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1.
  • Bielecki, Johan, et al. (författare)
  • Electrospray sample injection for single-particle imaging with x-ray lasers
  • 2019
  • Ingår i: Science advances. ; 5:5
  • Tidskriftsartikel (refereegranskat)abstract
    • The possibility of imaging single proteins constitutes an exciting challenge for x-ray lasers. Despite encouraging results on large particles, imaging small particles has proven to be difficult for two reasons: not quite high enough pulse intensity from currently available x-ray lasers and, as we demonstrate here, contamination of the aerosolized molecules by nonvolatile contaminants in the solution. The amount of contamination on the sample depends on the initial droplet size during aerosolization. Here, we show that, with our electrospray injector, we can decrease the size of aerosol droplets and demonstrate virtually contaminant-free sample delivery of organelles, small virions, and proteins. The results presented here, together with the increased performance of next-generation x-ray lasers, constitute an important stepping stone toward the ultimate goal of protein structure determination from imaging at room temperature and high temporal resolution.
2.
  • Carlsson, Gunilla H., et al. (författare)
  • The elusive ligand complexes of the DWARF14 strigolactone receptor
  • 2018
  • Ingår i: Journal of Experimental Botany. - 0022-0957 .- 1460-2431. ; 69:9, s. 2345-2354
  • Tidskriftsartikel (refereegranskat)abstract
    • Strigolactones, a group of terpenoid lactones, control many aspects of plant growth and development, but the active forms of these plant hormones and their mode of action at the molecular level are still unknown. The strigolactone protein receptor is unusual because it has been shown to cleave the hormone and supposedly forms a covalent bond with the cleaved hormone fragment. This interaction is suggested to induce a conformational change in the receptor that primes it for subsequent interaction with partners in the signalling pathway. Substantial efforts have been invested into describing the interaction of synthetic strigolactone analogues with the receptor, resulting in a number of crystal structures. This investigation combines a re-evaluation of models in the Protein Data Bank with a search for new conditions that may permit the capture of a receptor-ligand complex. While weak difference density is frequently observed in the binding cavity, possibly due to a low-occupancy compound, the models often contain features not supported by the X-ray data. Thus, at this stage, we do not believe that any detailed deductions about the nature, conformation, or binding mode of the ligand can be made with any confidence.
3.
  • Munke, Anna, et al. (författare)
  • Coherent diffraction of single Rice Dwarf Virus particles using soft X-rays at the Linac Coherent Light Source
  • 2018
  • Ingår i: Nature Scientific Data.
  • Tidskriftsartikel (övrigt vetenskapligt)abstract
    • Single particle imaging using X-ray Free Electron Lasers has recently made major advancements that have facilitated experiments on smaller samples compared to the earliest reported works on giant viruses and cells. Here, the technique was used to image the 70 nm Rice dwarf virus, for which the generated dataset is described here. The virus particles were aerosolized and injected into the X-ray beam of the Linac Coherent Light Source. A total number of 36534 diffraction patterns were recorded, of which approximately 10 % were classified as ‘single hits’ by the RedFlamingo software. With the anticipation to advance method development, the dataset along with usage instructions are deposited in the Coherent X-ray imaging data bank, free to access and analyze.
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4.
  • Valegård, Karin, et al. (författare)
  • Structural and functional analyses of Rubisco from arctic diatom species reveal unusual posttranslational modifications
  • 2018
  • Ingår i: Journal of Biological Chemistry. - 0021-9258 .- 1083-351X. ; 293:34, s. 13033-13043
  • Tidskriftsartikel (refereegranskat)abstract
    • The catalytic performance of the major CO2-assimilating enzyme, ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), restricts photosynthetic productivity. Natural diversity in the catalytic properties of Rubisco indicates possibilities for improvement. Oceanic phytoplankton contain some of the most efficient Rubisco enzymes, and diatoms in particular are responsible for a significant proportion of total marine primary production as well as being a major source of CO2 sequestration in polar cold waters. Until now, the biochemical properties and three-dimensional structures of Rubisco from diatoms were unknown. Here, diatoms from arctic waters were collected, cultivated, and analyzed for their CO2-fixing capability. We characterized the kinetic properties of five and determined the crystal structures of four Rubiscos selected for their high CO2-fixing efficiency. The DNA sequences of the rbcL, and rbcS genes of the selected diatoms were similar, reflecting their close phylogenetic relationship. The V-max and K-m for the oxygenase and carboxylase activities at 25 degrees C and the specificity factors (S-c/o) at 15, 25, and 35 degrees C were determined. The S-c/o values were high, approaching those of mono- and dicot plants, thus exhibiting good selectivity for CO(2 )relative to O-2. Structurally, diatom Rubiscos belong to form I C/D, containing small subunits characterized by a short beta A-beta B loop and a C-terminal extension that forms a beta-hairpin structure (beta E-beta F loop). Of note, the diatom Rubiscos featured a number of posttranslational modifications of the large subunit, including 4-hydroxyproline, beta-hydroxyleucine, hydroxylated and nitrosylated cysteine, mono- and dihydroxylated lysine, and trimethylated lysine. Our studies suggest adaptation toward achieving efficient CO2 fixation in arctic diatom Rubiscos.
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5.
  • Valegård, Karin, et al. (författare)
  • Structure of Rubisco from Arabidopsis thaliana in complex with 2-carboxyarabinitol-1,5-bis­phosphate
  • 2018
  • Ingår i: ACTA CRYSTALLOGRAPHICA SECTION D: STRUCTURAL BIOLOGY. - 2059-7983. ; 74:1, s. 1-9
  • Tidskriftsartikel (refereegranskat)abstract
    • The crystal structure of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) from Arabidopsis thaliana is reported at 1.5 Å resolution. In light of the importance of A. thaliana as a model organism for understanding higher plant biology, and the pivotal role of Rubisco in photosynthetic carbon assimilation, there has been a notable absence of an A. thaliana Rubisco crystal structure. A. thaliana Rubisco is an L8S8 hexadecamer comprising eight plastome-encoded catalytic large (L) subunits and eight nuclear-encoded small (S) subunits. A. thaliana produces four distinct small-subunit isoforms (RbcS1A, RbcS1B, RbcS2B and RbcS3B), and this crystal structure provides a snapshot of A. thaliana Rubisco containing the low-abundance RbcS3B small-subunit isoform. Crystals were obtained in the presence of the transition-state analogue 2-carboxy-D-arabinitol-1,5-bisphosphate. A. thaliana Rubisco shares the overall fold characteristic of higher plant Rubiscos, but exhibits an interesting disparity between sequence and structural relatedness to other Rubisco isoforms. These results provide the structural framework to understand A. thaliana Rubisco and the potential catalytic differences that could be conferred by alternative A. thaliana Rubisco small-subunit isoforms.
6.
  • Daurer, Benedikt J., et al. (författare)
  • Experimental strategies for imaging bioparticles with femtosecond hard X-ray pulses
  • 2017
  • Ingår i: IUCrJ. - 0972-6918 .- 2052-2525. ; 4, s. 251-262
  • Tidskriftsartikel (refereegranskat)abstract
    • This study explores the capabilities of the Coherent X-ray Imaging Instrument at the Linac Coherent Light Source to image small biological samples. The weak signal from small samples puts a significant demand on the experiment. Aerosolized Omono River virus particles of similar to 40 nm in diameter were injected into the submicrometre X-ray focus at a reduced pressure. Diffraction patterns were recorded on two area detectors. The statistical nature of the measurements from many individual particles provided information about the intensity profile of the X-ray beam, phase variations in the wavefront and the size distribution of the injected particles. The results point to a wider than expected size distribution (from similar to 35 to similar to 300 nm in diameter). This is likely to be owing to nonvolatile contaminants from larger droplets during aerosolization and droplet evaporation. The results suggest that the concentration of nonvolatile contaminants and the ratio between the volumes of the initial droplet and the sample particles is critical in such studies. The maximum beam intensity in the focus was found to be 1.9 * 10(12) photons per mu m(2) per pulse. The full-width of the focus at half-maximum was estimated to be 500 nm (assuming 20% beamline transmission), and this width is larger than expected. Under these conditions, the diffraction signal from a sample-sized particle remained above the average background to a resolution of 4.25 nm. The results suggest that reducing the size of the initial droplets during aerosolization is necessary to bring small particles into the scope of detailed structural studies with X-ray lasers.
7.
  • Gunn, Laura, 1986-, et al. (författare)
  • A unique structural domain in Methanococcoides burtonii ribulose-1,5-bisphosphatecarboxylase/oxygenase (Rubisco) acts as a small subunit mimic
  • 2017
  • Ingår i: Journal of Biological Chemistry. - 0021-9258 .- 1083-351X. ; 292:16, s. 6838-6850
  • Tidskriftsartikel (refereegranskat)abstract
    • The catalytic inefficiencies of the CO2-fixing enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) often limit plant productivity. Strategies to engineer more efficient plant Rubiscos have been hampered by evolutionary constraints, prompting interest in Rubisco isoforms from non-photosynthetic organisms. The methanogenic archaeon Methanococcoides burtonii contains a Rubisco isoform that functions to scavenge the ribulose-1,5-bisphosphate (RuBP) byproduct of purine/pyrimidine metabolism. The crystal structure of M. burtonii Rubisco (MbR) presented here at 2.6 Å resolution is composed of catalytic large subunits (LSu) assembled into pentamers of dimers, (L2)5 and differs from Rubiscos from higher plants where LSus are glued together by small subunits (SSu) into hexadecameric L8S8 enzymes. MbR contains a unique 29-amino-acid insertion near the C-terminus, which folds as a separate domain in the structure. This domain, which is visualized for the first time in this study, is located in a similar position to SSus in L8S8 enzymes between LSus of adjacent L2 dimers, where negatively charged residues co-ordinate around a Mg2+ ion in a fashion that suggests this domain may be important for the assembly process. The Rubisco assembly domain is thus an inbuilt SSu mimic that concentrates L2 dimers. MbR assembly is ligand-stimulated and we show that only 6-carbon molecules with a particular stereochemistry at the C3 carbon can induce oligomerization. Based on MbR structure, subunit arrangement, sequence, phylogenetic distribution and function, MbR and a subset of Rubiscos from the Methanosarcinales order are proposed to belong to a new Rubisco sub-group, named form IIIB.
8.
  • Larsson, Anna M., et al. (författare)
  • Crystal structures of β-carboxysome shell protein CcmP ligand binding correlates with the closed or open central pore
  • 2017
  • Ingår i: Journal of Experimental Botany. - OXFORD UNIV PRESS. - 0022-0957 .- 1460-2431. ; 68:14, s. 3857-3867
  • Tidskriftsartikel (refereegranskat)abstract
    • Cyanobacterial CO2 fixation is promoted by encapsulating and co-localizing the CO2-fixing enzymes within a protein shell, the carboxysome. A key feature of the carboxysome is its ability to control selectively the flux of metabolites in and out of the shell. The beta-carboxysome shell protein CcmP has been shown to form a double layer of pseudohexamers with a relatively large central pore (similar to 13 angstrom diameter), which may allow passage of larger metabolites such as the substrate for CO2 fixation, ribulose 1,5-bisphosphate, through the shell. Here we describe two crystal structures, at 1.45 angstrom and 1.65 angstrom resolution, of CcmP from Synechococcus elongatus PCC7942 (SeCcmP). The central pore of CcmP is open or closed at its ends, depending on the conformation of two conserved residues, Glu69 and Arg70. The presence of glycerol resulted in a pore that is open at one end and closed at the opposite end. When glycerol was omitted, both ends of the barrel became closed. A binding pocket at the interior of the barrel featured residual density with distinct differences in size and shape depending on the conformation, open or closed, of the central pore of SeCcmP, suggestive of a metabolite-driven mechanism for the gating of the pore.
9.
  • Ekeberg, Tomas, et al. (författare)
  • Single-shot diffraction data from the Mimivirus particle using an X-ray free-electron laser
  • 2016
  • Ingår i: Scientific Data. - 2052-4463. ; 3
  • Tidskriftsartikel (refereegranskat)abstract
    • Free-electron lasers (FEL) hold the potential to revolutionize structural biology by producing X-ray pules short enough to outrun radiation damage, thus allowing imaging of biological samples without the limitation from radiation damage. Thus, a major part of the scientific case for the first FELs was three-dimensional (3D) reconstruction of non-crystalline biological objects. In a recent publication we demonstrated the first 3D reconstruction of a biological object from an X-ray FEL using this technique. The sample was the giant Mimivirus, which is one of the largest known viruses with a diameter of 450 nm. Here we present the dataset used for this successful reconstruction. Data-analysis methods for single-particle imaging at FELs are undergoing heavy development but data collection relies on very limited time available through a highly competitive proposal process. This dataset provides experimental data to the entire community and could boost algorithm development and provide a benchmark dataset for new algorithms.
10.
  • Hantke, Max F., et al. (författare)
  • A data set from flash X-ray imaging of carboxysomes
  • 2016
  • Ingår i: Scientific Data. - 2052-4463. ; 3
  • Tidskriftsartikel (refereegranskat)abstract
    • Ultra-intense femtosecond X-ray pulses from X-ray lasers permit structural studies on single particles and biomolecules without crystals. We present a large data set on inherently heterogeneous, polyhedral carboxysome particles. Carboxysomes are cell organelles that vary in size and facilitate up to 40% of Earth’s carbon fixation by cyanobacteria and certain proteobacteria. Variation in size hinders crystallization. Carboxysomes appear icosahedral in the electron microscope. A protein shell encapsulates a large number of Rubisco molecules in paracrystalline arrays inside the organelle. We used carboxysomes with a mean diameter of 115±26 nm from Halothiobacillus neapolitanus. A new aerosol sample-injector allowed us to record 70,000 low-noise diffraction patterns in 12 min. Every diffraction pattern is a unique structure measurement and high-throughput imaging allows sampling the space of structural variability. The different structures can be separated and phased directly from the diffraction data and open a way for accurate, high-throughput studies on structures and structural heterogeneity in biology and elsewhere.
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