5,311 research outputs found
Evaluation of a Dual Isolation Width Acquisition Method for Isobaric Labeling Ratio Decompression
No full textIsobaric labeling is a highly precise
approach for protein quantification. However, due to the isolation
interference problem, isobaric tagging suffers from ratio underestimation
at the MS2 level. The use of narrow isolation widths is a rational
approach to alleviate the interference problem; however, this approach
compromises proteome coverage. We reasoned that although a very narrow
isolation window will result in loss of peptide fragment ions, the
reporter ion signals will be retained for a significant portion of
the spectra. On the basis of this assumption, we have designed a dual
isolation width acquisition (DIWA) method, in which each precursor
is first fragmented with HCD using a standard isolation width for
peptide identification and preliminary quantification, followed by
a second MS2 HCD scan using a much narrower isolation width for the
acquisition of quantitative spectra with reduced interference. We
leverage the quantification obtained by the “narrow”
scans to build linear regression models and apply these to decompress
the fold-changes measured at the “standard” scans. We
evaluate the DIWA approach using a nested two species/gene knockout
TMT-6plex experimental design and discuss the perspectives of this
approach
HSP90-CDC37-PP5 forms a structural platform for kinase dephosphorylation.
No full textActivation of client protein kinases by the HSP90 molecular chaperone system is affected by phosphorylation at multiple sites on HSP90, the kinase-specific co-chaperone CDC37, and the kinase client itself. Removal of regulatory phosphorylation from client kinases and their release from the HSP90-CDC37 system depends on the Ser/Thr phosphatase PP5, which associates with HSP90 via its N-terminal TPR domain. Here, we present the cryoEM structure of the oncogenic protein kinase client BRAFV600E bound to HSP90-CDC37, showing how the V600E mutation favours BRAF association with HSP90-CDC37. Structures of HSP90-CDC37-BRAFV600E complexes with PP5 in autoinhibited and activated conformations, together with proteomic analysis of its phosphatase activity on BRAFV600E and CRAF, reveal how PP5 is activated by recruitment to HSP90 complexes. PP5 comprehensively dephosphorylates client proteins, removing interaction sites for regulatory partners such as 14-3-3 proteins and thus performing a 'factory reset' of the kinase prior to release
Secretome of Cancer-Associated Fibroblasts (CAFs) Influences Drug Sensitivity in Cancer Cells.
No full textResistance is a major problem with effective cancer treatment and the stroma forms a significant portion of the tumor mass but traditional drug screens involve cancer cells alone. Cancer-associated fibroblasts (CAFs) are a major tumor stroma component and its secreted proteins may influence the function of cancer cells. The majority of secretome studies compare different cancer or CAF cell lines exclusively. Here, we present the direct characterization of the secreted protein profiles between CAFs and KRAS mutant-cancer cell lines from colorectal, lung, and pancreatic tissues using multiplexed mass spectrometry. 2573 secreted proteins were annotated, and differential analysis highlighted understudied CAF-enriched secreted proteins, including Wnt family member 5B (WNT5B), in addition to established CAF markers, such as collagens. The functional role of CAF secreted proteins was explored by assessing its effect on the response to 97 anticancer drugs since stromal cells may cause a differing cancer drug response, which may be missed on routine drug screening using cancer cells alone. CAF secreted proteins caused specific effects on each of the cancer cell lines, which highlights the complexity and challenges in cancer treatment and so the importance to consider stromal elements
Structural basis for the modulation of MRP2 activity by phosphorylation and drugs.
No full textMultidrug resistance-associated protein 2 (MRP2/ABCC2) is a polyspecific efflux transporter of organic anions expressed in hepatocyte canalicular membranes. MRP2 dysfunction, in Dubin-Johnson syndrome or by off-target inhibition, for example by the uricosuric drug probenecid, elevates circulating bilirubin glucuronide and is a cause of jaundice. Here, we determine the cryo-EM structure of rat Mrp2 (rMrp2) in an autoinhibited state and in complex with probenecid. The autoinhibited state exhibits an unusual conformation for this class of transporter in which the regulatory domain is folded within the transmembrane domain cavity. In vitro phosphorylation, mass spectrometry and transport assays show that phosphorylation of the regulatory domain relieves this autoinhibition and enhances rMrp2 transport activity. The in vitro data is confirmed in human hepatocyte-like cells, in which inhibition of endogenous kinases also reduces human MRP2 transport activity. The drug-bound state reveals two probenecid binding sites that suggest a dynamic interplay with autoinhibition. Mapping of the Dubin-Johnson mutations onto the rodent structure indicates that many may interfere with the transition between conformational states
Lateral Inverse Proximity Effect in Ti/Au Transition Edge Sensors
No full textWe report measured Tc of superconducting Ti/Au bilayer strips with a width W varying from 5 to 50 µm. The strips were fabricated based on a Ti/Au bilayer that consists of a 41-nm-thick Ti layer to which a 280-nm-thick Au layer was added. We find that the Tc drops as W decreases and the declining trend almost perfectly follows Tc/ [mK] = - 738.4 [μ m] 2/ W2+ 91.0 , where Tc(W= ∞) of 91 mK is consistent with the intrinsic Tc of the bilayer. The result is interpreted as a consequence of the lateral inverse proximity effect originated in normal-metal microstructures, namely Au overhangs that exist at the edges of the Ti/Au bilayer. The Tc shift from the intrinsic Tc should be anticipated in addition to the longitudinal proximity effect from superconducting Nb leads when one designs Ti/Au TESs.Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.ImPhys/Optic
Proteomic characterisation of triple negative breast cancer cells following CDK4/6 inhibition
No full textWhen used in combination with hormone treatment, Palbociclib prolongs progression-free survival of patients with hormone receptor positive breast cancer. Mechanistically, Palbociclib inhibits CDK4/6 activity but the basis for differing sensitivity of cancer to Palbociclib is poorly understood. A common observation in a subset of Triple Negative Breast Cancers (TNBCs) is that prolonged CDK4/6 inhibition can engage a senescence-like state where cells exit the cell cycle, whilst, remaining metabolically active. To better understand the senescence-like cell state which arises after Palbociclib treatment we used mass spectrometry to quantify the proteome, phosphoproteome, and secretome of Palbociclib-treated MDA-MB-231 TNBC cells. We observed altered levels of cell cycle regulators, immune response, and key senescence markers upon Palbociclib treatment. These datasets provide a starting point for the derivation of biomarkers which could inform the future use CDK4/6 inhibitors in TNBC subtypes and guide the development of potential combination therapies
Structure of a nucleosome-bound MuvB transcription factor complex reveals DNA remodelling
No full textGenes encoding the core cell cycle machinery are transcriptionally regulated by the MuvB family of protein complexes in a cell cycle-specific manner. Complexes of MuvB with the transcription factors B-MYB and FOXM1 activate mitotic genes during cell proliferation. The mechanisms of transcriptional regulation by these complexes are still poorly characterised. Here, we combine biochemical analysis and in vitro reconstitution, with structural analysis by cryo-electron microscopy and cross-linking mass spectrometry, to functionally examine these complexes. We find that the MuvB:B-MYB complex binds and remodels nucleosomes, thereby exposing nucleosomal DNA. This remodelling activity is supported by B-MYB which directly binds the remodelled DNA. Given the remodelling activity on the nucleosome, we propose that the MuvB:B-MYB complex functions as a pioneer transcription factor complex. In this work, we rationalise prior biochemical and cellular studies and provide a molecular framework of interactions on a protein complex that is key for cell cycle regulation
Citrobacter rodentium induces rapid and unique metabolic and inflammatory responses in mice suffering from severe disease.
No full textThe mouse pathogen Citrobacter rodentium is used to model infections with enterohaemorrhagic and enteropathogenic Escherichia coli (EHEC and EPEC). Pathogenesis is commonly modelled in mice developing mild disease (e.g., C57BL/6). However, little is known about host responses in mice exhibiting severe colitis (e.g., C3H/HeN), which arguably provide a more clinically relevant model for human paediatric enteric infection. Infection of C3H/HeN mice with C. rodentium results in rapid colonic colonisation, coinciding with induction of key inflammatory signatures and colonic crypt hyperplasia. Infection also induces dramatic changes to bioenergetics in intestinal epithelial cells, with transition from oxidative phosphorylation (OXPHOS) to aerobic glycolysis and higher abundance of SGLT4, LDHA, and MCT4. Concomitantly, mitochondrial proteins involved in the TCA cycle and OXPHOS were in lower abundance. Similar to observations in C57BL/6 mice, we detected simultaneous activation of cholesterol biogenesis, import, and efflux. Distinctly, however, the pattern recognition receptors NLRP3 and ALPK1 were specifically induced in C3H/HeN. Using cell-based assays revealed that C. rodentium activates the ALPK1/TIFA axis, which is dependent on the ADP-heptose biosynthesis pathway but independent of the Type III secretion system. This study reveals for the first time the unfolding intestinal epithelial cells' responses during severe infectious colitis, which resemble EPEC human infections
Revealing the influence of Mo addition on interphase precipitation in Ti-bearing low carbon steels
No full textMo is widely used as an effective microalloying element to improve mechanical performance of interphase precipitation steels, but the precise role of Mo in interphase precipitation behavior is not fully understood. In this contribution, interphase precipitation behavior in a series of Ti-Mo-bearing low carbon steels is systematically studied, and the role of Mo in interphase precipitates and its coarsening behavior is revisited. It is found that (Ti, Mo)C precipitates instead of TiC are formed in the Mo-containing alloys, and the average site fraction of Mo in (Ti, Mo)C is almost independent of the bulk Mo content. Moreover, the number density of interphase precipitates can be substantially enhanced by a minor addition of Mo, albeit it does not further rise with increasing the bulk Mo content. This is because the Mo fraction in (Ti, Mo)C rather than the bulk Mo content governs the driving force for precipitation nucleation and the interfacial energy of the (Ti, Mo)C/α and (Ti, Mo)C/γ interfaces. In addition to the reduced interfacial energy, decrease of Ti trans-interface diffusivity has been identified as another key reason for the enhanced carbide coarsening resistance in Mo-containing alloys.Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.Novel Aerospace Material
A redox switch in p21-CDK feedback during G2 phase controls the proliferation-cell cycle exit decision.
No full textReactive oxygen species (ROS) influence cell proliferation and fate decisions by oxidizing cysteine residues (S-sulfenylation) of proteins, but specific targets and underlying regulatory mechanisms remain poorly defined. Here, we employ redox proteomics to identify cell-cycle-coordinated S-sulfenylation events and investigate their functional role in proliferation control. Although ROS levels rise during cell cycle progression, the overall oxidation of the proteome remains constant, with dynamic S-sulfenylation restricted to a subset of cysteines. Among these, we identify a critical redox-sensitive cysteine residue (C41) in the cyclin-dependent kinase (CDK) inhibitor p21. C41 oxidation regulates the interaction of p21 with CDK2 and CDK4, controlling a double-negative feedback loop that determines p21 stability. When C41 remains reduced, p21's half-life increases in the G2 phase, resulting in more p21 inheritance to daughter cells, suppressing proliferation and promoting senescence after irradiation. Notably, we identify dynamic S-sulfenylation on further cell cycle regulators, implying coordination of cell cycle and redox control
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