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Wyniki wyszukiwania dla: RNA-PROTEIN INTERACTIONS
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Effects of interactions between variation in dopaminergic genes, traumatic life events, and anomalous self-experiences on psychosis proneness: Results from a cross-sectional study in a nonclinical sample
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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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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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Small regulatory bacterial RNAs regulating the envelope stress response
PublikacjaMost bacteria encode a large repertoire of RNA-based regulatory mechanisms. Recent discoveries have revealed that the expression of many genes is controlled by a plethora of base-pairing noncoding small regulatory RNAs (sRNAs), regulatory RNA-binding proteins and RNA-degrading enzymes. Some of these RNA-based regulated processes respond to stress conditions and are involved in the maintenance of cellular homeostasis. They achieve...
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Enhancing colloidal stability of nanodiamond via surface modification with dendritic molecules for optical sensing in physiological environments
PublikacjaPre-treatment of diamond surface in low-temperature plasma for oxygenation and in acids for carboxylation was hypothesized to promote the branching density of the hyperbranched glycidol polymer. This was expected to increase the homogeneity of the branching level and suppress interactions with proteins. As a result, composite nanodiamonds with reduced hydrodynamic diameters that are maintained in physiological environments were...
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Differential Response of MDA-MB-231 and MCF-7 Breast Cancer Cells to In Vitro Inhibition with CTLA-4 and PD-1 through Cancer-Immune Cells Modified Interactions
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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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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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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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Supramolecular structures formed by 2-aminopyridine derivatives. Part I. Hydrogenbonding networks via N-H...N interactions and the conformational polymorphism of N,N´-bis(2-piridyl)aryldiamines
PublikacjaOtrzymano serię N,N´-bis(2-pirydylo)arylodiamin w postaci monokryształów. Zgodnie z oczekiwaniami, powstawały dwie odmiany polimorficzne. Forma EE z układem wiązań R22(8) figuruje jako jednowymiarowe taśmy. Stwierdzono, że ugrupowanie 2-aminopirydylowe stanowi synton supramolekularny za pomocą którego można projektować struktury w ciele stałym. Właściwości tego syntonu były badane z wykorzystaniem metod dyfrakcyjnych oraz spektroskopii...
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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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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.
PublikacjaZaprezentowano 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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Interfacial water controls the process of adsorption of hyperactive antifreeze proteins onto the ice surface
PublikacjaA mechanism of interactions between the ice-binding surface of a hyperactive antifreeze protein molecule and the ice surface is proposed, involving the influence of water present between the two surfaces on the behavior of the approaching molecule. It is demonstrated that the interfacial water, even before its full solidification, can act as a factor that pushes away or pulls nearer the protein molecule to ensure its proper positioning....
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Extracting functional groups of ALLINI to design derivatives of FDA‐approved drugs: Inhibition of HIV‐1 integrase
PublikacjaHIV‐1 integrase (IN) is crucial for integration of viral DNA into the host genome and a promising target in development of antiretroviral inhibitors. In this work, six new compounds were designed by linking the structures of two different class of HIV‐1 IN inhibitors (active site binders and allosteric IN inhibitors (ALLINIs)). Among newly designed compounds, INRAT10b was found most potent HIV‐1 IN inhibitor considering different...
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Highly Conserved Homotrimer Cavity Formed by the SARS-CoV-2 Spike Glycoprotein: A Novel Binding Site
PublikacjaAn important stage in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) life cycle is the binding of the spike (S) protein to the angiotensin converting enzyme-2 (ACE2) host cell receptor. Therefore, to explore conserved features in spike protein dynamics and to identify potentially novel regions for drugging, we measured spike protein variability derived from 791 viral genomes and studied its properties by molecular...
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Comparative analysis of mRNA transcripts of HT-29 cell line expressed in identical quantities for pathogenic E. coli strains UM146 and UM147 with control Escherichia coli Nissle 1917
PublikacjaAim of study was comparative analysis of mRNA transcripts of HT-29 cell line, expressed in identical quantities for the combination of pathogenic and non-pathogenic Escherichia coli strains. HT-29 confluent monolayers infection with two pathogenic E. coli strains UM146 and UM147 resulted in two sets of mRNA transcripts that were identical with RNA transcripts obtained for non-pathogenic one strain E. coli Nissle 1917. In this study...
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Mechanism of recognition of parallel G-quadruplexes by DEAH/RHAU helicase DHX36 explored by molecular dynamics simulations
PublikacjaBecause of high stability and slow unfolding rates of G-quadruplexes (G4), cells have evolved specialized helicases that disrupt these non-canonical DNA and RNA structures in an ATP-dependent manner. One example is DHX36, a DEAH-box helicase, which participates in gene expression and replication by recognizing and unwinding parallel G4s. Here, we studied the molecular basis for the high affinity and specificity of DHX36 for parallel-type...
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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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The good, the bad, and the ugly: space use and intraguild interactions among three opportunistic predators—cat (Felis catus), dog (Canis lupus familiaris), and red fox (Vulpes vulpes)—under human pressure
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Influence of the ionic strength on the amyloid fibrillogenesis of hen egg white lysozyme
PublikacjaThe study investigates the role of the electrostatic interactions in the fibrillation of the hen egg white lysozyme (HEWL). In order to achieve this aim the influence of the cations Na+, Mg2+ and Al3+ on the amyloid fibril formation and amorphous aggregation was tested. The amyloids are formed in the solution without added salt but the Thioflavin T fluorescence gives the false-negative result. In these conditions, the HEWL fibrils...
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Properties of water in the region between a tubulin dimer and a single motor head of kinesin
PublikacjaA kinesin is a molecular motor that can perform movement on a microtubule track in a stepping-like manner. This motion is connected with processes of association and dissociation of kinesin and tubulin. Water is an important participant in these kinds of molecular interactions. This is why we have decided to investigate the dynamical and structural properties of water in the region between the kinesin catalytic domain and the tubulin...
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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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Simplified AutoDock force field for hydrated binding sites
Publikacjahas been extracted from the Protein Data Bank and used to test and recalibrate AutoDock force field. Since for some binding sites water molecules are crucial for bridging the receptor-ligand interactions, they have to be included in the analysis. To simplify the process of incorporating water molecules into the binding sites and make it less ambiguous, new simple water model was created. After recalibration of the force field on...
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“Dilute & Shoot” approach for rapid determination of trace amounts of nicotine in zero-level e-liquids by reversed phase liquid chromatography and hydrophilic interactions liquid chromatography coupled with tandem mass spectrometry-electrospray ionization
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“Dilute & Shoot” approach for rapid determination of trace amounts of nicotine in zero-level e-liquids by reversed phase liquid chromatography and hydrophilic interactions liquid chromatography coupled with tandem mass spectrometry-electrospray ionization
PublikacjaTwo analytical procedures are proposed where HILIC and RPLC techniques are coupled with tandem mass spectrometry detection for rapid determination of trace amounts of nicotine in zero-level liquids for electronic cigarettes. Samples are prepared on the basis of the approach “dilute & shoot” which makes this important step quick and not complicated. The chromatographic separation was carried out on a Zorbax XDB column (RPLC method)...
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Anion–cation interactions in a series of salts with substituted Hphen, Hbpy and H2bpy cations and [W(CN)8]4− anion: polymer with “super-short” N–H⋯N hydrogen bridges containing exclusively anions and H+
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Influence of Escherichia coli on Expression of Selected Human Drug Addiction Genes
PublikacjaThe impact of enteric microflora on the expression of genes associated with cocaine and amphetamine addiction was described. Human genome-wide experiments on RNA transcripts expressed in response to three selected Escherichia coli strains allowed for significant alteration (p > 0.05) of the linear regression model between HT-29 RNA transcripts associated with the KEGG pathway:hsa05030:Cocaine addiction after 3 h stimulation with...
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Effect of urea and glycine betaine on the hydration sphere of model molecules for the surface features of proteins
PublikacjaWater properties may significantly affect protein stability. Osmolytes are compounds that intrinsically affect water in many different ways and thus can influence proteins with this type of indirect mechanism. In this study, we characterize water properties in ternary solutions: model–water–osmolyte, with two model molecules: N-methylacetamide (NMA) and dimethyl sulfoxide (DMSO) and two osmolytes: glycine betaine (TMG)and urea....
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Analysis of the Factors Affecting Static In Vitro Pepsinolysis of Food Proteins
PublikacjaIn 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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Efficient three-dimensional fluorescence measurements for characterization of binding properties in some plants
PublikacjaThe main aim of this research was to characterize some plants and to determine their similarities and differences, using spectroscopic methods. The interactions of soluble polyphenols of different plants with human serum albumin (HSA) were investigated by 3D-fluorescence. The obtained fluorescence results allow to classify the investigated plants according to their binding properties. The HSA-binding capacities of these plants...
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Szczepionki przeciw toksoplazmozie - aktualny stan badań
PublikacjaArtykuł prezentuje współczesną wiedzę na temat opracowywania skutecznej szczepionki przeciwko toksoplazmozie. W publikacji zebrane zostały informacje dotyczące nowych strategii w konstruowaniu efektywnych szczepionek opartych na antygenach natywnych, rekombinantowych, DNA lub RNA pasożyta.
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Evaluation and cellular responses of modulators of TRF1/TRF2 protein’s function as potential anticancer drugs interfering with telomeric shelterin’s function
PublikacjaA number of proteins that interact with telomeres have been identified in human cells, indicating the high plasticity of human nucleoprotein complex organization. The most important complex is the "shelterin" complex, which consists of six proteins: TRF1, TRF2, TIN2, POT1, TPP1. The TRF1 and TRF2 directly bind to telomeric double-stranded DNA and the TIN2 protein. The TIN2 protein also binds to the TPP1 protein, stabilizing the...
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Zastosowanie addytywów w separacji pianowej białek serwatkowych i białek mlecznych
PublikacjaZaproponowano proces separacji pianowej do wydzielania białek ze strumieni poprodukcyjnych przemysłu mleczarskiego Ponadto zaproponowano zastosowanie w separacji pianowej białek serwatkowych i mlecznych addytywów dopuszczonych ustawą do stosowania w żywności. Jako cel pracy przyjęto uzyskanie wyników uzasadniających wybór takich addytywów, które intensyfikują przebieg i polepszają wynik procesu separacji pianowej białek. W części...
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Monitoring of lysozyme thermal denaturation by volumetric measurements and nanoDSF technique in the presence of N-butylurea
PublikacjaThe results of thermal studies of denaturation of hen egg white lysozyme (HEWL) in water and an aqueous solution of N-butylurea (BU) are presented. High-precision densimetric measurements were used to characterize and analyze the changes of the specific volume, v, during temperature elevation. The temperature of the midpoint of protein denaturation was also determined by nanoDSF technique (differential scanning fluorimetry). The...
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Molecular mechanism and energetics of coupling between substrate binding and product release in the F 1 -ATPase catalytic cycle
PublikacjaF1-ATPase is a motor protein that couples the rotation of its rotary γ subunit with ATP synthesis or hydrolysis. Single-molecule experiments indicate that nucleotide binding and release events occur almost simultaneously during the synthesis cycle, allowing the energy gain due to spontaneous binding of ADP to one catalytic β subunit to be directly harnessed for driving the release of ATP from another rather than being dissipated...
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Tailoring Diffusional Fields in Zwitterion/Dopamine Copolymer Electropolymerized at Carbon Nanowalls for Sensitive Recognition of Neurotransmitters
PublikacjaThe importance of neurotransmitter sensing in the diagnosis and treatment of many psychological illnesses and neurodegenerative diseases is non-negotiable. For electrochemical sensors to become widespread and accurate, a long journey must be undertaken for each device, from understanding the materials at the molecular level to real applications in biological fluids. We report a modification of diamondized boron-doped carbon nanowalls...
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Posttranscriptional coordination of splicing and miRNA biogenesis in plants
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Molecular simulation study of cooperativity in hydrophobic association
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AmiP from hyperthermophilic Thermus parvatiensis prophage is a thermoactive and ultrathermostable peptidoglycan lytic amidase
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In silico epitope prediction of Borrelia burgdorferi sensu lato antigens for the detection of specific antibodies
PublikacjaDespite many years of research, serodiagnosis of Lyme disease still faces many obstacles. Difficulties arise mainly due to the low degree of amino acid sequence conservation of the most immunogenic antigens among B. burgdorferi s.l. genospecies, as well as differences in protein production depending on the environment in which the spirochete is located. Mapping B-cell epitopes located on antigens allows for a better understanding...
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Analytical Strategies and Applications in Lipidomics
PublikacjaLipidomics is a field of study aiming at a comprehensive analysis of a set of lipids in biological systems. This includes both quantitative and qualitative characterization of lipid profiles, comparative studies of lipidomes, and analysis of lipid-protein interactions. Lipids are structurally diversified that make their analysis a challenging task. The constant advances in analytical technologies, especially in the field of high-performance...
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Identification of antigen Ag43 in uropathogenic Escherichia coli Dr+ strains and defining its role in the pathogenesis of urinary tract infections
PublikacjaUrinary tract infections (UTIs) caused by uropathogenic Escherichia coli (UPEC) are among the most common bacterial infectious diseases in the developed world. The urovirulence of UPEC is mainly associated with the surface-exposed fimbrial adhesins and adhesins of the autotransporter (AT) family. The best studied of theses proteins is antigen 43 (Ag43) mediating cell aggregation, adhesion and biofilm development as the causes of...
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Wykorzystanie wiązań niekowalencyjnych do otrzymywania jedno- i dwuskładnikowych struktur supramolekularnych
PublikacjaPrzedstawiona rozprawa doktorska dotyczy badań nad wykorzystaniem oddziaływań międzycząsteczkowych do projektowania i syntezy uporządkowanych struktur krystalicznych, ze szczególnym uwzględnieniem wiązań halogenowych i chalkogenowych jako stosunkowo nowych i bardzo atrakcyjnych z punktu widzenia inżynierii kryształu. Praca podzielona jest na kilka części. Pierwsza z nich stanowi wstęp teoretyczny obejmujący opis, założenia oraz...
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Modeling the Structure, Dynamics, and Transformations of Proteins with the UNRES Force Field
PublikacjaThe physics-based united-residue (UNRES) model of proteins ( www.unres.pl ) has been designed to carry out large-scale simulations of protein folding. The force field has been derived and parameterized based on the principles of statistical-mechanics, which makes it independent of structural databases and applicable to treat nonstandard situations such as, proteins that contain D-amino-acid residues. Powered by Langevin dynamics...
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Targeting Spike‐ACE2 Interface of SARS‐CoV‐2 and its Omicron Variant: A Comparative Screening of Potential Inhibitors for Existing and Anticipating Variants Using Molecular Modelling Approach
PublikacjaThe recent COVID pandemic has shown major impact on public health and economic crisis. Despite the development of many vaccines and drugs against the severe acute respiratory syndrome (SARS) coronavirus 2, the pandemic still persists. The continued spread of the virus is largely driven by the emergence of viral variants such as α, β, γ, delta, epsilon spike, omicron and its subvariants (BA.1,2,3) which can evade the current vaccines...
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Protective effect of Aronia melanocarpa polyphenols against cadmium-induced disorders in bone metabolism: A study in a rat model of lifetime human exposure to this heavy metal
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Butyrylcholinesterase signal sequence self-aggregates and enhances amyloid fibril formation in vitro
PublikacjaAlzheimer’s disease (AD) pathogenesis has been attributed to extracellular aggregates of amyloid β (Aβ) plaques and neurofibrillary tangles in the human brain. It has been reported that butyrylcholinesterase (BChE) also accumulates in the brain Aβ plaques in AD. We have previously found that the BChE substitution in 5′UTR caused an in-frame N-terminal extension of 41 amino acids of the BChE signal peptide. The resultant variant...
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Elucidating of oxidative distress in COVID-19 and methods of its prevention
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Cellular uptake of biotransformed graphene oxide into lung cells
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