout the experiment. It is necessary to determine whether any two scattering profiles are similar so that noise can be reduced by averaging over similar curves. For experiments by different researchers to be inter-comparable, the progression of radiation damage is most usefully tracked as a function of the dose absorbed by the sample. RADDOSE-3D is a free and open source software program used to calculate the time- and space-resolved three-dimensional distribution of the dose absorbed by a protein crystal in a macromolecular crystallography experiment; however, there is no equivalent software available for SAXS. Radiation damage studies in SAXS thus currently require the experimenters to correctly parameterize the experiment and manually calculate a single estimate of the dose within the sample. In a paper published by Brooks-Bartlett et al. [(2017), J. Synchrotron. Rad. 24, doi:101107/S1600577516015083], extensions to RADDOSE-3D are presented, which enable the convenient calculation of doses for SAXS experiments, reducing the burden of manually performing the calculation. Additionally, the authors have created a visualisation package to assess the similarity of SAXS frames and used these tools to assess the efficacy of various radioprotectant compounds for increasing the radiation tolerance of the glucose isomerase protein sample.


Poulsen C.,EMBL Hamburg | Poulsen C.,Copenhagen University | Panjikar S.,EMBL Hamburg | Panjikar S.,Australian Synchrotron | And 5 more authors.
PLoS ONE | Year: 2014

Members of the WXG100 protein superfamily form homo- or heterodimeric complexes. The most studied proteins among them are the secreted T-cell antigens CFP-10 (10 kDa culture filtrate protein, EsxB) and ESAT-6 (6 kDa early secreted antigen target, EsxA) from Mycobacterium tuberculosis. They are encoded on an operon within a gene cluster, named as ESX-1, that encodes for the Type VII secretion system (T7SS). WXG100 proteins are secreted in a full-length form and it is known that they adopt a four-helix bundle structure. In the current work we discuss the evolutionary relationship between the homo- and heterodimeric WXG100 proteins, the basis of the oligomeric state and the key structural features of the conserved sequence pattern of WXG100 proteins. We performed an iterative bioinformatics analysis of the WXG100 protein superfamily and correlated this with the atomic structures of the representative WXG100 proteins. We find, firstly, that the WXG100 protein superfamily consists of three subfamilies: CFP-10-, ESAT-6- and sagEsxA-like proteins (EsxA proteins similar to that of Streptococcus agalactiae). Secondly, that the heterodimeric complexes probably evolved from a homodimeric precursor. Thirdly, that the genes of hetero-dimeric WXG100 proteins are always encoded in bi-cistronic operons and finally, by combining the sequence alignments with the X-ray data we identify a conserved C-terminal sequence pattern. The side chains of these conserved residues decorate the same side of the C-terminal α-helix and therefore form a distinct surface. Our results lead to a putatively extended T7SS secretion signal which combines two reported T7SS recognition characteristics: Firstly that the T7SS secretion signal is localized at the C-terminus of T7SS substrates and secondly that the conserved residues YxxxD/E are essential for T7SS activity. Furthermore, we propose that the specific α-helical surface formed by the conserved sequence pattern including YxxxD/E motif is a key component of T7SS-substrate recognition. © 2014 Poulsen et al.


Samygina V.R.,Russian Academy of Sciences | Sokolov A.V.,Institute of Experimental Medicine NWB RAMS | Bourenkov G.,EMBL Hamburg | Petoukhov M.V.,EMBL Hamburg | And 5 more authors.
PLoS ONE | Year: 2013

Copper-containing ferroxidase ceruloplasmin (Cp) forms binary and ternary complexes with cationic proteins lactoferrin (Lf) and myeloperoxidase (Mpo) during inflammation. We present an X-ray crystal structure of a 2Cp-Mpo complex at 4.7 Å resolution. This structure allows one to identify major protein-protein interaction areas and provides an explanation for a competitive inhibition of Mpo by Cp and for the activation of p-phenylenediamine oxidation by Mpo. Small angle X-ray scattering was employed to construct low-resolution models of the Cp-Lf complex and, for the first time, of the ternary 2Cp-2Lf-Mpo complex in solution. The SAXS-based model of Cp-Lf supports the predicted 1:1 stoichiometry of the complex and demonstrates that both lobes of Lf contact domains 1 and 6 of Cp. The 2Cp-2Lf-Mpo SAXS model reveals the absence of interaction between Mpo and Lf in the ternary complex, so Cp can serve as a mediator of protein interactions in complex architecture. Mpo protects antioxidant properties of Cp by isolating its sensitive loop from proteases. The latter is important for incorporation of Fe3+ into Lf, which activates ferroxidase activity of Cp and precludes oxidation of Cp substrates. Our models provide the structural basis for possible regulatory role of these complexes in preventing iron-induced oxidative damage. © 2013 Samygina et al.


Ghasparian A.,University of Zürich | Riedel T.,University of Zürich | Koomullil J.,University of Zürich | Moehle K.,University of Zürich | And 9 more authors.
ChemBioChem | Year: 2011

Engineered nanoparticles have been designed based on the self-assembling properties of synthetic coiled-coil lipopeptide building blocks. The presence of an isoleucine zipper within the lipopeptide together with the aggregating effects of an N-terminal lipid drives formation of 20-25 nm nanoparticles in solution. Biophysical studies support a model in which the lipid is buried in the centre of the nanoparticle, with 20-30 trimeric helical coiled-coil bundles radiating out into solution. A promiscuous T-helper epitope and a synthetic B-cell epitope mimetic derived from the circumsporozoite protein of Plasmodium falciparum have been linked to each lipopeptide chain, with the result that 60-90 copies of each antigen are displayed over the surface of the nanoparticle. These nanoparticles elicit strong humoral immune responses in mice and rabbits, including antibodies able to cross-react with the parasite, thereby, supporting the potential value of this delivery system in synthetic vaccine design. Viral protection: Synthetic virus-like particles (SVLPs) are produced from self-assembling coiled-coil lipopeptide building blocks (see figure). SVLPs allow multivalent display of B-cell epitope mimetics, are highly immunogenic, and can be used to elicit strong epitope- and pathogen-specific humoral immune responses without the use of adjuvants. © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


List F.,EMBL Hamburg | List F.,University of Regensburg | Vega M.C.,EMBL Hamburg | Vega M.C.,CSIC - Biological Research Center | And 4 more authors.
Chemistry and Biology | Year: 2012

Nitrogen is incorporated into various metabolites by multifunctional glutamine amidotransferases via reactive ammonia generated by glutaminase hydrolysis of glutamine. Although this process is generally tightly regulated by subsequent synthase activity, little is known about how the glutaminase is inhibited in the absence of an activating signal. Here, we use imidazoleglycerolphosphate synthase as a model to investigate the mechanism of glutaminase regulation. A structure of the bienzyme-glutamine complex reveals that the glutaminase active site is in a catalysis-competent conformation but the ammonia pathway toward the synthase active site is blocked. Mutation of two residues blocking the pathway leads to a complete uncoupling of the two reactions and to a 2800-fold amplification of glutaminase activity. Our data advance the understanding of coupling enzymatic activities in glutamine amidotransferases and raise hypotheses of the underlying molecular mechanism. © 2012 Elsevier Ltd.


Tamura H.,Max Planck Institute For Terrestrische Mikrobiologie | Tamura H.,Research Institute for Biological science RIBS Okayama | Salomone-Stagni M.,EMBL Hamburg | Fujishiro T.,Max Planck Institute For Terrestrische Mikrobiologie | And 6 more authors.
Angewandte Chemie - International Edition | Year: 2013

Inhibition mechanism: Isocyanides strongly inhibit [Fe]-hydrogenase. X-ray crystallography and X-ray absorption spectroscopy revealed that the isocyanide binds to the trans position, versus the acyl carbon of the Fe center, and is covalently bound to the pyridinol hydroxy oxygen. These results also indicated that the hydroxy group is essential for H2 activation. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Blanchet C.E.,EMBL Hamburg | Zozulya A.V.,EMBL Hamburg | Kikhney A.G.,EMBL Hamburg | Kikhney A.G.,German Electron Synchrotron | And 9 more authors.
Journal of Applied Crystallography | Year: 2012

A setup is presented for automated high-throughput measurements of small-angle X-ray scattering (SAXS) from macromolecular solutions on the bending-magnet beamline X33 of EMBL at the storage ring DORIS-III (DESY, Hamburg). A new multi-cell compartment allows for rapid switching between in-vacuum and in-air operation, for digital camera assisted control of cell filling and for colour sample illumination. The beamline is equipped with a Pilatus 1 M-W pixel detector for SAXS and a Pilatus 300 k-W for wide-angle scattering (WAXS), and results from the use of the Pilatus detectors for scattering studies are reported. The setup provides a broad resolution range from 100 to 0.36 nm without the necessity of changing the sample-to-detector distance. A new optimized robotic sample changer is installed, permitting rapid and reliable automated sample loading and cell cleaning with a required sample volume of 40 l. All the devices are fully integrated into the beamline control software system, ensuring fully automated and user-friendly operation (attended, unattended and remote) with a throughput of up to 15 measurements per hour. © 2012 International Union of Crystallography Printed in Singapore-all rights reserved.


Sauer F.,EMBL Hamburg | Vahokoski J.,EMBL Hamburg | Song Y.-H.,EMBL Hamburg | Wilmanns M.,EMBL Hamburg
EMBO Reports | Year: 2010

Large filament proteins in muscle sarcomeres comprise many immunoglobulin-like domains that provide a molecular platform for self-assembly and interactions with heterologous protein partners. We have unravelled the molecular basis for the head-to-tail interaction of the carboxyl terminus of titin and the amino-terminus of obscurin-like-1 by X-ray crystallography. The binary complex is formed by a parallel intermolecular Β-sheet that presents a novel immunoglobulin-like domain-mediated assembly mechanism in muscle filament proteins. Complementary binding data show that the assembly is entropy-driven rather than dominated data by specific polar interactions. The assembly observed leads to a V-shaped zipper-like arrangement of the two filament proteins. © 2010 European Molecular Biology Organization.


Esch D.,Max Planck Institute for Molecular Biomedicine | Vahokoski J.,EMBL Hamburg | Groves M.R.,EMBL Hamburg | Pogenberg V.,EMBL Hamburg | And 10 more authors.
Nature Cell Biology | Year: 2013

Terminally differentiated cells can be reprogrammed to pluripotency by the forced expression of Oct4, Sox2, Klf4 and c-Myc. However, it remains unknown how this leads to the multitude of epigenetic changes observed during the reprogramming process. Interestingly, Oct4 is the only factor that cannot be replaced by other members of the same family to induce pluripotency. To understand the unique role of Oct4 in reprogramming, we determined the structure of its POU domain bound to DNA. We show that the linker between the two DNA-binding domains is structured as an α-helix and exposed to the protein's surface, in contrast to the unstructured linker of Oct1. Point mutations in this α-helix alter or abolish the reprogramming activity of Oct4, but do not affect its other fundamental properties. On the basis of mass spectrometry studies of the interactome of wild-type and mutant Oct4, we propose that the linker functions as a protein-protein interaction interface and plays a crucial role during reprogramming by recruiting key epigenetic players to Oct4 target genes. Thus, we provide molecular insights to explain how Oct4 contributes to the reprogramming process. © 2013 Macmillan Publishers Limited. All rights reserved.


News Article | December 16, 2016
Site: phys.org

SAXS envelopes of Glucose Isomerase generated from frames collected early (bottom left) and late (top right) in the experiment. Credit: Brooks-Bartlett et al Biological small-angle X-ray scattering (SAXS) is an experimental technique that provides low-resolution structural information on macromolecules. The surge of popularity of the technique is a result of recent improvements in both software and hardware, allowing for high-throughput data collection and analysis, reflected in the increasing number of dedicated SAXS beamlines such as BM29 at the ESRF, P12 at EMBL Hamburg and B21 at Diamond Light Source. However, as for most other macromolecular structural techniques, radiation damage is still a major factor hindering the success of experiments. The high solvent proportion of biological SAXS samples means that hydroxyl, hydroperoxyl radicals and hydrated electrons are produced in abundance by the radiolysis of water when it is irradiated with X-rays. These radicals can then interact with the protein molecules, ultimately leading to protein aggregation, fragmentation or unfolding. Furthermore, molecular repulsion due to protein charging can also decrease the scattering at low angles. Common methods used to reduce radiation damage to biological SAXS samples are generally concerned with limiting the X-ray exposure to any given volume of sample. In an analogous manner, cryo-cooling samples down to 100 K for SAXS (cryoSAXS) has been reported to increase the dose tolerance of SAXS samples by at least two orders of magnitude. Applications of the above radiation damage mitigation approaches are unable to completely circumvent its detrimental effects, in particular the change of the scattering profile throughout the experiment. It is necessary to determine whether any two scattering profiles are similar so that noise can be reduced by averaging over similar curves. For experiments by different researchers to be inter-comparable, the progression of radiation damage is most usefully tracked as a function of the dose absorbed by the sample. RADDOSE-3D is a free and open source software program used to calculate the time- and space-resolved three-dimensional distribution of the dose absorbed by a protein crystal in a macromolecular crystallography experiment; however, there is no equivalent software available for SAXS. Radiation damage studies in SAXS thus currently require the experimenters to correctly parameterize the experiment and manually calculate a single estimate of the dose within the sample. In a paper published by Brooks-Bartlett et al. [(2017), J. Synchrotron. Rad. 24, doi:101107/S1600577516015083], extensions to RADDOSE-3D are presented, which enable the convenient calculation of doses for SAXS experiments, reducing the burden of manually performing the calculation. Additionally, the authors have created a visualisation package to assess the similarity of SAXS frames and used these tools to assess the efficacy of various radioprotectant compounds for increasing the radiation tolerance of the glucose isomerase protein sample. Explore further: New beamline at MAX II opens for research More information: Jonathan C. Brooks-Bartlett et al, Development of tools to automate quantitative analysis of radiation damage in SAXS experiments, Journal of Synchrotron Radiation (2017). DOI: 10.1107/S1600577516015083

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