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Proteins are typically targeted to the proteasome for degradation through the attachment of ubiquitin chains and the proteasome initiates degradation at a disordered region within the target protein. Yet some proteins with ubiquitin chains and disordered regions escape degradation. Here we investigate how the position of the ubiquitin chain on the target protein relative to the disordered region modulates degradation and show that the distance between the two determines whether a protein is degraded efficiently. This distance depends on the type of the degradation tag and is likely a result of the separation on the proteasome between the receptor that binds the tag and the site that engages the disordered region.
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http://dx.doi.org/10.1101/2023.08.08.552540 | DOI Listing |
Open Res Eur
July 2025
REQUIMTE LAQV Porto, Porto, Porto District, Portugal.
The 2024 Nobel Prizes in Chemistry and Physics mark a watershed moment in the convergence of artificial intelligence (AI) and molecular biology. This article explores how AI, particularly deep learning and neural networks, has revolutionized protein science through breakthroughs in structure prediction and computational design. It highlights the contributions of 2024 Nobel laureates John Hopfield, Geoffrey Hinton, David Baker, Demis Hassabis, and John Jumper, whose foundational work laid the groundwork for AI tools such as AlphaFold.
View Article and Find Full Text PDFAdv Mater
September 2025
Research Center for Crystal Materials, CAS Key Laboratory of Functional Materials and Devices for Special Environmental Conditions, Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Urumqi, 830011, P. R. China.
The generation of coherent deep-ultraviolet (DUV) radiation via nonlinear frequency conversion remains a major scientific and technological challenge in modern optics. To date, only a very limited number of nonlinear optical (NLO) crystals-such as KBBF, ABF, and quartz-have been experimentally demonstrated to support measurable direct second-harmonic generation (SHG) at wavelengths of 177 nm or shorter. There is a pressing need to develop alternative materials or strategies that enable efficient frequency conversion in the DUV region.
View Article and Find Full Text PDFCell Rep
September 2025
Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA. Electronic address:
RNA polymerase II (RNAPII) is regulated by sequence-specific transcription factors (TFs) and the pre-initiation complex (PIC): TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIH, and Mediator. TFs, Mediator, and RNAPII contain intrinsically disordered regions (IDRs) and form phase-separated condensates, but how IDRs control RNAPII function remains poorly understood. Using purified PIC factors, we developed a real-time in vitro fluorescence transcription (RIFT) assay for second-by-second visualization of transcription at hundreds of promoters simultaneously.
View Article and Find Full Text PDFJ Mol Biol
September 2025
Department of Biochemistry and Biophysics Oregon State University, Corvallis, Oregon, USA. Electronic address:
Ferlins are vesicle trafficking proteins composed of folded C2 domains conjugated by linkers which are largely disordered. Although a role for the C2 domains as calcium sensors has been established it remains unclear whether the linkers function beyond acting as passive spacers. We examined the C2A-C2B linker sequences of vertebrate ferlins and found both putative short linear motifs (SLiMs) as well as membrane binding sequences for members of the protein family.
View Article and Find Full Text PDFAdv Biol Regul
September 2025
Laboratory of Cancer Cell Architecture, Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic. Electronic address:
Biomolecular condensates (BMCs) are membrane-less organelles formed through liquid-liquid phase separation, primarily driven by multivalent interactions between scaffold and client molecules. These dynamic compartments enable cells to spatially and temporally organize biochemical reactions by locally concentrating specific biomolecules, thereby enhancing the frequency of productive molecular interactions and increasing reaction rates. BMCs are integral to normal cellular physiology, with well-characterized examples including the nucleolus and Cajal bodies.
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