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  • Kraken3D  (1)
  • Protein aggregation  (1)
  • affinity labeling  (1)
  • 1
    Digitale Medien
    Digitale Medien
    Springer
    The protein journal 9 (1990), S. 445-451 
    ISSN: 1573-4943
    Schlagwort(e): Phosphoribulokinase ; affinity labeling ; bromoacetylethanolamine phosphate
    Quelle: Springer Online Journal Archives 1860-2000
    Thema: Chemie und Pharmazie
    Notizen: Abstract The chloroplast enzyme phosphoribulokinase is reversibly deactivated by oxidation of Cys16 and Cys55 to a disulfide. Although not required for catalysis, Cys16 is an active-site residue positioned at the nucleotide-binding domain (Porter and Hartman, 1988). The hyperreactivity of Cys16 has heretofore limited further active-site characterization by chemical modification. To overcome this limitation, the partially active enzyme,S-methylated at Cys16, has been probed with a potential affinity reagent. Treatment of methylated enzyme with bromoacetylethanolamine phosphate results in essentially complete loss of catalytic activity. Inactivation follows pseudo-first-order kinetics and exhibits a rate saturation with an apparentK d of 3–4 mM. ATP, but not ribulose 5-phosphate, affords substantial protection. Complete inactivation correlates with incorporation of 1 mol of [14C]reagent per mole of enzyme subunit. Amino acid analysis of the [14C]-labeled enzyme demonstrates that only cysteine is modified, and mapping of tryptic digests shows that Cys55 is a major site of alkylation. These results indicate that Cys55 is also located in the ATP-binding domain of the active-site.
    Materialart: Digitale Medien
    Standort Signatur Erwartet Verfügbarkeit
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  • 2
    Digitale Medien
    Digitale Medien
    Springer
    Planta 181 (1990), S. 349-357 
    ISSN: 1432-2048
    Schlagwort(e): Light/dark regulation ; Phosphoribulokinase ; Protein aggregation ; Spinacia (phosphoribulokinase)
    Quelle: Springer Online Journal Archives 1860-2000
    Thema: Biologie
    Notizen: Abstract Phosphoribulokinase (PRK; EC 2.1.7.19) is active in illuminated chloroplasts and inactive in darkened chloroplasts. This regulatory mechanism is mediated by thioredoxin-dependent reduction of a kinase disulfide in vivo. Extracts of spinach (Spinacia oleracea L.) leaves in the presence of 10 mM dithiothreitol contain a single 80-kDa form of PRK as judged by gel filtration. Gel filtration of thiol-free extracts of light-harvested tissue shows the presence of two inactive forms of PRK, the 80-kDa form and an aggregate (〉 550 kDa) form, but treatment of both forms with dithiothreitol restores kinase activity. Gel filtration following extraction of dark-harvested tissue in the absence of dithiotreitol demonstrates the presence of only the heavier form. Inclusion of 400 mM (NH4)2SO4 in the homogenization buffer during extraction of light-harvested tissue suppresses the formation of the high-M r form of PRK, but does not eliminate the aggregate form observed in extracts of dark-harvested leaves. However, prolonged treatment of extracts from dark-harvested tissue with 400 mM (NH4)2SO4 results in conversion of the high-M r form of phosphoribulokinase to the low-M r form. The data are consistent with the heavier form of phosphoribulokinase being the normal in-vivo aggregation state in the dark, while the lighter form is the normal aggregation state in the light. This research was sponsored jointly by the science and education administration of the U.S. Department of Agriculture under Grant No. 88-37130-3722 from the Competitive Research Grants Office and by the Office of Health and Environmental Research, U.S. Department of Energy under Contract DE-AC05-84OR21400 with Martin Marietta Energy Systems Inc., Oak Ridge, Tenn., USA. The author is Postdoctoral Investigator supported by the U.S. Department of Agriculture through Subcontract No. 88-37130-3722 from the Biology Division of Oak Ridge National Laboratory to the University of Tennessee.
    Materialart: Digitale Medien
    Standort Signatur Erwartet Verfügbarkeit
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  • 3
    Publikationsdatum: 2022-10-20
    Beschreibung: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Oliveira, T. C. A., Lin, Y.-T., & Porter, M. B. Underwater sound propagation modeling in a complex shallow water environment. Frontiers in Marine Science, 8, (2021): 751327, https://doi.org/10.3389/fmars.2021.751327.
    Beschreibung: Three-dimensional (3D) effects can profoundly influence underwater sound propagation in shallow-water environments, hence, affecting the underwater soundscape. Various geological features and coastal oceanographic processes can cause horizontal reflection, refraction, and diffraction of underwater sound. In this work, the ability of a parabolic equation (PE) model to simulate sound propagation in the extremely complicated shallow water environment of Long Island Sound (United States east coast) is investigated. First, the 2D and 3D versions of the PE model are compared with state-of-the-art normal mode and beam tracing models for two idealized cases representing the local environment in the Sound: (i) a 2D 50-m flat bottom and (ii) a 3D shallow water wedge. After that, the PE model is utilized to model sound propagation in three realistic local scenarios in the Sound. Frequencies of 500 and 1500 Hz are considered in all the simulations. In general, transmission loss (TL) results provided by the PE, normal mode and beam tracing models tend to agree with each other. Differences found emerge with (1) increasing the bathymetry complexity, (2) expanding the propagation range, and (3) approaching the limits of model applicability. The TL results from 3D PE simulations indicate that sound propagating along sand bars can experience significant 3D effects. Indeed, for the complex shallow bathymetry found in some areas of Long Island Sound, it is challenging for the models to track the interference effects in the sound pattern. Results emphasize that when choosing an underwater sound propagation model for practical applications in a complex shallow-water environment, a compromise will be made between the numerical model accuracy, computational time, and validity.
    Beschreibung: TO thanks FCT/MCTES for the financial support to CESAM (UIDP/50017/2020 + UIDB/50017/2020), through national funds. The funding support from the Office of Naval Research for Y-TL via the grant N00014-21-1-2416 was also acknowledged. MP was supported by the Office of Naval Research under contracts N68335-17-C-0553 and N00014-18-C-7007.
    Schlagwort(e): Underwater soundscape ; 3D PE ; Bellhop3D ; Kraken3D ; Long Island Sound ; Sand bars
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Standort Signatur Erwartet Verfügbarkeit
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