Publications by authors named "Luciano Di Stefano"
Article Synopsis
- Data-Independent Acquisition (DIA) enhances co-immunoprecipitation analysis by reducing quantitation variability and improving the detection of specific interactors compared to Data-Dependent Acquisition (DDA).
- A comparison of DIA and DDA across various bioinformatics workflows revealed that DIA can effectively generate spectral libraries without needing separate DDA experiments, and software struggles with indistinct signals from mock pull-downs.
- Spectronaut and DIA-NN provided the best control of coefficient of variation in protein quantification, while using DIA for both building spectral libraries and quantifying proteins leads to more consistent results and fewer missing values.
Article Synopsis
- - Immunoprecipitation (IP) paired with mass spectrometry is a powerful method for mapping how proteins interact, especially when using tagged cell collections, but many protein interactions remain unexplored due to limitations in current high-throughput techniques.
- - A major challenge in IP is maintaining stable interactions when transferring samples, as this can result in losing real interactions and failing to identify them later.
- - The authors developed a high-content screening approach that investigates how different chemical conditions affect IP results, allowing for quick optimization of methods to better capture protein complexes.
Article Synopsis
- The LINE-1 retrotransposon is a significant genetic element in humans, contributing to about a third of our genome via a 'copy and paste' method driven by its enzyme, ORF2p, which is linked to diseases like cancer and autoimmunity.
- Recent studies using X-ray crystallography and cryo-electron microscopy have revealed new structural details of ORF2p, including previously unknown domains and a dynamic conformation that changes during the retrotransposition process.
- The findings enhance our understanding of L1 replication and its effects on immune responses, creating potential pathways for drug development targeting L1 and related cellular processes.
Inorganic materials depleted of heavy stable isotopes are known to deviate strongly in some physicochemical properties from their isotopically natural counterparts. Here we explored for the first time the effect of simultaneous depletion of the heavy carbon, hydrogen, oxygen and nitrogen isotopes on the bacterium E. coli and the enzymes expressed in it.
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- LINE-1 (L1) retrotransposons create diverse ribonucleoproteins (RNPs) during their replication and the host's efforts to limit them, but their exact makeup is still not well understood.
- The composition of L1-associated macromolecules varies according to factors like the L1 life cycle stage, whether it’s dealt with productively or suppressed, and the specific cell type involved.
- This chapter presents techniques for identifying and analyzing the protein and RNA components of L1 macromolecules from tissues, using embryonal carcinoma cell lines (like N2102Ep) and colorectal cancer tissues as primary examples.
Article Synopsis
- * Targeting ATM, ATR, or DNA topoisomerases can cause significant aggregation of proteins, particularly those prone to aggregation such as Huntingtin with an expanded polyglutamine repeat, due to a breakdown in cellular chaperone systems.
- * Inhibition of the HSP70 chaperone system worsens protein aggregation, while the chaperone HSPB5 can help suppress this aggregation, indicating a connection between genotoxic stress and protein aggregation similar to conditions seen in protein-related diseases.
Fast photochemical oxidation of proteins (FPOP) is a MS-based method that has proved useful in studies of protein structures, interactions, conformations, and protein folding. The success of this method relies on the irreversible labeling of solvent-exposed amino acid side chains by hydroxyl radicals. FPOP generates these radicals through laser-induced photolysis of hydrogen peroxide.
View Article and Find Full Text PDFRadionuclides are increasingly used in hospitals for diagnostic and therapeutic purposes, such as functional research, diagnostic imaging, and in the performance of radioiodine therapy. Their use produces radioactive waste, and risks environmental contamination. The present study involves 486 samples of radioactive waste produced in hospitals in Abruzzo, Italy, during 2000 - 2015.
View Article and Find Full Text PDFDespite significant affinity to carbonyl oxygens, thermal hydrogen atoms attach to unmodified polypeptides at a very low rate, while the hydrogen-hydrogen exchange rate is high. Here, using the novel omnitrap setup, we found that attachment to polypeptides is much more facile when radical site is already present, but the rate decreases for larger radical ions. The likely explanation is the intramolecular hydrogen atom rearrangement in hydrogen-deficient radicals to a more stable or less accessible site.
View Article and Find Full Text PDFIn this paper, the first study of cationic cyanine dye Astrazon Orange-R by combined spectroscopic and theoretical investigation is presented. It is shown that molecular modeling of Astrazon Orange-R is in very good agreement with experiment, allowing us to gain insight into its complicated photophysics. A solvent viscosity controlled relaxation of excited states, involving cyanine isomerization, is also outlined.
View Article and Find Full Text PDF2,4-, 2,5-, 2,6- and 3,5-dihydroxyacetophenone (DHA) used as matrices in matrix-assisted ultraviolet laser desorption/ionization mass spectrometry (UV-MALDI-MS) were studied by steady-state and transient absorption spectroscopy, together with DFT calculations at the B3LYP level of theory. All compounds have low fluorescence quantum yields, possibly due to an efficient excited-state intramolecular proton transfer (ESIPT). Laser flash photolysis (LFP) results showed that, only for 2,4-DHA, a phototautomer could be detected at λ = 400 nm.
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