Bone-like GdF3 was synthesized and applied for phosphopeptide enrichment for the first time. As a new kind of efficient phosphopeptide affinity probe, GdF3 exhibits high efficiency in the mediation of the dephosphorylation reaction. In addition, DFT calculations were introduced to theoretically explain the unique property of GdF3 compared to GdPO4, which is promising and can be potentially significant in protein phosphorylation research.
Histone lysine methylation can be removed by proteins containing JmjC domains in a sequence- and methylation state-specific manner. JARID1B, a protein containing PHD and JmjC domains, is a histone demethylase specific for H3K4me2 and H3K4me3 which requires Fe(II) and α-ketoglutarate (α-KG) as cofactors to remove the methyl group. JARID1B has also been shown to play a critical role in the development of breast cancer. JARID1B contains JmjN, Arid and JmjC domains, a C5HC2 zinc-finger domain and three PHD domains. The first PHD domain (PHD1(JARID1B); residues 306-360) is located at the N-terminus and is important for both histone demethylase activity and histone-tail recognition of JARID1B. Here, the expression, purification and crystallization of PHD1(JARID1B) is reported. A PHD1(JARID1B) crystal was grown by the hanging-drop vapour-diffusion method in reservoir solution consisting of 0.1 M HEPES pH 7.0, 2.2 M ammonium sulfate at 277 K. A zinc SAD data set was collected from a PHD1(JARID1B) crystal. The diffraction pattern of the PHD1(JARID1B) crystal extended to 1.65 Å resolution using synchrotron radiation. The crystal belonged to space group P4(3), with unit-cell parameters a = 51.7, b = 51.7, c = 36.2 Å.
WWP2 is a HECT-domain ubiquitin ligase of the Nedd4 family, which is involved in various important biological processes, such as protein degradation, membrane-protein sorting and transportation, the immune response, pluripotency of embryonic stem cells, tumourigenesis and metastasis. The HECT domain provides the intrinsic ubiquitin ligase activity of WWP2. Here, the expression, purification, crystallization and crystallographic analysis of the HECT domain of human WWP2 (HECT WWP2 ) are reported. HECT WWP2 has been crystallized and the crystals diffracted to 2.50 Å resolution. They belonged to space group P 4 1 2 1 2 and the structure has been solved via molecular replacement. The overall structure of HECT WWP2 has an inverted T-shape. This structure displays a high degree of conservation with previously published structures of Nedd4 subfamily members.
Abstract The 5′-end capping of nascent pre-mRNA represents the initial step in RNA processing, with evidence demonstrating that guanosine addition and 2′-O-ribose methylation occur in tandem with early steps of transcription by RNA polymerase II, especially at the pausing stage. Here, we determine the cryo-EM structures of the paused elongation complex in complex with RNGTT, as well as the paused elongation complex in complex with RNGTT and CMTR1. Our findings show the simultaneous presence of RNGTT and the NELF complex bound to RNA polymerase II. The NELF complex exhibits two conformations, one of which shows a notable rearrangement of NELF-A/D compared to that of the paused elongation complex. Moreover, CMTR1 aligns adjacent to RNGTT on the RNA polymerase II stalk. Our structures indicate that RNGTT and CMTR1 directly bind the paused elongation complex, illuminating the mechanism by which 5’-end capping of pre-mRNA during transcriptional pausing.
Osteoarthritis (OA), a common chronic joint disease, is characterized by cartilage degeneration and subchondral bone reconstruction. NF-κB signaling pathway-activated inflammation and NLRP3-induced pyroptosis play essential roles in the development of OA. In this study, we examine whether paroxetine can inhibit pyroptosis and reduce osteoclast formation, thereby delaying the destruction of knee joints.We employed high-density cultures, along with quantitative polymerase chain reactions and Western blotting techniques, to investigate the effects of paroxetine on extracellular matrix synthesis and degradation. The expression levels of NF-κB and pyroptosis-related signaling pathway proteins were examined by Western blotting and immunofluorescence. Furthermore, the impact of paroxetine on RANKL-induced osteoclast formation was evaluated through TRAP staining and F-actin ring fluorescence detection. To investigate the role of paroxetine in vivo, we constructed a mouse model with destabilization of the medial meniscus (DMM) surgery. Safranin O-Fast Green staining, Hematoxylin-Eosin staining, and immunohistochemistry were conducted to observe the extent of knee joint cartilage deformation. In addition, TRAP staining was used to observe the formation of osteoclasts in the subchondral bone.In the in vitro experiments with ATDC5, paroxetine treatment attenuated IL-1β-induced activation of the pyroptosis-related pathway and suppressed extracellular matrix catabolism by inhibiting the NF-kB signaling pathway. In addition, paroxetine treatment decreased the expression of RANKL-induced osteoclast marker genes and reduced osteoclast formation. In animal experiments conducted in vivo, mice treated with paroxetine exhibited thicker knee cartilage with a smoother surface compared to the DMM group. Additionally, the formation of osteoclasts in the subchondral bone was reduced in the paroxetine-treated mice. Further analysis revealed that paroxetine treatment played a role in preserving the balance of the extracellular matrix and delaying knee joint degeneration.Paroxetine can inhibit pyroptosis and reduce osteoclast formation via inhibiting the NF-κB signaling pathway, suggesting that it may have therapeutic effects in patients with OA.
Background The escalating global burden of diabetes and its associated cognitive impairment underscores the urgency for effective interventions. Bergenin shows promise in regulating glucose metabolism, mitigating inflammation, and improving cognitive function. Zebrafish models offer a unique platform for assessing drug efficacy and exploring pharmacological mechanisms, complemented by subsequent investigations in cell and rat models. Methods The experimental subjects included zebrafish larvae (CZ98: Tg (mpeg1:EGFP) ihb20Tg/+ ), adult zebrafish (immersed in 2% glucose), BV2 cell line (50 mM glucose + 10 μm Aβ 1-42 ), and a streptozotocin (STZ) bilateral intracerebroventricular injection rat model. Bergenin’s effects on the toxicity, behavior, and cognitive function of zebrafish larvae and adults were evaluated. The Morris water maze assessed cognitive function in rats. Neuronal histopathological changes were evaluated using HE and Nissl staining. qPCR and Western blot detected the expression of glycolysis enzymes, inflammatory factors, and Bergenin’s regulation of PPAR/NF-κB pathway in these three models. Results 1) In zebrafish larvae, Bergenin interventions significantly reduced glucose levels and increased survival rates while decreasing teratogenicity rates. Microglial cell fluorescence in the brain notably decreased, and altered swimming behavior tended to normalize. 2) In adult zebrafish, Bergenin administration reduced BMI and blood glucose levels, altered swimming behavior to slower speeds and more regular trajectories, enhanced recognition ability, decreased brain glucose and lactate levels, weakened glycolytic enzyme activities, improved pathological changes in the telencephalon and gills, reduced expression of pro-inflammatory cytokines, decreased ins expression and increased expression of irs1 , irs2a , and irs2b , suggesting a reduction in insulin resistance. It also altered the expression of pparg and rela . 3) In BV2 cell line, Bergenin significantly reduced the protein expression of glycolytic enzymes (GLUT1, HK2, PKFKB3, and PKM2), lowered IL-1β, IL-6, and TNF-α mRNA expression, elevated PPAR-γ protein expression, and decreased P-NF-κB-p65 protein expression. 4) In the rat model, Bergenin improves learning and memory abilities in STZ-induced rats, mitigates neuronal damage in the hippocampal region, and reduces the expression of inflammatory factors IL-1β, IL-6, and TNF-α. Bergenin decreases brain glucose and lactate levels, as well as glycolytic enzyme activity. Furthermore, Bergenin increases PPARγ expression and decreases p-NF-κB p65/NF-κB p65 expression in the hippocampus. Conclusion Bergenin intervenes through the PPAR-γ/NF-κB pathway, redirecting glucose metabolism, alleviating inflammation, and preventing high glucose-induced neuronal damage.
Abstract DNMT1 is an important epigenetic regulator that plays a key role in the maintenance of DNA methylation. Here we determined the crystal structure of DNMT1 in complex with USP7 at 2.9 Å resolution. The interaction between the two proteins is primarily mediated by an acidic pocket in USP7 and Lysine residues within DNMT1’s KG linker. This intermolecular interaction is required for USP7-mediated stabilization of DNMT1. Acetylation of the KG linker Lysine residues impair DNMT1–USP7 interaction and promote the degradation of DNMT1. Treatment with HDAC inhibitors results in an increase in acetylated DNMT1 and decreased total DNMT1 protein. This negative correlation is observed in differentiated neuronal cells and pancreatic cancer cells. Our studies reveal that USP7-mediated stabilization of DNMT1 is regulated by acetylation and provide a structural basis for the design of inhibitors, targeting the DNMT1–USP7 interaction surface for therapeutic applications.
Abstract Nascent pre-mRNA undergoes 5′ end capping as the first step of processing. Early evidences demonstrated the guanosine addition and 2′-O-ribose methylation spatiotemporally correlated with transcription machinery at the early stage of transcription. Here, we determined cryo-EM structures of PEC (paused elongation complex)-RNGTT (RNA guanylyltransferase and 5′ phosphatase) and PEC-RNGTT-CMTR1 (cap-specific mRNA (nucleoside-2′-O-)-methyltransferase). The structures show that RNGTT docks to the root of Pol II stalk through its OB fold. Within RNGTT, the OB fold binds N-terminal of triphosphatase domain and facilitates positioning its catalytic cavity facing towards the RNA exit tunnel. RNGTT dephosphorylates and guanylates PEC-bound RNAs of 17nt, 19nt, 20nt, but not 22nt, in length. CMTR1 arrayed with RNGTT on the Pol II surface through distinct interfaces. Our structures unravel that capping enzymes RNGTT and CMTR1 directly docks to paused elongation complex, and shed light on how pre-mRNA capping couples with Pol II at the specific transcription stage.
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