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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., Journal of Chemical Physics 2026 Vol. 165 No. 9 Article 094902
We derive the stress tensor of a flexible polymer solution within the Gaussian-chain self-consistent field theory (SCFT) without invoking the ground-state dominance (GSD) approximation. Starting from a covariant formulation of the single-chain partition function in a background metric, we obtain the symmetric stress tensor expressed through the full Edwards propagators. The result contains the local ...
Added: September 2, 2026
Belousov Y., Кискин М. А., Sidoruk A. et al., Australian Journal of Chemistry 2022 Vol. 75 No. 9 P. 572–580
Four new complexes [Ln(pfaa)3(H2O)2]n (Ln = Eu (1), Tb (2)) and [Ln2Cd2(pfaa)10 (phen)2(EtOH)2]·2MeCN (Ln = Eu (3), Tb (4), phen = 1,10-phenanthroline) based on pentaphorphenylacetic acid (Hpfaa) have been prepared and completely investigated. The structures of compounds 1 and 3 were studied by single crystal X-ray diffraction analysis: the isostructural complexes 1 and 2 represent ...
Added: August 26, 2026
Mazur D., Petr E. Brandyshev, Doronin S. et al., Electrochimica Acta 2026 Vol. 577 Article 149729
The electric double layer (EDL) at a single-crystal metal surface is controlled not only by the electrolyte composition and the electrode potential, but also by the atomic structure of the surface itself. This makes the Ag(hkl)/NaF interface a stringent test for continuum theories of the EDL. In the third part of our series, we examine ...
Added: August 20, 2026
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
Novikov A., New Journal of Chemistry 2026 Vol. 50 P. 13931–13957
The rational design of coinage metal nanocarriers requires a mechanistic understanding of metal-drug binding and predictive descriptors that translate molecular interactions into design rules. Using DFT (B3LYP-D3BJ/def2-TZVP, SMD water), we systematically investigated the binding of 5-fluorouracil (5-FU) and levodopa (l-DOPA) to neutral and cationic homo- and heteronuclear dimers of Au, Ag, and Cu (Au2, Ag2, ...
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
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
Kertesz-Farkas A., Myers M. P., Protein and peptide letters 2014 Vol. 21 No. 8 P. 858–863
Identification and elimination of noise peaks in mass spectra from large proteomics data streams simultaneously improves the accuracy of peptide identification and significantly decreases the size of the data. There are a number of peak filtering strategies that can achieve this goal. Here we present a simple algorithm wherein the number of highest intensity peaks ...
Added: November 18, 2015
Kertesz-Farkas A., Myers M. P., Current Bioinformatics 2012 Vol. 7 No. 2 P. 212–220
Mass spectrometry based proteomics analysis can produce many thousands of spectra in a single experiment, and much of this data, frequently greater than 50%, cannot be properly evaluated computationally. Therefore a number of strategies have been developed to aid the processing of mass spectra and typically focus on the identification and elimination of noise, which ...
Added: November 18, 2015
Kertesz-Farkas A., Noble W., Journal or Proteome Research 2015 Vol. 14 No. 8 P. 3027–3038
Added: September 25, 2015