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Search results for: PROTEIN—LIGAND BINDING
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Binding free energy of selected anticancer compounds to DNA - theoreticalcalculations
PublicationPraca dotyczy swobodnej energii wiązania z DNA trzech związków o działaniu przeciwnowotworowym (mitoksantronu i dwóch pochodnych pirymidoakrydyny). Obliczenia wykorzystywały metody Poissona-Boltzmanna (udział elektrostatyczny) i metody SASA (udział nieelektrostatyczny). W wyniku badań zaproponowano struktury kompleksów jakie tworzą badane ligandy z DNA.
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The Influence of Binding Agents on Stiffness of Mineral-cement-emulsion Mixtures
PublicationThis paper attempts to determine the behavior of mineral-cement-emulsion mixture (MCE) under load, whether is it similar to asphalt mixtures (viscoelastic behavior) or to cement treated materials (elastic behavior). To answer this question nine mineral- cement-emulsion mixtures with different combinations of cement and emulsion content were tested in laboratory using Simple Performance Test (SPT). For each mixture stiffness moduli...
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Understanding the interactions between protein stabilizers and the peptide bond through the analysis of the volumetric and compressibility properties for the model systems
PublicationThis work confirms our earlier supposition, that volumetric and acoustic parameters for simple model proposed by us are directly related to stabilizing/destabilizing effect of osmolytes on proteins structure. The apparent molar volumes, V and the apparent molar isentropic compressions, KS,, of glycine and N,N,N –trimethylglycine (betaine) were determined from densities and speed of sound measurements in aqueous solution of N-methylacetamide...
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Predicting Value of Binding Constants of Organic Ligands to Beta-Cyclodextrin: Application of MARSplines and Descriptors Encoded in SMILES String
PublicationThe quantitative structure–activity relationship (QSPR) model was formulated to quantify values of the binding constant (lnK) of a series of ligands to beta–cyclodextrin (β-CD). For this purpose, the multivariate adaptive regression splines (MARSplines) methodology was adopted with molecular descriptors derived from the simplified molecular input line entry specification (SMILES) strings. This approach allows discovery of regression...
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Reactions of (Ph)tBuP-P(SiMe3)Li·3THF with [(PNP)TiCl2] and [MeNacNacTiCl2·THF]. Synthesis of first PNP titanium(IV) complex with phosphanylphosphinidene ligand [(PNP)Ti(Cl){η2-P-P(Ph)tBu}]
PublicationLithium derivative of diphosphane (Ph)tBuP-P(SiMe3)Li (1) was isolated for the first time and investigated in reactions with β-diketiminate (MeNacnac− = [Ar]NC(Me)CHC(Me)N[Ar]; Ar = 2,6-iPr2C6H3) and PNP-pincer (PNP = N[2-PiPr2-4-methylphenyl]2) Ti(III) complexes. The β-diketiminate titanium(III) complex containing phosphanylphosphido ligand [MeNacNacTi(Cl){η2-P(SiMe3)-P(Ph)tBu}] (2) was prepared in reaction of [MeNacNacTiCl2·THF]...
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Role of Silicon in Counteracting Cadmium Stress in Pea Plants (Pisum sativum L.): Insights Into Cadmium Binding Mechanisms and Pectin Methylesterase Activity
PublicationPurpose: The aim of this study was to investigate the role of silicon (Si) in counteracting a cadmium (Cd) stress to pea plants (Pisum sativum L.) and to identify the mechanism by which Cd is bound within pea roots. Methods: These goals were achieved through (i) a histochemical study of Cd localization in pea roots, (ii) spectrophotometric determination of pectin content and the activity...
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Unwinding Au+···Au+ Bonded Filaments in Ligand-Supported Gold(I) Polymer under Pressure
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An investigation on the chemistry of the R2P=P ligand: reactions of a phosphanylphosphinidene complex of tungsten(VI) with electrophilic reagents
PublicationThe nucleophilic properties of the title compound [(2,6-i-Pr2C6H3N)2(Cl)W(η2-t-Bu2PvP)]Li·3DME (1) were investigated in reactions with selected electrophilic reagents such as MeI, M(CO)5THF (M = Cr, Mo, W), AlCl3, and GaCl3. Methylation of 1 by MeI yields phosphanylphosphido complexes [(2,6-i-Pr2C6H3N)2W(X)(1,2-η-t-Bu2PvP–CH3)] (X = Cl, I) (2-Cl/2-I) with the formation of a new P–C bond. Moreover, 1 reacts with electrophilic compounds...
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Gold(III) complexes with chloride and cyanopyridines: Facilitated hydrolysis of nitrile ligand to amide and antibacterial activity
PublicationA range of novel simple gold(III) compounds has been synthesized in their monocrystalline form, including two previously unknown chloro-complexes of Au3+ with 2-cyanopyridine or 3-cyanopyridine, respectively. Our investigations have revealed the intricate nature of the reaction between 2-cyanopyridine and tetrachloroauric acid, yielding at least three distinct products. The main product, obtained in high yield, is a salt featuring...
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Highly selective impedimetric determination of Haemophilus influenzae protein D using maze-like boron-doped carbon nanowall electrodes
PublicationThis study reports a novel impedimetric immunosensor for protein D detection in purified and bacterial (Haemophilus influenzae, Hi) samples. The detection was based on antigen recognition by anti-protein D antibodies (apD) immobilised at the maze-like boron-doped carbon nanowall electrodes (B:CNW). The B:CNW electrodes were synthesised, and their surface was characterised by scanning electron microscopy (SEM) and X-ray photoelectron...
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Characterization of single-stranded DNA-binding proteins from the psychrophilic bacteria Desulfotalea psychrophila, Flavobacterium psychrophilum, Psychrobacter arcticus, Psychrobacter cryohalolentis, Psychromonas ingrahamii, Psychroflexus torquis, and Photobacterium profundum
PublicationBackground: Single-stranded DNA-binding proteins (SSBs) play essential roles in DNA replication, recombination and repair in Bacteria, Archaea and Eukarya. In recent years, there has been an increasing interest in SSBs, since they find numerous applications in diverse molecular biology and analytical methods. Results: We report the characterization of single-stranded DNA-binding proteins from the psychrophilic bacteria Desulfotalea...
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Binding modes of a new epoxysuccinyl–peptide inhibitor of cysteine proteases. Where and how do cysteine proteases express their selectivity?
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Reactivity study of a β-diketiminate titanium(III) complex with a phosphanylphosphido ligand towards chlorophosphanes. A new method of synthesis of β-diketiminate titanium(IV) complexes with versatile phosphanylphosphinidenes
PublicationThe reactivity of ab-diketiminate titanium(III) complex with a phosphanylphosphido ligand, [MeNacNacTi(Cl){g2-P(SiMe3)-PtBu2}] (1)(MeNacNac= [Ar]NC(Me)CHC(Me)N[Ar]; Ar = 2,6-iPr2Ph), was investigatedtowards selected chlorophosphanes, such astBu2PCl,iPr2PCl, Cy2PCl, (Cy)tBuPCl, (Me)tBuPCl, (Ph)tBuPCl, Ph2PCl, (iPr2N)tBuPCl and (Et2N)2PCl. The reactions withtBu2PCl and Ph2PCl lead mainly to theearlier described complex [MeNacNacTi(Cl){g2-P-PtBu2}]...
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Pea Protein for Hempseed Oil Nanoemulsion Stabilization
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Some applications of thermophiles and their enzymes for protein processing
PublicationPrzedstawiono charakterystykę, właściwości oraz możliwości zastosowań enzymów proteolitycznych wytwarzanych przez termofile. Zaletą tych biokatalizatorów jest między innymi duża odporność na działanie rozpuszczalników organicznych, detergentów i innych czynników denaturujących białka oraz mała wrażliwość na zmiany pH. Dokonano też przeglądu czynników powodujących dużą stabilność proteaz z termofili.
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Apple pectin complexes with whey protein isolate
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Polysaccharide–Protein Complexes in a Coarse-Grained Model
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ANALYSIS OF THE p53 PROTEIN GENE EXPRESSION MODEL
PublicationWe study the asymptotic behaviour of the solutions of the p53-Mdm2 model proposed by Monk (2003). The p53 gene is crucial for cellular inhibition of the angiogenesis process, while Mdm2 is a negative regulator of the p53 tumor-suppressor. We investigate the stability of the positive steady state and perform some numerical experiments.
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Silica In Silico: A Molecular Dynamics Characterization of the Early Stages of Protein Embedding for Atom Probe Tomography
PublicationA novel procedure for the application of atom probe tomography (APT) to the structural analysis of biological systems, has been recently proposed, whereby the specimen is embedded by a silica matrix and ablated by a pulsed laser source. Such a technique, requires that the silica primer be properly inert and bio-compatible, keeping the native structural features of the system at hand, while condensing into an amorphous, glass-like...
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Induced circularly polarized luminescence for revealing DNA binding with fluorescent dyes
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Common functionally important motions of the nucleotide‐binding domain of H sp70
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Binding energies of Eu2+ and Eu3+ ions in β-Ca2SiO4 doped with europium
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Sequence variants of p21 gene of the MRL/MpJ mouse: a possible association with the deficit of p21 protein and regenerative phenotype.
PublicationThe MRL/MpJ mouse is known for its enhanced regeneration abilities that manifested themselves by scarless ear-hole wound closure. The deficit of p21 found in the MRL is associated with the regenerative capacity as the p21 gene knockout in a mouse strain unrelated to the MRL mouse results in an ear-hole closure effect, similar to that observed in the MRL mouse. Cdkn1a gene encodes p21 protein, a cyclin-dependent kinase inhibitor,...
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Regulation of the First Committed Step in Lipopolysaccharide Biosynthesis Catalyzed by LpxC Requires the Essential Protein LapC (YejM) and HslVU Protease
PublicationWe previously showed that lipopolysaccharide (LPS) assembly requires the essential LapB protein to regulate FtsH-mediated proteolysis of LpxC protein that catalyzes the first committed step in the LPS synthesis. To further understand the essential function of LapB and its role in LpxC turnover, multicopy suppressors of ΔlapB revealed that overproduction of HslV protease subunit prevents its lethality by proteolytic degradation...
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UNRES-GPU for Physics-Based Coarse-Grained Simulations of Protein Systems at Biological Time- and Size-Scales
PublicationThe dynamics of the virus like particles (VLPs) corresponding to the GII.4 Houston, GII.2 SMV, and GI.1 Norwalk strains of human noroviruses (HuNoV) that cause gastroenteritis was investigated by means of long-time (about 30 μs in the laboratory timescale) molecular dynamics simulations with the coarse-grained UNRES force field. The main motion of VLP units turned out to be the bending at the junction between the P1 subdomain (that...
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Docking is not enough: 17-trifluoromethylphenyl trinor PGF2α is only a very weak ligand of neurokinin-1 receptor
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Function and Frustration of Multi-Drug ABC Exporter Protein and Design of Model Proteins for Drug Delivery Using Protein Hydration Thermodynamics
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Statistical Method for Analysis of Interactions Between Chosen Protein and Chondroitin Sulfate in an Aqueous Environment
PublicationWe present the statistical method to study the interaction between a chosen protein and another molecule (e.g., both being components of lubricin found in synovial fluid) in a water environment. The research is performed on the example of univariate time series of chosen features of the dynamics of mucin, which interact with chondroitin sulfate (4 and 6) in four different saline solutions. Our statistical approach is based on recurrence...
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The hydration properties of protein stabilizer, trimethylamine-N-oxide in aqueous solutions of N-methylacetamide – The volumetric and compressibility studies between 288.15 and 308.15 K
PublicationApparent molar volumes and apparent molar isentropic compressions of the protein stabilizer, trimethylamine-N-oxide (TMAO) were determined from the densities and speed of sound measured at T = (288.15, 298.15 and 308.15) K in aqueous solutions of N-methylacetamide (NMA) at four different concentrations (2, 4, 6 and 8 mol/kg). The concentration dependencies of the calculated quantities extrapolated to the infinite dilution lead...
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Role of the disulfide bond in stabilizing and folding of the fimbrial protein DraE from uropathogenic Escherichia coli
PublicationDr fimbriae are homopolymeric adhesive organelles of uropathogenic Escherichia coli composed of DraE subunits, responsible for the attachment to host cells. These structures are characterized by enormously high stability resulting from the structural properties of an Ig-like fold of DraE. One feature of DraE and other fimbrial subunits that makes them peculiar among Ig-like domain-containing proteins is a conserved disulfide bond...
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Hybrid materials comprising trimethylglycinamide groups: immobilization consequences for anion binding affinities
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Imidazo-thiazine, -diazinone and -diazepinone derivatives. Synthesis, structure and benzodiazepine receptor binding
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Molecular insights into receptor binding energetics and neutralization of SARS-CoV-2 variants
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A tight-binding model of a carbon nanotube interacting with TiO2 rutile (110) surface
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Assessment of Adjustment of GNSS Railway Measurements with Parameter-Binding Conditions in a Stationary Scenario
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NK1 receptor binding of a few low molecular weight 3,5-bistrifluoromethylbenzene derivatives
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Fentanyl Family at the Mu-Opioid Receptor: Uniform Assessment of Binding and Computational Analysis
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Single-stranded DNA-binding proteins (SSBs) - sources and applicationsin molecular biology
PublicationBiałka wiążące się do jednoniciowego DNA (SSB) odgrywają ważną rolę w replikacji, rekombinacji i naprawie DNA u bakterii, archea i eukariota. Ostatnio wzrosło zainteresowanie białkami SSB jako przydatnymi narzędziami w metodach badawczych biologii molekularnej, analitycznych i diagnostycznych. Większość znanych prokariotycznych białek SSB zbudowanych jest z czterech podjednostek (homotetramer) z jedną domeną wiążąca (OB) jednoniciowe...
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Assessment of Adjustment of GNSS Railway Measurements with Parameter-Binding Conditions in a Stationary Scenario
PublicationThe study aims to assess the applicability of the ordinary least squares method, robust estimation, and conditions-binded adjustment in processing the six synchronous coordinate pairs of global navigation satellite system (GNSS) receivers. The research is part of the research project InnoSatTrack, focused on the enhancement of the determination of geometrical parameters of railway tracks using GNSS, inertial, and other sensors....
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Copper containing protein sites - structure, properties and models
PublicationEnzymy organizmów żywych katalizują wiele reakcji stosowanych w przemyśle chemicznym. Przykładem potencjalnego zastosowania enzymu w produkcji jest synteza L-Dopy przy udziale tyrozynazy. Ze względu na możliwe praktyczne zastosowanie w katalizie, otrzymano i opisano wiele prostych modeli miejsc aktywnych enzymów. W artykule opisano niektóre modele białek zawierających miedź.
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Effect of increased protein intake on the risk of female infertility
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Electrosynthesis of potato starch–whey protein isolate complexes
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The SERRATE protein is involved in alternative splicing in Arabidopsis thaliana
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The SERRATE protein is involved in alternative splicing in Arabidopsis thaliana
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Role of Oligosaccharide Chain Polarity in Protein–Glycosaminoglycan Interactions
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The protein folding problem: global optimization of force fields
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Lipid-protein interactions in membranes: a molecular modelling study
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A bifunctional chimeric protein consisting of MutS and beta-galactosidase
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A bifunctional chimeric protein consisting of MutS and beta-galactoside
PublicationPraca pokazuje konstrukcję DNA plazmidowego kodującego bifunkcjonalne białko chimeryczne złożone z MutS Thermus thermophilus i beta-galaktozydazy E.coli, optymalizację jego ekspresji i oczyszczania. Białko to testowano w metodzie wykrywania mutacji punktowych, wykorzystując kolorymetryczne mierzenie aktywności domeny reporterowej beta galaktozydazy.
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c-Myc Protein Level Affected by Unsymmetrical Bisacridines Influences Apoptosis and Senescence Induced in HCT116 Colorectal and H460 Lung Cancer Cells
PublicationUnsymmetrical bisacridines (UAs) are highly active antitumor compounds. They contain in their structure the drugs previously synthesized in our Department: C-1311 and C-1748. UAs exhibit different properties than their monomer components. They do not intercalate to dsDNA but stabilize the G-quadruplex structures, particularly those of the MYC and KRAS genes. Since MYC and KRAS are often mutated and constitutively expressed in cancer...