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Proteomics-based scoring of cellular response to stimuli for improved characterization of signaling pathway activity
Proteomics. 2023. Vol. 53. No. 5. Article 2200275.
Kazakova E., Solovyeva E., Levitsky L., Bubis J., Emekeeva D., Antonets A., Alexey A. Nazarov, Gorshkov M., Tarasova I.
Omics technologies focus on uncovering the complex nature of molecular mechanisms in cells and organisms, including biomarkers and drug targets discovery. Aiming at these tasks, we see that information extracted from omics data is still underused. In particular, characteristics of differentially regulated molecules can be combined in a single score to quantify the signaling pathway activity. Such a metric can be useful for comprehensive data interpretation to follow: (1) developing molecular responses in time; (2) potency of a drug on a certain cell culture; (3) ranking the signaling pathway activity in stimulated cells; and (4) integration of the omics data and assay-based measurements of cell viability, cytotoxicity, and proliferation. With recent advances in ultrafast mass spectrometry for quantitative proteomics allowing data collection in a few minutes, proteomics score for cellular response to stimuli can become a fast, accurate, and informative complement to bioassays. Here, we utilized an interquartile-based selection of differentially regulated features and a variety of schemes for quantifying cellular responses to come up with the quantitative metric for total cellular response and pathway activity. Validation was performed using antiproliferative and virus assays and label-free proteomics data collected for cancer cells subjected to drug stimulation.
Budkov Y., Kalikin N., Journal of Chemical Physics 2026 Vol. 165 Article 064506
A self-consistent statistical-mechanical theory of the Hall effect in electrolyte solutions is developed by extending the self-consistent Debye–Hückel–Onsager (SCDHO) framework to crossed electric and magnetic fields. The theory incorporates non-local ionic charge distributions via Slater-type form factors, regularizing the Coulomb interaction at short range, and accounts for dielectric friction through ion-specific coefficients, employing experimental values ...
Added: August 12, 2026
Voropaeva D., S. Novikova, I. Stenina et al., Solid State Ionics 2026 Vol. 445 Article 117288
Composite gel polymer electrolytes based on a perfluorinated sulfonic acid cation-exchange MF-4SC membrane
containing surface-sulfonated nanoparticles of aluminum oxide, cerium (IV) oxide, and titanium oxide (sAl2O3,
sCeO2, and sTiO2, respectively) were prepared by casting from a dispersion in N,N-dimethylformamide and
plasticized with a 1,3-dioxolane/1,2-dimethoxyethane mixture. The influence of the filler nature on ionic conductivity,
solvent uptake, activation energy, lithium ...
Added: July 30, 2026
Korogod D., Shapeev A., Ivan S. Novikov, Physical Review B: Condensed Matter and Materials Physics 2026 Vol. 114 No. 2 Article 024104
We present two models with explicit long-range electrostatics in the form of Coulomb interactions. Both models include point charges depending on their local atomic environments, and the second model also conserves a total charge of an atomic system. We combine the proposed long-range models with the local moment tensor potential (MTP) and demonstrate that they ...
Added: July 22, 2026
Moshkina E., Molokeev M., Zolotov A. et al., Journal of Alloys and Compounds 2026 Vol. 1077 Article 189412
A wide series of substitutions in a subsystem of small radii cations M = Al, Cr, Fe, Ga, Sc is possible in rare-earth borates ReM3(BO3)4 with the huntite structure. However, the existence of these compounds where M = Mn still raises doubts. The study presents a synthetic approach developed in the framework of the flux method allowing for the required ...
Added: June 29, 2026
Schneider M., Zaripov D., Dokin R. et al., Journal of Chemical Theory and Computation 2026 Vol. 22 No. 9 P. 4405–4414
Density functional theory (DFT) is the workhorse of modern reactions and materials modeling. While the exact functional remains unknown, many approximations to it have been constructed either by hand-crafting functional forms to satisfy exact constraints or by machine learning. In this work, we show how both of these approaches can be fused to build both ...
Added: June 26, 2026
Laurinavichyute V., Levin E. E., Mironkova A. A. et al., Surfaces and Interfaces 2026 Vol. 81 Article 108389
In this work we characterize mixed Mo-W acidic deposition solutions with Mo content ranging from 0 to 100 mol.% by Raman and UV–Vis spectroscopy. The obtained distribution diagram of mixed isopolyanions allows one to explain the observed change in film deposition rate with increase in Mo content. It was found that the initial decrease in ...
Added: June 24, 2026
Filippova A. V., Yurchenko N. Y., Smirnov S. A. et al., Journal of Alloys and Compounds 2026 No. 1074 Article 189162
This study investigates the effects of post-processing heat treatment at 300–500 °C on the microstructure, hardness, and tensile properties of laser powder bed fusion (PBF-LB) processed Al-bronze processed with energy densities (ED) in the range of 125–938 J/mm3. In the as-printed state, sharp needle-like α + β′ laths form at lower ED whereas with increasing ED, the β′ ...
Added: June 12, 2026
Obijiofor O., Novikov A., New Journal of Chemistry 2026 Vol. 50 No. 23 P. 9749–9768
Rational design of gold-based nanocarriers for neurotherapeutics requires atomic-scale understanding of drug-material interactions. Density functional theory calculations were performed to investigate levodopa (L-DOPA) adsorption on small gold clusters (Au2–Au4) with cationic, neutral, and anionic charges, with additional validation on a larger Au10 cluster using multiple low-energy isomers. Binding free energies (ΔGbind), charge transfer, and electronic descriptors ...
Added: June 3, 2026
Das A., Saikia J., Maji N. et al., ChemNanoMat 2026 Vol. 12 No. 5 Article e202500733
Developing efficient photoactive materials from bio-derived resources is vital yet challenging for achieving effective water splitting performance. In this work, nano carbon dots (CDs) of zero-dimensional (0D) were synthesized from papaya peel through a simple and eco-friendly process and subsequently anchored onto the two-dimensional (2D) layered structure of graphitic carbon nitride (g-C3N4, GCN) at various ...
Added: June 2, 2026
Wary R. R., Mahato B., Sharma N. et al., The Journal of Physical Chemistry Letters 2026 Vol. 17 No. 17 P. 5099–5107
Development of heterojunction materials is an efficient approach for enhancing photocatalytic and photoelectrochemical processes. We develop a ZnO/CuO heterojunction via Cu doping into a ZnO matrix. Structural characterization confirmed that Cu was effectively incorporated into ZnO without any structural changes. The improved optical properties and reduced charge carrier recombination of the doped samples were confirmed ...
Added: June 2, 2026
Ostovari Moghaddam A., Mehrabi-Kalajahi S., Hossein Vasigh S. A. et al., The Journal of Physical Chemistry Letters 2026 Vol. 17 No. 13 P. 3978–3985
Water electrolysis is a key technology for sustainable energy conversion and hydrogen generation. Recently, high-entropy oxides (HEOs) have emerged as promising materials because they allow tuning of structural, electronic, and catalytic properties in multifunctional systems. Here, we report the synthesis of a multicomponent La(FeCoCuTiNiMnMgSnZn)O3 perovskite, and its hybridization with reduced graphene oxide (rGO) to form a ...
Added: June 1, 2026
Chowdhury U., Mondal S., Dey S. et al., Journal of the american chemical society 2026 Vol. 148 No. 23 P. 24538–24550
Covalent functionalization offers a versatile platform to engineer carbon nanotube properties for optoelectronics applications. We demonstrate by atomistic quantum dynamics simulation that covalent functionalization can renormalize the CNT band gap, split the degenerate CNT band edge states, and strongly influence charge carrier separation and recombination dynamics. Open-ring CNT functionalization (O-CNT) largely retains the π-conjugation, whereas ...
Added: June 1, 2026
Jiménez-Grávalos F., Alexander S. Novikov, Pendás Á. M., Communications in Computational Chemistry 2026 Vol. 8 No. 2 P. 203–210
Chalcogen bonds (ChBs) are often interpreted as 𝜎-hole driven electrostatic interactions between a chalcogen atom and a Lewis base, yet their covalent character remains under active discussion. Here, we present a real-space, reference-free study of prototypical X2Ch···X– complexes (X = F, Cl; Ch = O, S) using the Interacting Quantum Atoms (IQA) energy decomposition within ...
Added: May 27, 2026
Uskov F., Korobkov S., Birin K. P. et al., Journal of Photochemistry and Photobiology A: Chemistry 2026 Vol. 474 Article 116936
Oxidation of sulfides by singlet oxygen has been extensively studied, yet the structure-photoactivity relationship of these photosensitizers remains underinvestigated. In the present work the photocatalytic performance of a set of functionalized palladium(II) porphyrinates was comprehensively investigated in the photocatalytic oxidation of sulfides to reveal mutual influence of structural peculiarities onto the photosensitizing properties. The photophysical ...
Added: May 27, 2026
Mezentsev I., Dudarova N., Druzina A. et al., Journal of Photochemistry and Photobiology A: Chemistry 2026 Vol. 479 Article 117316
Novel cobalt bis(dicarbollide) based terminal alkynes with charge-compensated group in a spacer were synthesized by the nucleophilic ring-opening reactions of cyclic oxonium derivatives of cobalt bis(dicarbollide) with N,N-dimethylbut-3-yn-1-amine. A series of zwitterionic conjugates of cobalt bis(dicarbollide) with BODIPY were synthesized using the copper(I)-catalyzed azide-alkyne cycloaddition reaction. The absorption-emission spectra of the synthesized fluorescent conjugates of cobalt ...
Added: May 27, 2026
Toukach P., Smirnova N. S., Zdorovenko E. L. et al., Analytical Chemistry 2026 Vol. 98 No. 15 P. 10988–10996
Pyruvylation is one of the immunochemically relevant modifications of O-antigens in bacterial and fungal cells. Therefore, fast and relatively simple analytical methods for identifying this modification are highly demanded. 13C NMR spectroscopy is the best candidate for this purpose, but its successful application requires using reference structures and reliable databases. In this work, we collected ...
Added: May 25, 2026
Зверева О., Kliuev F., Lebedeva N. et al., Organic Letters 2025 Vol. 27 No. 50 P. 13711–13716
Added: May 23, 2026
Mikhail A. Losev, Andrey S. Kozlov, Afanasyev O. et al., ACS Catalysis 2026 Vol. 16 No. 10 P. 9380–9386
A convenient, stable, and non-toxic substance, tetrabutylammonium difluorotriphenylsilicate (TBAT), can be used as an organocatalyst in all stages of polymer lifetime: synthesis, modification, and recycling. The fluorine-containing initiator showed high activity in the polymerization of siloxanes compared to classic organocatalytic systems. Using kinetically controlled ROP, a high-molecular-weight PDMS (Mn up to 820 𝑘𝑔/𝑚𝑜𝑙) was prepared at room ...
Added: May 22, 2026
Sabatier P., Beusch C., Maltseva D. et al., Nature Communications 2021 No. 12 Article 6558
Detailed characterization of cell type transitions is essential for cell biology in general and particularly for the development of stem cell-based therapies in regenerative medicine. To systematically study such transitions, we introduce a method that simultaneously measures protein expression and thermal stability changes in cells and provide the web-based visualization tool ProteoTracker. We apply our ...
Added: November 12, 2021
Kopylov A., Ponomarenko E., Ilgisonis E. et al., Journal of Proteome Research 2019 Vol. 18 No. 1 P. 120–129
This work continues the series of the quantitative measurements of the proteins encoded by different chromosomes in the blood plasma of a healthy person. Selected Reaction Monitoring with Stable Isotope-labeled peptide Standards (SRM SIS) and a gene-centric approach, which is the basis for the implementation of the international Chromosome-centric Human Proteome Project (C-HPP), were applied ...
Added: October 7, 2019
Kuznetsova K., Ivanov M., Pyatnitskiy M. et al., Biochemistry. Biokhimiia 2019 Vol. 84 No. 1 P. 71–78
The brain proteome of Drosophila melanogaster was characterized by liquid chromatography/high-resolution mass spectrometry and compared to the earlier characterized Drosophila whole-body and head proteomes. Raw data for all the proteomes were processed in a similar manner. Approximately 4000 proteins were identified in the brain proteome that represented, as expected, the subsets of the head and ...
Added: October 7, 2019
Ponomarenko E., Poverennaya E., Ilgisonis E. et al., International Journal of Analytical Chemistry 2016 P. 1–6
This work discusses bioinformatics and experimental approaches to explore the human proteome, a constellation of proteins expressed in different tissues and organs. As the human proteome is not a static entity, it seems necessary to estimate the number of different protein species (proteoforms) and measure the number of copies of the same protein in a ...
Added: March 14, 2018
Kliuchnikova A., Samokhina N., Ilina I. et al., Proteomics 2016 Vol. 16 No. 13 P. 1938–1946
Twenty-nine human aqueous humor samples from patients with eye diseases such as cataract and glaucoma with and without pseudoexfoliation syndrome were characterized by LC-high resolution MS analysis. In total, 269 protein groups were identified with 1% false discovery rate including 32 groups that were not reported previously for this biological fluid. Since the samples were analyzed individually, but not pooled, 36 proteins were identified ...
Added: March 14, 2018
Kertesz-Farkas A., Myers M. P., Current Bioinformatics 2012 Vol. 7 No. 2 P. 221–230
Bottom-up proteomics (mass spectrometry analysis of peptides obtained by proteolysis and separated by liquid chromatography, (LCMS/MS)) is one of the most frequently used techniques for identifying and characterizing proteins in biological samples. A key element of the analysis is database searching when the mass spectra of the peptides are compared with a database of theoretically ...
Added: November 18, 2015