Search results for: PROTEIN MODEL
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Modulation of mRNA and protein levels of CYP1A1, 1A2, and 1B1 in nontumorigenic breast epithelial cells (MCF10A) by cabbage juice and its active components
PublicationZbadano wpływ soków z kapusty oraz występujących w nich pochodnych indolowych i sulforafanu na poziom ekspresji enzymów odpowiedzialnych za metabolizm ksenobiotyków w tym estrogenów. Wykazano, że soki z kapusty i izolowane substancje mają podobny wpływ na poziom mRNA i białek enzymatycznych.
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New plasma preparation approach to enrich metabolome coverage in untargeted metabolomics: plasma protein bound hydrophobic metabolite release with proteinase K
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Expression of Estrogen Receptor Coactivator Proline-, Glutamic Acid- and Leucine-Rich Protein 1 within Paraspinal Muscles in Adolescents with Idiopathic Scoliosis
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Anticancer imidazoacridinone C-1311 inhibits hypoxia-inducible factor-1α (HIF-1α), vascular endothelial growth factor (VEGF) and angiogenesis
PublicationAntitumor imidazoacridinone C-1311 is a DNA-reactive topoisomerase II and FLT3 receptor tyrosine kinase inhibitor. Here, we demonstrate the mechanism of C-1311 inhibitory action on novel targets: hypoxia-inducible factor-1α (HIF-1α), vascular-endothelial growth factor (VEGF), and angiogenesis. In a cell-free system, C-1311 prevented HIF-1α binding to an oligonucleotide encompassing a canonical hypoxia-responsive element (HRE),...
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Performance of electrochemical immunoassays for clinical diagnostics of SARS-CoV-2 based on selective nucleocapsid N protein detection: Boron-doped diamond, gold and glassy carbon evaluation
PublicationThe 21st century has already brought us a plethora of new threats related to viruses that emerge in humans after zoonotic transmission or drastically change their geographic distribution or prevalence. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first spotted at the end of 2019 to rapidly spread in southwest Asia and later cause a global pandemic, which paralyzes the world since then. We have designed novel...
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Ligand-Modified Boron-Doped Diamond Surface: DFT Insights into the Electronic Properties of Biofunctionalization
PublicationWith the increasing power of computation systems, theoretical calculations provide a means for quick determination of material properties, laying out a research plan, and lowering material development costs. One of the most common is Density Functional Theory (DFT), which allows us to simulate the structure of chemical molecules or crystals and their interaction. In developing a new generation of biosensors, understanding the nature...
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The Boltzmann sequence-structure channel
PublicationWe rigorously study a channel that maps binary sequences to self-avoiding walks in the two-dimensional grid, inspired by a model of protein statistics. This channel, which we also call the Boltzmann sequence-structure channel, is characterized by a Boltzmann/Gibbs distribution with a free parameter corresponding to temperature. In our previous work, we verified experimentally that the channel capacity has a phase transition for...
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ESCASA : Analytical estimation of atomic coordinates from coarse‐grained geometry for nuclear‐magnetic‐resonance ‐assisted protein structure modeling. I. Backbone and Hβ protons
PublicationA method for the estimation of coordinates of atoms in proteins from coarse-grained geometry by simple analytical formulas (ESCASA), for use in nuclear-magnetic-resonance (NMR) data-assisted coarse-grained simulations of proteins is proposed. In this paper, the formulas for the backbone Hα and amide (HN) protons, and the side-chain Hβ protons, given the Cα-trace, have been derived and parameterized, by using the interproton distances...
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Ultrasound assisted synthesis of 3-alkynyl substituted 2-chloroquinoxaline derivatives: their in silico assessment as potential ligands for N-protein of SARS-CoV-2
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Toxoplasma gondii: Enzyme-Linked Immunosorbent Assay using different fragments of recombinant microneme protein 1 (MIC1) for detection of immunoglobulin G antibodies
PublicationTrzy rekombinantowe fragmenty białka antygenowego MIC1 Toxoplasma gondii (r-MIC1ex2, r-MIC1ex34 i r-MIC1) zostały wyprodukowane jako białka fuzyjne (zawierające dwie domeny oligohistydynowe na N- i C-końcu) w komórkach bakteryjnych Escherichia coli. Homogenne preparaty antygenów rekombinantowych otrzymane z zastosowaniem jednoetapowego oczyszczania metodą chromatografii metalopowinowactwa, wykorzystano następnie do immunoidentyfikacji...
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Physics-Based Potentials for the Coupling between Backbone- and Side-Chain-Local Conformational States in the United Residue (UNRES) Force Field for Protein Simulations
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Pro-apoptotic action of protein-carbohydrate fraction isolated from coelomic fluid of the earthworm Dendrobaena veneta against human colon adenocarcinoma cells
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Funkcjonalne właściwości preparatu białek mięśniowych z kręgosłupów dorsza bałtyckiego = Functional properties of a muscle protein preparation from Baltic cod spine
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Prime-Boost Vaccination with Toxoplasma Lysate Antigen, but Not with a Mixture of Recombinant Protein Antigens, Leads to Reduction of Brain Cyst Formation in BALB/c Mice
PublicationIntroduction Infection with the ubiquitous parasite Toxoplasma gondii is a threat for immunocompro- mised patients and pregnant women and effective immune-prophylaxis is still lacking. Methods Here we tested a mixture of recombinant T . gondii antigens expressed in different develop- mental stages, i.e., SAG1, MAG1 and GRA7 (SMG), and a lysate derived from T . gondii tachyzoites (TLA) for prophylactic vaccination against cyst formation....
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Modeling SARS‐CoV‐2 proteins in the CASP‐commons experiment
PublicationCritical Assessment of Structure Prediction (CASP) is an organization aimed at advancing the state of the art in computing protein structure from sequence. In the spring of 2020, CASP launched a community project to compute the structures of the most structurally challenging proteins coded for in the SARS-CoV-2 genome. Forty-seven research groups submitted over 3000 three-dimensional models and 700 sets of accuracy estimates on...
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Aberration of the enzymatic activity of Fhit tumor suppressor protein enhances cancer cell death upon photodynamic therapy similarly to that driven by wild-type Fhit
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A Hierarchical Multiscale Approach to Protein Structure Prediction: Production of Low‐Resolution Packing Arrangements of Helices and Refinement of the Best Models with a United‐Residue Force Field
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A surface-exposed DraD protein of uropathogenic Escherichia coli bearing Dr fimbriae may be expressed and secreted independently from DraC usher and DraE adhesin
PublicationOperon dra uropatogennych szczepów Escherichia coli Dr+ odpowiedzialny jest za proces bakteryjnej adhezji i inwazji. Operon dra kodujący fimbrie Dr zawiera sześć otwartych ramek odczytu - draA, draB, draC, draD, draP oraz draE. Fimbrie Dr zlokalizowane na powierzchni komórki bakteryjnej, zbudowane są z podjednostek białka DraE. Niewiele wiadomo na temat powierzchniowej ekspresji białka DraD oraz jego roli w procesie biogenezy fimbrii...
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Natural fish oil improves the differentiation and maturation of oligodendrocyte precursor cells to oligodendrocytes in vitro after interaction with the blood–brain barrier
PublicationThe blood–brain barrier (BBB) tightly controls the microenvironment of the central nervous system (CNS) to allow neurons to function properly. Additionally, emerging studies point to the beneficial effect of natural oils affecting a wide variety of physiological and pathological processes in the human body. In this study, using an in vitro model of the BBB, we tested the influence of natural fish oil mixture (FOM) vs. borage oil...
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Impact of selected amino acids of HP0377 (Helicobacter pylori thiol oxidoreductase) on its functioning as a CcmG (cytochrome c maturation) protein and Dsb (disulfide bond) isomerase
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Cu(II) complexes with peptides from FomA protein containing -His-Xaa-Yaa-Zaa-His and -His-His-motifs. ROS generation and DNA degradation
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DMSO and TMAO—Differences in Interactions in Aqueous Solutions of the K-Peptide
PublicationInteractions between a solvent and their co-solute molecules in solutions of peptides are crucial for their stability and structure. The K-peptide is a synthetic fragment of a larger hen egg white lysozyme protein that is believed to be able to aggregate into amyloid structures. In this study, a complex experimental and theoretical approach is applied to study systems comprising the peptide, water, and two co-solutes: trimethylamide...
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Implementation of Molecular Dynamics and Its Extensions with the Coarse-Grained UNRES Force Field on Massively Parallel Systems: Toward Millisecond-Scale Simulations of Protein Structure, Dynamics, and Thermodynamics
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Identification of X-DING-CD4, a new member of human DING protein family that is secreted by HIV-1 resistant CD4+ T cells and has anti-viral activity
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Fatty Acid-Binding Protein 7 (FABP-7), Glutamic Acid and Neurofilament Light Chain (NFL) as Potential Markers of Neurodegenerative Disorders in Psoriatic Patients—A Pilot Study
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Effect of Manual Therapy Compared to Ibuprofen on Primary Dysmenorrhea in Young Women—Concentration Assessment of C-Reactive Protein, Vascular Endothelial Growth Factor, Prostaglandins and Sex Hormones
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Voltammetric and biological studies of folate-targeted non-lamellar lipid mesophases
PublicationFolate-targeted lipid nanostructures are promising strategies for the development of biocompatible drug delivery systems. The objective of this study was to evaluate the efficacy of drug delivery to cancer cells by folate-targeted lipid mesophases, cubosomes (CUB) and hexosomes (HEX), loaded with doxorubicin (DOX). Three cancer-derived cell lines (KB, HeLa, T98G) exhibiting different expressional levels of folate receptor protein...
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Interaction of human serum albumin with volatiles and polyphenols from some berries
PublicationHeadspace solid-phase microextraction coupled with comprehensive two-dimensional gas chromatography with time-of-flight mass spectrometry (HS-SPME/GC GCeTOFMS) identified 19 and quantified 6 monoterpenes in gooseberries, blueberries and cranberries. As a protein model human serum albumin (HSA) was used in interaction with terpenes. Specific binding of terpenes to HSA under the physiological conditions was a result of the formation...
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Short-term Cultivation of Porcine Cumulus Cells Influences the Cyclin-dependent Kinase 4 (Cdk4) and Connexin 43 (Cx43) Protein Expression—A Real-time Cell Proliferation Approach
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Towards temperature-dependent coarse-grained potentials of side-chain interactions for protein folding simulations. I: Molecular dynamics study of a pair of methane molecules in water at various temperatures
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The activity of latent benzoperimidine esters to inhibit P-glycoprotein and multidrug resistance-associated protein 1 dependent efflux of pirarubicin from several lines of multidrug resistant tumor cells.
PublicationZaprezentowano wyniki badań biologicznych przeprowadzonych dla nowej grupy związków: estrów benzoperymidyny z zastosowaniem wybranych linii komórek nowotworowych: wrażliwych i opornych o oporności P-gp-zależnej, MRP1-zależnej i o oporności związanej z nadekspresją białek MRP1/LRP. Metodą spektrofluorymetryczną zbadano zdolność estrów benzoperymidyny do hamowania eksportu aktywnego pirarubicyny z komórek opornych. Estry benzoperymidyny...
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Ageing-Time Dependent Changes of Angiotensin I-Converting Enzyme-Inhibiting Activity of Protein Hydrolysates Obtained from Dry-Cured Pork Loins Inoculated with Probiotic Lactic Acid Bacteria
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Identification and molecular modeling of a novel lipase from an Antarctic soil metagenomic library.
PublicationIn this work, we present the construction of a metagenomic library in Escherichia coli using pUC19 vector and environmental DNA directly isolated from Antarctic topsoil and screened for lipolytic enzymes. The screening on agar supplemented with olive oil and rhodamine B revealed one clone with lipolytic activity (Lip1) out of 11,000 E. coli clones. This clone harbored a plasmid, pLip1, which has an insert of 4722 bp that has been...
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Pre-treatment of bio fraction waste prior to fermentation processes
PublicationCurrent efforts are taken to increase resource efficiency, close material loops, and improve sustainable waste and by-products management. Thus, networking agro-food by-products and converting them into valuable products completely exhausting the potential of the raw material becomes significant. Model lignocellulosic and starch based biomass were subjected to pre-treatment with the application of acidic compounds, i.e. sulphuric...
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Karaś P., Kochanowicz K., Pitek M., Domański P., Obuchowski I., Tomiczek B., Liberek K.: Evolution towards simplicity in bacterial small heat shock protein system// eLife -, (2023), s.1-21
PublicationEvolution can tinker with multi-protein machines and replace them with simpler single-protein systems performing equivalent functions in an equally efficient manner. It is unclear how, on a molecular level, such simplification can arise. With ancestral reconstruction and biochemical analysis, we have traced the evolution of bacterial small heat shock proteins (sHsp), which help to refold proteins from aggregates using either...
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Significant Decrease in Glycated Hemoglobin, 2h-Post-Load Glucose and High-Sensitivity C-Reactive Protein Levels in Patients with Abnormal Body Mass Index after Therapy with Manual Lymphatic Drainage
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Torsional elasticity and energetics of F1-ATPase
PublicationFoF1-ATPase is a rotary motor protein synthesizing ATP from ADP driven by a cross-membrane proton gradient. The proton flow through the membrane-embedded Fo generates the rotary torque that drives the rotation of the asymmetric shaft of F1. Mechanical energy of the rotating shaft is used by the F1 catalytic subunit to synthesize ATP. It was suggested that elastic power transmission with transient storage of energy in some compliant...
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An examination of an Antarctic soil metagenomic-derivate putative methylthioadenosine phosphorylase gene as a novel reporter gene for promoter trapping
PublicationThe rsfp gene was discovered during examination ofan Antarctic soil-derived metagenome library and encodesa bacterial methylthioadenosine phosphorylase (GenBank accession number GQ202582). In a previous study, we found that E. coli colonies expressing the rsfp gene reveal strong pink fluorescence after exposure to UV light when grown on culture medium supplemented with rhodamine B (Cieśliński et al., 2009). In contrast to that,...
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Keratin-Butyrate Scaffolds Promote Skin Wound Healing in Diabetic Rats Through Down-Regulation of IL-1β and Up-Regulation of Keratins 16 and 17
PublicationImpaired wound healing particularly in diabetics creates a significant healthcare burden. The study aimed to evaluate the effect of keratin-butyrate fibers (FKDP +0.1%NaBu) in a full-thickness skin wound model in 30 diabetic rats. Physicochemical examination showed that the obtained dressing possesses a heterogeneous structure and butyrate was slowly released into the wound. Moreover, the obtained dressing is nontoxic and supports...
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A review on computer‐aided chemogenomics and drug repositioning for rational COVID ‐19 drug discovery
PublicationApplication of materials capable of energy harvesting to increase the efficiency and environmental adaptability is sometimes reflected in the ability of discovery of some traces in an environment―either experimentally or computationally―to enlarge practical application window. The emergence of computational methods, particularly computer-aided drug discovery (CADD), provides ample opportunities for the rapid discovery and development...
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Analysis of the Factors Affecting Static In Vitro Pepsinolysis of Food Proteins
PublicationIn this meta-analysis, we collected 58 publications spanning the last seven decades that reported static in vitro protein gastric digestion results. A number of descriptors of the pepsinolysis process were extracted, including protein type; pepsin activity and concentration; protein concentration; pH; additives; protein form (e.g., ‘native’, ‘emulsion’, ‘gel’, etc.); molecular weight of the protein; treatment; temperature; and...
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DL_MG: A Parallel Multigrid Poisson and Poisson–Boltzmann Solver for Electronic Structure Calculations in Vacuum and Solution
PublicationThe solution of the Poisson equation is a crucial step in electronic structure calculations, yielding the electrostatic potential -- a key component of the quantum mechanical Hamiltonian. In recent decades, theoretical advances and increases in computer performance have made it possible to simulate the electronic structure of extended systems in complex environments. This requires the solution of more complicated variants of the...
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Antifungal Effect of Penicillamine Due to the Selective Targeting of L-Homoserine O-Acetyltransferase
PublicationDue to the apparent similarity of fungal and mammalian metabolic pathways, the number of established antifungal targets is low, and the identification of novel ones is highly desirable. The results of our studies, presented in this work, indicate that the fungal biosynthetic pathway of L-methionine, an amino acid essential for humans, seems to be an attractive perspective. The MET2 gene from Candida albicans encoding L-homoserine...
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Electrochemical determination of neurotransmitter serotonin using boron/nitrogen co-doped diamond-graphene nanowall-structured particles
PublicationElectrode fouling is a major issue in biological detection due to the adhesion of the protein itself and polymerization of biomolecules on the electrode surface, impeding the electron transfer ability and decreasing the current response. To overcome this issue, the use of anti-fouling material, especially boron-doped diamond (BDD) electrode, is an alternative way. However, the electrocatalytic activity of BDD is inadequate compared...
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The structurally similar TRFH domain of TRF1 and TRF2 dimers shows distinct behaviour towards TIN2
PublicationThe telomere repeat binding-factor 1 and 2 (TRF1 and TRF2) proteins of the shelterin complex bind to duplex telomeric DNA as homodimers, and the homodimerization is mediated by their TRFH (TRF-homology) domains. We performed molecular dynamic (MD) simulations of the dimer forms of TRF1TRFH and TRF2TRFH in the presence/absence of the TIN2TBM (TIN2, TRF-interacting nuclear protein 2, TBM, TRF-binding motif) peptide. The MD results...
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Dibutyl phthalate disrupts conserved circadian rhythm in Drosophila and human cells
PublicationPeople are constantly exposed to phthalates, due to their common use in the production of plastics, pharmaceuticals, cosmetics and skin care products. The ability of phthalates to disrupt endocrine signaling, leading to developmental, reproductive and metabolic defects, has been studied, yet how phthalates interfere with these biological functions is still unclear. To uncover DBP interacting molecular pathways, we raised Drosophila...
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Role of the Solvation Water in Remote Interactions of Hyperactive Antifreeze Proteins with the Surface of Ice
PublicationMost protein molecules do not adsorb onto ice, one of the exceptions being so-called antifreeze proteins. In this paper, we describe that there is a force pushing an antifreeze protein molecule away from the ice surface when it is not oriented with its ice-binding plane toward the ice and that this pushing force may be also present even when the protein is oriented with its ice-binding plane toward the ice. This force is absent...
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Molecular dynamics study on the role of solvation water in the adsorption of hyperactive AFP to the ice surface
PublicationUsing computer simulations, the early stages of the adsorption of the CfAFP molecule to the ice surface were analyzed. We found that the ice and the protein interact at least as early as when the protein is about 1 nm away from the ice surface. These interactions are mediated by interfacial solvation water and are possible thanks to the structural ordering of the solvent. This ordering leads to positional preference of the protein...
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Water-mediated long-range interactions between the internal vibrations of remote proteins
PublicationIt is generally acknowledged that the mobility of protein atoms and the mobility of water molecules in the solvation layer are connected. In this article, we answer the question whether a similar interdependence exists between the motions of atoms of proteins separated by the hydration layers of variable thickness. The system consisted of a kinesin catalytic domain and a tubulin dimer. It was studied using molecular dynamics simulations....
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Characterization of a cryptic plasmid pSFKW33 from Shewanella sp. 33b
PublicationA cryptic plasmid pSFKW33 from psychrotrophic bacterium Shewanella sp. 33B, an isolate from the Gulf of Gdansk (the Baltic Sea), was sequenced and characterized. It is an 8021 bpcircular molecule with 38% GC content, which shows a distinctive nucleotide sequence without homology to other known plasmids. The nucleotide sequence analysis predicts eight open reading frames. The deduced amino acid sequence of ORF-1 shared significant...