mant atpγs  (Jena Bioscience)

Journal: bioRxiv

Article Title: Linking the kinetic mechanism to structural dynamics required for nucleotide hydrolysis by an alphavirus nsP2 RNA helicase

doi: 10.64898/2026.05.08.723793

Figure Lengend Snippet: (A) Chemical structure of ′(3′)-O-(N-methyl-anthraniloyl) ATPγS (mant-ATPγS). (B) ATPγS is not hydrolyzed by nsP2. Under the conditions tested, 50 nM nsP2 converted ∼80% of 1 mM ATP to ADP within 30 minutes, whereas no detectable hydrolysis of 1 mM ATPγS was observed after 120 minutes. No luminescence signal was detected in reactions containing ATP or ATPγS in the absence of enzyme (data not shown). (C) Representative tryptophan to mant FRET emission spectra collected using excitation at 80 nm. nsP2 alone (1 μM) exhibits an emission peak at 350 nm, whereas mant-ATPγS alone (10 μM) shows weak emission at 445 nm under 280-nm excitation. Addition of mant-ATPγS to nsP2 products an increase in 445-nm emission, consistent with FRET arising from formation of the nsP2·mant-ATPγS complex. Data in panels D-G were generated by subtracting mant-ATPγS-only emission at 445 nm from spectra collected in the presence of nsP2. (D) Direct binding of mant-ATPγS to nsP2. ns2P (0. 25 μM) was titrated with 0.002 5 μM mant-ATPγS. Data represent mean ± SD ( n = 3). (E-G) Competitive binding experiments. nsP2 (0. 5 μM) was incubated with 0.1 μM mant-ATPγS and increasing concentrations of unlabeled competitor. ATPγS (E; 0-10 μM), ADP (F; 0-9 mM), or inorganic phosphate (Pi) and tripolyphosphate (TPP) (G; 0-40 mM) were added as indicated. Fluorescence data in panels E and F were normalized to percent relative fluorescence, with the signal in the absence of competitor defined as 100%. Data were fit by nonlinear regression, and IC₅₀ values were converted to inhibition constants ( K i ) using the Cheng-Prusoff equation.

Article Snippet: Mant-ATP and mant-ATPγS were from Jena Bioscience.

Techniques: Generated, Binding Assay, Incubation, Fluorescence, Inhibition

Journal: bioRxiv

Article Title: Linking the kinetic mechanism to structural dynamics required for nucleotide hydrolysis by an alphavirus nsP2 RNA helicase

doi: 10.64898/2026.05.08.723793

Figure Lengend Snippet: (A) Exp rimental design for ATPγS association kinetics. nsP2 was rapidly mixed with mant-ATPγS under stopped-flow conditions, and binding was monitored by tryptophan-to-mant FRET. (B) ATPγS association kinetics. Representative fluorescence time courses following rapid mixing of mant-ATPγS (0.1 μM) with increasing concentrations of nsP2 (0.5-3 μM). (C) Observed rate constants ( k obs ) extracted from single-phase fits to the association traces in panel B were replotted as a function of nsP2 concentration (n = 3 independent experiments). Linear regression was used to determine the second-order association rate constant ( k ₒₙ). (D) Experimental design for ATPγS dissociation kinetics. Pre-formed nsP2·mant-ATPγS complexes were rapidly mixed with excess unlabeled ATPγS to initiatw ligand displacement. (E) ATPγS dissociation kinetics. Time-dependent loss of sensitized Mant fluorescence following competition with unlabeled ATPγS. Traces were fit to a two-phase exponential decay, revealing fast and slow dissociation components ( k off,fast and k off,slow ). (F) Experimental design for ATP dissociation in the presence of inhibitor. Pre-formed nsP2·mant-ATP complexes were rapidly mixed with excess unlabeled ATP in the presence of the nsP2 inhibitor RA-NSP2- (5 μM). (G) ATP dissociation kinetics in the presence of inhibitor. Representative fluorescence decay trace fit to a single-phase exponential model, yielding the apparent ATP dissociation rate constant ( k off ).

Article Snippet: Mant-ATP and mant-ATPγS were from Jena Bioscience.

Techniques: Binding Assay, Fluorescence, Concentration Assay

Journal: bioRxiv

Article Title: Linking the kinetic mechanism to structural dynamics required for nucleotide hydrolysis by an alphavirus nsP2 RNA helicase

doi: 10.64898/2026.05.08.723793

Figure Lengend Snippet:

Article Snippet: Mant-ATP and mant-ATPγS were from Jena Bioscience.

Techniques: Binding Assay, Fluorescence, Concentration Assay

Journal: Aging Cell

Article Title: Aging Triggers an Intestinal Energy Crisis and HDL3 Deficiency Disrupting Gut–Liver Axis Homeostasis

doi: 10.1111/acel.70445

Figure Lengend Snippet: Mitochondrial dysfunction‐mediated ATP deficiency suppresses HDL3 synthesis in aging intestinal cells. (a) Representative images (scale bar: 5 μm) of intestinal cell microstructure measured by TEM, n = 18 images from n = 3 independent experiments; (b) ileum ATP levels, n = 5; (c) representative images (scale bar: 5 μm) of IME microstructure measured by TEM, n = 18 images from n = 3 independent experiments; (d) IME ATP levels, n = 5; (e) glycolysis assay measured as cytoplasmic acidification, the fluorescence signal was enhanced with the increase of acidification degree, n = 4; (f) oxygen consumption, as mitochondrial respiration depletes the oxygen within the assay medium, quenching of the fluorescent dye is reduced, and the fluorescence signal increases proportionately, n = 4; (g, h) OXPHOS protein expression levels in the ileum, n = 3; and (i) exogenous ATPγS‐AM (50 μM) partially restored HDL3 synthesis in senescent IME cells, whereas native ATP (50 μM) had no significant effect, n = 5. Data are express as the mean ± SEM. * p < 0.05, ** p < 0.01. D‐Gal: D‐galactose; NC, normal control.

Article Snippet: In the normal control groups (10 replicates), the medium was replaced with complete DMEM, whereas in the model control groups (10 replicates), the medium was replaced with D‐galactose (200 mM, dissolved in complete DMEM) and cultured for 24 h. After successful establishment of the aging model, the medium was discarded, and the model control group (D‐Gal) (replaced with complete DMEM containing ApoA1 10 μg/mL), ATP intervention group (D‐Gal‐ATP) was replaced with complete DMEM containing ApoA1 10 μg/mL and ATP 50 μM, ATPγS‐AM intervention group (D‐Gal‐ATPγS‐AM) was replaced with complete DMEM containing ApoA1 10 μg/mL and ATPγS‐AM 50 μM, NMN intervention group (D‐Gal‐NMN) was replaced with complete DMEM containing ApoA1 10 μg/mL and NMN 5 μM, the agonist CS‐6253 (MedChem Express, Shanghai, China) intervention group (D‐GAL‐CS‐6253) was replaced with complete DMEM containing ApoA1 10 μg/mL and CS‐6253 1 μM; and the NMN and CS‐6253 synergistic group (D‐Gal‐NMN‐CS‐6253) was replaced with complete DMEM containing ApoA1 10 μg/mL, NMN 5 μM, and CS‐6253 1 μM.

Techniques: Fluorescence, Expressing, Control

Journal: Aging Cell

Article Title: Aging Triggers an Intestinal Energy Crisis and HDL3 Deficiency Disrupting Gut–Liver Axis Homeostasis

doi: 10.1111/acel.70445

Figure Lengend Snippet: ABCA1 downregulation limits HDL3 synthesis in aging. (a) Relative mRNA expression of ABCA1 , ApoA1 , LPL , and ANGPTL3 in ileum, n = 5; (b, c) representative images (scale bar: 50 μm) and quantitative analysis of ABCA1, ApoA1, LPL, and ANGPTL3, measured by IHC staining, n = 3; and (d) activation of ABCA1 expression combined with ATPγS‐AM supplementation enhances cellular HDL3 synthesis capacity n = 5. Data are express as the mean ± SEM. ** p < 0.01. ABCA1, ATP‐binding cassette transporter 1; ANGPTL3, angiopoietin‐like3; CS‐6253, ABCA1 activators; D‐Gal, D‐galactose; HDL3, high‐density lipoprotein 3; IHC, immunohistochemistry; IME, intestinal mucosa epithelial; LPL, lipoprotein lipase; NC, normal control.

Article Snippet: In the normal control groups (10 replicates), the medium was replaced with complete DMEM, whereas in the model control groups (10 replicates), the medium was replaced with D‐galactose (200 mM, dissolved in complete DMEM) and cultured for 24 h. After successful establishment of the aging model, the medium was discarded, and the model control group (D‐Gal) (replaced with complete DMEM containing ApoA1 10 μg/mL), ATP intervention group (D‐Gal‐ATP) was replaced with complete DMEM containing ApoA1 10 μg/mL and ATP 50 μM, ATPγS‐AM intervention group (D‐Gal‐ATPγS‐AM) was replaced with complete DMEM containing ApoA1 10 μg/mL and ATPγS‐AM 50 μM, NMN intervention group (D‐Gal‐NMN) was replaced with complete DMEM containing ApoA1 10 μg/mL and NMN 5 μM, the agonist CS‐6253 (MedChem Express, Shanghai, China) intervention group (D‐GAL‐CS‐6253) was replaced with complete DMEM containing ApoA1 10 μg/mL and CS‐6253 1 μM; and the NMN and CS‐6253 synergistic group (D‐Gal‐NMN‐CS‐6253) was replaced with complete DMEM containing ApoA1 10 μg/mL, NMN 5 μM, and CS‐6253 1 μM.

Techniques: Expressing, Immunohistochemistry, Activation Assay, Binding Assay, Control

Journal: bioRxiv

Article Title: The vacuolar tauopathy-associated mutation D395G confers redox sensitivity to p97/VCP

doi: 10.64898/2026.04.16.718620

Figure Lengend Snippet: a, Domain structure of p97, highlighting the D395G mutation located in the D1 domain. b, Schematic representation of preparation of ubiquitinated Ub₄-mEOS3.2 for the p97 substrate unfolding assay (top). Green Ub₄-mEOS3.2 was polyubiquitinated using E1, E2-25K, and ubiquitin, and subsequently photoconverted to its red form under UV illumination, as previously described . The purified substrate was then used in unfolding assays in the presence of the Ufd1-Npl4 complex. Compared with p97 WT (grey), p97 D395G (blue) exhibits reduced substrate unfolding activity (bottom). All measurements were performed with at least three technical replicates. c, NMR characterization of p97 D395G using the ND1L construct, comprising the NTD, D1 domain and linker. Key probes for NTD conformation and bound nucleotide are indicated in the schematic above. ATPγS induces an NTD ‘up’ conformation, similar to p97 WT . In the presence of ADP and the ATP reg , predominantly ‘down’ with a minor ‘up’ conformation is observed, in contrast to p97 WT . For comparison, spectra of the prototypical MSP-1-associated mutant p97 R95G in presence of ADP are shown, which display signals at an averaged position between NTD ‘up’ and ‘down’ conformation, indicating fast conformational exchange on the NMR time scale. This establishes that p97 D395G displays distinct molecular defects from MSP-1-type mutants. d, Cryo-EM reconstructions of p97 D395G under different conditions (ATPγS, ATP reg , and ADP). The N-terminal domain (NTD) is colored grey, and the D1 and D2 ATPase domains are shown in blue. Schematic representations on the left indicate the corresponding nucleotide-bound states. e, Backbone RMSD of a p97 D395G protomer relative to p97 WT in different nucleotide states, calculated without the NTD. p97 D395G structures in ATPγS (PDB: 28VN), ADP (PDB: 28VL), and ADP.P i (PDB: 28XW) states were aligned using the main chain atoms of the D1 and D2 domains to the published p97 WT models in the ATPγS (PDB: 5FTN), ADP (PDB: 5FTK), and ADP.P i (PDB: 8OOI) states, respectively. The inset shows a magnified view of the α 5 helix in the D2 domain of p97 D395G in ADP.P i state.

Article Snippet: Nucleotide states were prepared with 5 mM ADP, or 5 mM ATPγS (Jena Bioscience, Jena, Germany) with 4 mM MgCl 2 , respectively.

Techniques: Mutagenesis, Ubiquitin Proteomics, Purification, Activity Assay, Construct, Comparison, Cryo-EM Sample Prep