35 research outputs found
Supplementary material: Efficient in vivo screening method for the identification of C4 photosynthesis inhibitors based on cell suspensions of the single-cell C4 plant Bienertia sinuspersici
No full textData described in Minges et al. (2019) Efficient in vivo screening method for the identification of C4 photosynthesis inhibitors based on cell suspensions of the single-cell C4 plant Bienertia sinuspersici. doi: 10.3389/fpls.2019.01350
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Raw diffraction images of pyruvate phosphate dikinase (PPDK), PDB 5JVN
No full text<p>Raw diffration images and processing input files/logs of pyruvate phosphate dikinase (PPDK) from the C<sub>3</sub> plant <em>Flaveria pringlei</em>. The data was used for PDB entry <a href="https://www.ebi.ac.uk/pdbe/entry/pdb/5jvn">5JVN</a> (<a href="https://www.doi.org/10.1038/srep45389">Minges et al. 2017</a>). Data was collected in two helical scans from the same crystal, each consisting of 3600 images (360°/scan, 0.1°/image). Data were cut according to accumulated radiation damage at 3445 and 3400 images respectively. All data was collected from loop-harvested crystals at beamline ID29 at the European Synchrotron Radiation Facility (ESRF, Grenoble, France) using a wavelength of 0.976252 Å and a Pilatus 6M (Dectris, Baden, Switzerland) detector.</p>
<p>The crystal belonged to the spacegroup P622 with unit cell constants a, b ~ 250 Å, c ~ 84 Å, α, β, γ ~ 90°.</p>
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eLabFTW – das freie elektronische Laborjournal
No full texteLabFTW ist eine freie und offene Software zur elektronischen Verwaltung und Dokumentation experimenteller Arbeiten. Weiterhin ist eine Datenbankfunktionalität implementiert, welche die Organisation unterschiedlichster Informationen wie z. B. Versuchsvorschriften vereinfacht. Durch seinen flexiblen Aufbau ist eLabFTW in praktisch allen experimentell arbeitenden Laboren einsetzbar und kann dort mit sehr geringem Aufwand auch auf eigener Hardware in Betrieb genommen werden. Zusätzlich ist die Eingliederung an zentrale Infrastrukturen, beispielsweise zur Benutzerverwaltung möglich. Über eine umfangreiche Programmierschnittstelle (API) kann weiterhin eine Anbindung an externe Programme erfolgen, worüber beispielsweise eine automatisierte Dokumentation von Messergebnissen realisiert werden kann.</p
CRC 1430 Metadata Block Configuration for Dataverse
No full textThis dataset contains TSV files for the configuration of metadata blocks for data repositories based on Dataverse. The metadata block helps to describe datasets from the domain of life science and chemistry as performed in the CRC 1430. To add a metadata block to a Dataverse installation use the instructions in the Dataverse Admin Guide. In addition to the TSV files, a YAML representation of the metadata blocks is provided which provide a structured way to edit the underlying data. The YAML files may be converted to TSV format using the yml2block software.
Methods
Together with researchers from the CRC 1430, a metadata schema was developed based on and extending the Dataverse-provided Life Sciences schema. Additional metadata blocks were created de novo for basic chemical metadata and mapping to other internally used databases such as the electronic lab notebook. Metadata fields and controlled vocabulary terms of the CRC 1430 metadata schema were first defined in YAML format and then converted into the TSV files format required by Dataverse for including customized metadata blocks using the yml2block software. These TSV files were used in the internal CRC 1430 Dataverse as metadata blocks to support FAIR data storage and foster data exchange.</p
Small-molecule inhibition of pyruvate phosphate dikinase targeting the nucleotide binding site.
No full textPyruvate phosphate dikinase (PPDK) is an essential enzyme of C4 photosynthesis in plants, catalyzing the ATP-driven conversion of pyruvate to phosphoenolpyruvate (PEP). It is further used by some bacteria and unicellular protists in the reverse, ATP-forming direction. Many weed species use C4 photosynthesis in contrast to world's major crops, which are C3 plants. Hence inhibitors of PPDK may be used as C4-specific herbicides. By screening a library of 80 commercially available kinase inhibitors, we identified compounds derived from bisindolylmaleimide (bisindolylmaleimide IV, IC50 = 0.76 ± 0.13 μM) and indirubin (indirubin-3'-monoxime, IC50 = 4.2 ± 0.9 μM) that showed high inhibitory potency towards PPDK and are among the most effective PPDK inhibitors described today. Physiological studies on leaf tissues of a C4 model plant confirmed in vivo inhibition of C4-driven photosynthesis by these substances. Moreover, comparative docking studies of non-inhibitory bisindolylmaleimide derivatives suggest that the selectivity towards PPDK may be increased by addition of functional groups to the core structure
Interfering Peptides Targeting Protein–Protein Interactions in the Ethylene Plant Hormone Signaling Pathway as Tools to Delay Plant Senescence
No full textTrapped intermediate state of plant pyruvate phosphate dikinase indicates substeps in catalytic swiveling domain mechanism
No full textPyruvate phosphate dikinase (PPDK) is an essential enzyme of both the C photosynthetic pathway and cellular energy metabolism of some bacteria and unicellular protists. In C plants, it catalyzes the ATP- and Pi-dependent formation of phosphoenolpyruvate (PEP) while in bacteria and protozoa the ATP-forming direction is used. PPDK is composed out of three distinct domains and exhibits one of the largest single domain movements known today during its catalytic cycle. However, little information about potential intermediate steps of this movement was available. A recent study resolved a discrete intermediate step of PPDK's swiveling movement, shedding light on the details of this intriguing mechanism. Here we present an additional structural intermediate that possibly represents another crucial step in the catalytic cycle of PPDK, providing means to get a more detailed understanding of PPDK's mode of function
