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The N-terminal transactivation domain (TAD) of p53 is a disordered region with multiple phosphorylation sites. Phosphorylation at Thr18 is crucial for the release of p53 from its negative regulator, MDM2. In stressed cells, CK1δ is responsible for phosphorylating Thr18, but requires Ser15 to be phosphorylated. To understand the mechanistic underpinnings of this sequential phosphorylation, molecular modeling and molecular dynamics simulation studies of these phosphorylation events were carried out. Our models suggest that a positively charged region on CK1δ near the adenosine triphosphate (ATP) binding pocket, which is conserved across species, sequesters the negatively charged pSer15, thereby constraining the positioning of the rest of the peptide, such that the side chain of Thr18 is positioned close to the γ-phosphate of ATP. Furthermore, our studies show that the phosphorylated p53 TAD1 (p53pSer15) peptide binds more strongly to CK1δ than does p53. p53 adopts a helical structure when bound to CK1δ, which is lost upon phosphorylation at Ser15, thus gaining higher flexibility and ability to morph into the binding site. We propose that upon phosphorylation at Ser15 the p53 TAD1 peptide binds to CK1δ through an electrostatically driven induced fit mechanism resulting in a flanking fuzzy complex.
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http://dx.doi.org/10.1002/prot.26393 | DOI Listing |
Biosens Bioelectron
September 2025
Department of Biological Sciences, Faculty of Science, National University of Singapore, 117543, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore; Precision Medicine Translational Research Programme (TRP), Yong Loo Lin School
DNAzymes possessing kinase-like activities have long held theoretical promise, yet their practical implementation has remained significantly limited. Notably, DNAzyme kinase 1 (DK1), discovered over two decades ago, exhibits a unique self-phosphorylation capability upon encountering specific substrates like ATP, but its broad-based and programmable applications have not yet been fully realized. In this study, we innovatively couple DK1's autophosphorylation mechanism with the PfAgo to establish a novel programmable cascade sensing platform named RASTEN (Robust pfAgo-based Strategy for POC Testing Non-nucleic Acid and Nucleic Acid).
View Article and Find Full Text PDFACS Chem Biol
September 2025
Institute for Biomedicine and Glycomics, Griffith University, Queensland, 4111 Brisbane, Australia.
Small-molecule metabolic chemical probes are tailored chemical biology tools that are designed to detect and visualize biological processes within a cell or an organism. Nucleoside analogues are a subset of metabolic probes that enable the study of DNA synthesis, proliferation kinetics, and cell cycle progression. However, most available nucleoside analogue probes have been designed for use in mammalian cells, limiting their use in other species, where there are metabolic pathway differences.
View Article and Find Full Text PDFPhysiol Rep
September 2025
Division of Pulmonary, Critical Care, Sleep, and Allergy Medicine, University of Arizona, Tucson, Arizona, USA.
Post-acute sequelae of SARS-CoV-2 (PASC or "long COVID") and chronic fatigue syndrome/myalgic encephalitis (CFS/ME) share symptoms such as exertional dyspnea. We used exercise oxygen pathway analysis, comprising six parameters of oxygen transport and utilization, to identify limiting mechanisms in both conditions. Invasive cardiopulmonary exercise testing was performed on 15 PASC patients, 11 CFS/ME patients, and 11 controls.
View Article and Find Full Text PDFCrit Rev Biochem Mol Biol
August 2025
Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL, USA.
The aerobic respiratory chain is vital to bacterial and eukaryotic cell energy transformation. Embedded in the mitochondrial inner membrane and the bacterial plasma membrane, the respiratory chain couples sequential redox reactions with ion pumping, thereby generating the motive force that is used to drive ATP synthesis. Due to the essential role of oxidative phosphorylation in cellular life, the electron transport chain proteins, their cofactors, and ATP synthase components serve as a target for antibacterial, antifungal, and antiparasitic drugs.
View Article and Find Full Text PDFCell
August 2025
Department of Modomics Biology and Medicine, Institute of Development, Aging and Cancer (IDAC), Tohoku University, Sendai 980-8575, Japan; Department of Modomics Pharmacology, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan. Electronic address: fanyan.wei.d3@toh
RNA contains diverse post-transcriptional modifications, and its catabolic breakdown yields numerous modified nucleosides requiring correct processing, but the mechanisms remain unknown. Here, we demonstrate that three RNA-derived modified adenosines, N-methyladenosine (mA), N,N-dimethyladenosine (mA), and N-isopentenyladenosine (iA), are sequentially metabolized into inosine monophosphate (IMP) to mitigate their intrinsic cytotoxicity. After phosphorylation by adenosine kinase (ADK), they undergo deamination by adenosine deaminase-like (ADAL).
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