Journal: Biochimica et Biophysica Acta (BBA) - General Subjects

Abbreviation

Biochim. biophys. acta, Gen. subj.

Publisher

Elsevier

Journal Volumes

ISSN

0304-4165
1872-8006

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2014 - 201952020 - 20253
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Publications 1 - 8 of 8
  • Characterization of the N- and C-terminal domain interface of the three main apoE isoforms: A combined quantitative cross-linking mass spectrometry and molecular modeling study
    Item type: Journal Article
    Mohammadi, Azadeh; Deroo, Stéphanie; Leitner, Alexander; et al. (2025)
    Biochimica et Biophysica Acta (BBA) - General Subjects
    Apolipoprotein E (apoE) polymorphism is associated with different pathologies such as atherosclerosis and Alzheimer's disease. Knowledge of the three-dimensional structure of apoE and isoform-specific structural differences are prerequisites for the rational design of small molecule structure modulators that correct the detrimental effects of pathological isoforms. In this study, cross-linking mass spectrometry (XL-MS) targeting Asp, Glu and Lys residues was used to explore the intramolecular interactions in the E2, E3 and E4 isoforms of apoE. The resulting quantitative XL-MS data combined with molecular modeling revealed isoform-specific characteristics of the N- and C-terminal domain interfaces as well as the isoform-dependent dynamic equilibrium of these interfaces. Finally, the data identified a network of salt bridges formed by R61-R112-E109 residues in the N-terminal helical bundle as a modulator of the interaction with the C-terminal domain making this network a potential drug target.
  • Impact of protein and ligand impurities on ITC-derived protein-ligand thermodynamics
    Item type: Journal Article
    Gruener, Stefan; Neeb, Manuel; Barandun, Luzi Jakob; et al. (2014)
    Biochimica et Biophysica Acta (BBA) - General Subjects
  • The structure of cyanophycinase in complex with a cyanophycin degradation intermediate
    Item type: Journal Article
    Sharon, Itai; Grogg, Marcel; Hilvert, Donald; et al. (2022)
    Biochimica et Biophysica Acta (BBA) - General Subjects
    Background: Cyanophycinases are serine protease family enzymes which are required for the metabolism of cyanophycin, the natural polymer multi-L-arginyl-poly(L-aspartic acid). Cyanophycinases degrade cyanophycin to β-Asp-Arg dipeptides, which enables use of this important store of fixed nitrogen. Methods: We used genetic code expansion to incorporate diaminopropionic acid into cyanophycinase in place of the active site serine, and determined a high-resolution structure of the covalent acyl-enzyme intermediate resulting from attack of cyanophycinase on a short cyanophycin segment. Results: The structure indicates that cyanophycin dipeptide residues P1 and P1′ bind shallow pockets adjacent to the catalytic residues. We observe many cyanophycinase - P1 dipeptide interactions in the co-complex structure. Calorimetry measurements show that at least two cyanophycin dipeptides are needed for high affinity binding to cyanophycinase. We also characterized a putative cyanophycinase which we found to be structurally very similar but that shows no activity and could not be activated by mutation of its active site. General significance: Despite its peptidic structure, cyanophycin is resistant to degradation by peptidases and other proteases. Our results help show how cyanophycinase can specifically bind and degrade this important polymer.
  • Uptake of Marasmius oreades agglutinin disrupts integrin-dependent cell adhesion
    Item type: Journal Article
    Juillot, Samuel; Cott, Catherine; Madl, Josef; et al. (2016)
    Biochimica et Biophysica Acta (BBA) - General Subjects
    Background Fruiting body lectins have been proposed to act as effector proteins in the defense of fungi against parasites and predators. The Marasmius oreades agglutinin (MOA) is a lectin from the fairy ring mushroom with specificity for Galα1-3Gal containing carbohydrates. This lectin is composed of an N-terminal carbohydrate-binding domain and a C-terminal dimerization domain. The dimerization domain of MOA shows in addition calcium-dependent cysteine protease activity, similar to the calpain family. Methods Cell detachment assay, cell viability assay, immunofluorescence, live cell imaging and Western blot using MDCKII cell line. Results In this study, we demonstrate in MDCKII cells that after internalization, MOA protease activity induces profound physiological cellular responses, like cytoskeleton rearrangement, cell detachment and cell death. These changes are preceded by a decrease in FAK phosphorylation and an internalization and degradation of β1-integrin, consistent with a disruption of integrin-dependent cell adhesion signaling. Once internalized, MOA accumulates in late endosomal compartments. Conclusion Our results suggest a possible toxic mechanism of MOA, which consists of disturbing the cell adhesion and the cell viability. General significance After being ingested by a predator, MOA might exert a protective role by diminishing host cell integrity.
  • The key to predicting the stability of protein mutants lies in an accurate description and proper configurational sampling of the folded and denatured states
    Item type: Journal Article
    Eichenberger, Andreas P.; van Gunsteren, Wilfred F.; Riniker, Sereina; et al. (2015)
    Biochimica et Biophysica Acta (BBA) - General Subjects
  • A non-covalent "click chemistry" strategy to efficiently coat highly porous MOF nanoparticles with a stable polymeric shell
    Item type: Journal Article
    Aykaç, Ahmet; Noiray, Magali; Malanga, Milo; et al. (2017)
    Biochimica et Biophysica Acta (BBA) - General Subjects
  • Role of leucine zipper-like motifs in the oligomerization of Pseudomonas putida phasins
    Item type: Journal Article
    Tarazona, Natalia A.; Maestro, Beatriz; Revelles, Olga; et al. (2019)
    Biochimica et Biophysica Acta (BBA) - General Subjects
  • Nanodiamonds for bioapplications–specific targeting strategies
    Item type: Journal Article
    Terada, Daiki; Genjo, Takuya; Segawa, Takuya Fabian; et al. (2020)
    Biochimica et Biophysica Acta (BBA) - General Subjects
    Background Nanodiamonds (NDs) provide a unique multitasking system for drug delivery and fluorescent imaging in biological environments. Owing to their quantum properties, NDs are expected to be employed as multifunctional probes in the future for the accurate visualization of biophysical parameters such as temperature and magnetic fields. However, the use of NDs for the selective targeting of the biomolecules of interest within a complicated biological system remains a challenge. One of the most promising solutions is the appropriate surface design of NDs based on organic chemistry and biochemistry. The engineered NDs have high biocompatibility and dispersibility in a biological environment and hence undergo cellular uptake through specific pathways. Scope of review This review focuses on the selective targeting of NDs for biomedical and biophysical applications from the viewpoint of ND surface functionalizations and modifications. These pretreatments make possible the specific targeting of biomolecules of interest on or in a cell by NDs via a designed biochemical route. Major conclusions The surface of NDs is covalently or noncovalently modified with silica, polymers, or biomolecules to reshape them, control their size, and enhance the colloidal stability and biomolecular selectivity toward the biomolecules of interest. Electroporation, chemical treatment, injection, or endocytosis are the methods generally adopted to introduce NDs into living cells. The pathway, efficiency, and the cell viability depend on the selected method. General significance In the biomedical field, the surface modification facilitates specific delivery of a drug, leading to a higher therapeutic efficacy. In biophysical applications, the surface modification paves the way for the accurate measurement of physical parameters to gain a better understanding of various cell functions.
Publications 1 - 8 of 8