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Wyniki wyszukiwania dla: BINDING ANALYSIS
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Structure-function analysis of decay-accelerating factor: identification ofresidues important for binding of the Escherichia coli Dr adhesin and complement regulation
PublikacjaZidentyfikowano ważne dla wiązania adhezyny Dr uropatogennych Escherichiacoli reszty aminokwasowe w ludzkim receptorze DAF SCR-3.
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Analysis of interactions responsible for vasopressin binding to human neurohypophyseal hormone receptors—molecular dynamics study of the activated receptor–vasopressin–Gα systems
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Characterization of a single-stranded DNA-binding-like Protein from Nanoarchaeum equitans - a nucleic acid binding protein with broad substrate specificity
PublikacjaBackground SSB (single-stranded DNA-binding) proteins play an essential role in all living cells and viruses, as they are involved in processes connected with ssDNA metabolism. There has recently been an increasing interest in SSBs, since they can be applied in molecular biology techniques and analytical methods. Nanoarchaeum equitans, the only known representative of Archaea phylum Nanoarchaeota, is a hyperthermophilic, nanosized,...
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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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The Influence of Binding Agents on Stiffness of Mineral-cement-emulsion Mixtures
PublikacjaThis 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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Synthesis, structure, DNA binding and anticancer activity of mixed ligand ruthenium(II) complex
PublikacjaIn order to obtain a potential chemotherapeutic which is not affected on the normal BALB/3T3 cell line, a new arene ruthenium(II) complex {[RuCl(L1)(η6-p-cymene)]PF6}2 · H2O has been synthesized by a direct reaction of precursor, [{(η6-p-cymene)Ru(μ-Cl)}2Cl2], with N,N-chelating ligand (L1 - 2,2′-bis(4,5-dimethylimidazole). The compound has been fully characterized by elemental analysis, X-ray diffraction, IR, UV–Vis and 1H, 13C...
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A Colorimetric Microplate Assay for DNA-Binding Activity of His-Tagged MutS Protein
PublikacjaA simple microplate method was designed for rapid testing DNA-binding activity of proteins. The principle of the assay involves binding of tested DNA by his-tagged protein immobilized on a nickel-coated ELISA plate, following colorimetric detection of biotinylated DNA with avidin conjugated to horseradish peroxidase. The method was used to compare DNA mismatch binding activities of MutS proteins from three bacterial species. The...
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Induced circularly polarized luminescence for revealing DNA binding with fluorescent dyes
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Novel single-stranded DNA-binding protein from psyvhrophilic bacterium Psychrobacter arcticus
PublikacjaTo study the biochemical properties of SSB from Psychrobacter arcticus (ParSSB), we have cloned the ssb genes obtained by PCR and have developed Escherichia coli overexpression systems. The gene consists of an open reading frame of 642 nucleotides encoding SSB protein of 213 amino acids with a calculated molecular mass of 22.8 kDa. The amino-acid sequence of ParSSB exhibits 49% identity and 57% similarity to Escherichia coli SSB....
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Identification and properties of the psychrophilic bacterium Desulfolatea psychrophila single-stranded DNA binding proteins
PublikacjaTo study the biochemical properties of SSB from Desulfolatea psychrophila (DpsSSB), we have cloned the ssb genes obtained by PCR and have developed Escherichia coli overexpression systems. The gene consists of an open reading frame of 426 nucleotides encoding SSB protein of 142 amino acids with a calculated molecular mass of 15.6 kDa and it is the smallest known bacterial SSB protein indentified to date. The amino-acid sequence...
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Assessment of Adjustment of GNSS Railway Measurements with Parameter-Binding Conditions in a Stationary Scenario
PublikacjaThe 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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Identification and characterization of single-stranded DNA-binding protein from the facultative psychrophilic bacteria Pseudoalteromonas haloplanktis
PublikacjaSingle-stranded DNA-binding protein (SSB) plays an important role in DNA metabolism such as DNAreplication, repair, and recombination, and is essential for cell survival. This study reports on the ssb-likegene cloning, gene expression and characterization of a single-stranded DNA-binding protein of Pseudoal-teromonas haloplanktis (PhaSSB) and is the first report of such a protein from psychrophilic microorganism.PhaSSB possesses...
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The role of additives in improving the flammability and calorific value of leather shavings and the binding of chromium compounds in ash
PublikacjaLeather processing companies are struggling with the problem of increasing costs of post-production waste disposal. Therefore, the issue of thermal waste disposal at the plant and the use of generated heat in the production process is becoming more and more popular. Leather waste on its own does not allow for autothermal combustion despite the sufficient higher heating value (HHV). Therefore the Authors proposed to improve the...
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Novel single-stranded DNA-binding proteins from extreme psychrophilic bacterium Psychromonas ingrahamii 37
PublikacjaWe report the identification and characterization of the single-stranded DNA binding protein (SSB) from extreme psychrophilic bacterium Psychromonas ingrahamii 37 (PinSSB) that grows expotentially at -12°C and may well grow at even lower temperatures. PinSSB is one of the largest known bacterial SSB protein consisting 222 amino acid residues with a calculated molecular mass of 25.1 kDa. The analysis by gel filtration chromatography...
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In Vitro Studies on the Relationship Between the Antioxidant Activities of Some Berry Extracts and Their Binding Properties to Serum Albumin
PublikacjaThe aim of this study was to investigate the possibility to use the bioactive components from cape gooseberry (Physalis peruviana), blueberry (Vaccinium corymbosum), and cranberry (Vaccinium macrocarpon) extracts as a novel source against oxidation in food supplementation. The quantitative analysis of bioactive compounds (polyphenols, flavonoids, flavanols, carotenoids, and chlorophyll) was based on radical scavenging spectrophometric assays...
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Novel DNA-binding protein from Nanoarchaeum equitans Kin4-M binds all kinds of nucleic acids
PublikacjaNanoarchaeum equitans is the only known representative of Archaea phylum Nanoarchaeota and stands out as one of the tiniest known living organism. What is more it has smallest genome, which is only 490.885 base pairs long. It is also one of the most compact genomes. According to predictions about 95% of the DNA encodes proteins or stable RNA. Nanoarchaeum equitans lacks genes for most vital metabolic pathways including lipid, cofactor,...
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An insight into the mixed quantum mechanical-molecular dynamics simulation of a ZnII-Curcumin complex with a chosen DNA sequence that supports experimental DNA binding investigations
PublikacjaAn important aspect of research pertaining to Curcumin (HCur) is the need to arrest its degradation in aqueous solution and in biological milieu. This may be achieved through complex formation with metal ions. For this reason, a complex of HCur was prepared with ZnII, that is not likely to be active in redox pathways, minimizing further complications. The complex is monomeric, tetrahedral, with one HCur, an acetate and a molecule...
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Exploring thiophene-2-acetate and thiophene-3-acetate binding modes towards the molecular and supramolecular structures and photoluminescence properties of Pb(ii) polymers
PublikacjaTo evaluate the impact of the flexible positional isomeric ligands thiophene-2-acetate (2tpacCOO) andthiophene-3-acetate (3tpacCOO) on the construction and self-assembly process of Pb(II) polymers, twonovel compounds, [Pb(2tpacCOO)2(H2O)]n(1) and [Pb(3tpacCOO)2]n(2), were preparedviaanonhydro-thermal method with respect to green chemistry rules. The obtained polymers were fully characterized byelemental analysis, TG/DTG and PXRD,...
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Density functional theory calculations on entire proteins for free energies of binding: Application to a model polar binding site
PublikacjaIn drug optimization calculations, the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method can be used to compute free energies of binding of ligands to proteins. The method involves the evaluation of the energy of configurations in an implicit solvent model. One source of errors is the force field used, which can potentially lead to large errors due to the restrictions in accuracy imposed by its empirical nature....
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Comparison of Cadmium Cd2+ and Lead Pb2+ Binding by Fe2O3@SiO2‐EDTA Nanoparticles – Binding Stability and Kinetic Studies
PublikacjaThis study describes the synthesis and characterization of ethylenediaminetetraacetic acid (EDTA) functionalized magnetic nanoparticles of 20 nm in size – Fe3O4@SiO2‐EDTA – which were used as a novel magnetic adsorbent for Cd(II) and Pb(II) binding in aqueous medium. These nanoparticles were obtained in two‐stage synthesis: covering by tetraethyl orthosilicate and functionalization with EDTA derivatives. Nanoparticles were characterized...
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Probing the binding selected metal ions and biologically active substances to the antimicrobial peptide LL-37 using DSC, ITC measurements and calculations
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Lower rim substituted p-tert-butylcalix[4]arene; Part 14. Synthesis, structures and binding studies of calix[4]arene thioamides
PublikacjaA number of p-tert-butylcalix[4]arene thioamides were synthesized and characterized by 1H-NMR and elemental analysis. Compounds 1-5 are O-substituted derivatives with -CH2-C(=S)-N-X groups, where NX = morpholidyl, NEt2, NHC2H4Ph, NHCH2Ph and NHEt,respectively. The X-ray structures of the ligands 1, 3, 5 and of the complex 3Pb(ClO4)2, (compound 6), are presented and their slightly distorted cone conformation is established. The...
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An excess electron binding to the `purple' zwitterion quinonoid
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Identification and characterization of single-stranded-DNA-binding proteins from Thermus thermophilus and Thermus aquaticus - new arrangement of binding domains
PublikacjaOkreślono molekularne właściwości białek SSB-podobnych z Thermus thermophi-lus i T. aquaticus. Zbadano aktywność białek oraz termostabilność. Ponadto, dowiedziono homodimeryczność obu białek i ustalono minimalną sekwencję wiążącą ssDNA.
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Recycling of waste tires in the light of binding law in Poland
PublikacjaA risings of large quantities of used rubber products, especially used tires has been increasing every year in Poland, in 2006 it was 160 thousand. The waste management and recycling of used tires become a major environmental problem. Well known methods of utilization of used tires are presented in this article. The main problem is ignorance of the law by tyre manufactures and users. In Poland first act on waste introduces ban...
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DAF - and collagen-binding properties of chimeric Dr fimbriae
PublikacjaEkspozycja białek heterologicznych na powierzchni mikroorganizmów jest jedną z nowych strategii stosowanych w mikrobiologii, biotechnologii oraz projektowaniu nowoczesnych szczepionek. W niniejszej pracy zbadano możliwość wykorzystania białka podjednostkowego DraE fimbrii Dr uropatogennych szczepów Escherichia coli jako nośnika heterologicznych sekwencji. W rejon odpowiadający N-terminalnej domenie 2 białka DraE wprowadzono epitopową...
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Characterization of single-stranded DNA-binding proteins from the psychrophilic bacteria
PublikacjaSingle-stranded DNA-binding proteins (SSBs) are indispensable elements in the cells of all living organisms. SSB proteins interact with ssDNA insequence in an independent manner, preventing them from forming secondary structures and from degradation by nucleases. In this way, SSB-binding proteins participate in all processes involving ssDNA, such as replication, repair and recombination. Although there are differences in amino...
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Characterization of single-stranded DNA-binding proteins from the psychrophilic bacteria
PublikacjaSingle-stranded DNA-binding proteins (SSBs) are indispensable elements in the cells of all living organisms. SSB proteins interact with ssDNAinsequence in an independent manner, preventing them from forming secondary structures and from degradation by nucleases. In this way, SSB-binding proteins participate in all processes involving ssDNA, such as replication, repair and recombination.Although there are differences in amino acid...
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Computational methods for calculation of binding free energy for ligand-receptor complexes
PublikacjaAccurate description of the molecular complexes energetic influence is required for understanding of many biological functions carried out by proteins. Therefore, estimation of binding free energy for ligand-receptor complexes is of highest importance for structure-based ligand design and drug discovery approaches.Experimental methods of determination of difference in Gibbs'es free energy have many limitations. Thus, computational...
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Data on solutions of Hes1 system
Dane BadawczeHes1 protein (hairy and enhancer of split 1) belongs to the helix-loop-helix (bHLH) family of transcription proteins, i.e. DNA-binding proteins in the promoter region or in another region where regulation of transcription processes occurs. The database collects data on solutions of the Hes1 systems with multiple binding sites and the dimer formation...
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In vitro antioxidative and binding properties of phenolics in traditional, citrus and exotic fruits
PublikacjaMany polyphenols bind proteins, therefore our research was focused on the potential of protein binding to polyphenols of investigated fruits and their health-related effects. The contents of polyphenols and related antioxidant activities of traditional, citrus and exotic fruits were compared. The presence of polyphenols (flavonoids and phenolic acids) in the investigated samples and their interaction with human serum albumin (HSA)...
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Analysis of a gene expression model
PublikacjaWe study a mathematical model of gene transcription and protein synthesis with negative feedback. We consider a system of equations taking into account the number of active binding sites, the way in which dimers bind to DNA and time delay in translation process. For a simplified model that consist of three ordinary differential equations with time delay we derive conditions for stability of the positive steady state and for the...
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Effect of Ion and Binding Site on the Conformation of Chosen Glycosaminoglycans at the Albumin Surface
PublikacjaAlbumin is one of the major components of synovial fluid. Due to its negative surface charge, it plays an essential role in many physiological processes, including the ability to form molecular complexes. In addition, glycosaminoglycans such as hyaluronic acid and chondroitin sulfate are crucial components of synovial fluid involved in the boundary lubrication regime. This study presents the influence of Na+, Mg2+ and Ca2+ ions...
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Functionalized azobenzocrown ethers as sensor materials—The synthesis and ion binding properties
PublikacjaNew 13- and 16-membered azobenzocrown ethers with aromatic amino, amide, ether–ester or ether–amide residue in para position to an azo moiety were obtained. Acid–base properties and ion binding ability of the colored compounds were studied by spectroscopic methods: UV–vis, fluorimetry and 1H NMR spectroscopy. Selected azobenzocrowns were tested as ionophores in ion-selective membrane electrodes (ISEs) – classic and miniature all...
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Structure of liquid gold from tight-binding driven molecular-dynamics
PublikacjaPraca przedstawia wyniki symulacji ciekłego złota w nadkomórce periodycznej przy użyciu stworzonego przez autorów programu komputerowego, za pomocą połączonych metod dynamiki molekularnej (MD) i ciasnego wiązania (TB). Omówiono strukturę tak symulowanej cieczy, porównując ją z dostępnymi danymi doświadczalnymi oraz wynikami innych symulacji, pod kątem radialnej i kątowej funkcji rozkładu i elektronowej gęstości stanów.A tight-binding...
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Syntheses and DNA binding of new cationic porphyrin–tetrapeptide conjugates
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Binding of new cationic porphyrin–tetrapeptide conjugates to nucleoprotein complexes
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Copper binding by the cystatin C fragment. The role of histidine residues
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Carotenoid binding to proteins: Modeling pigment transport to lipid membranes
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Binding free energy of selected anticancer compounds to DNA - theoreticalcalculations
PublikacjaPraca 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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Positron binding to alkali-metal hydrides: The role of molecular vibrations
PublikacjaThe bound vibrational levels for J=0 have been computed for the series of alkali-metal hydride molecules from LiH to RbH, including NaH and KH. For all four molecules the corresponding potential-energy curves have been obtained for each isolated species and for its positron-bound complex (e+XH). It is found that the calculated positron affinity values strongly depend on the molecular vibrational state for which they are obtained...
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Optimising DNA binding to carbon nanotubes by non-covalent methods
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Obtaining ionic forces by the total-energy tight-binding method
PublikacjaZastosowanie metody ciasnego wiązania w sformułowaniu nieortogonalnym do obliczania sił atomowych w symulacji metodą dynamiki molekularnej pozwala na stworzenie modelu charakteryzującego się lepszą przenośnością, w porównaniu z potencjałami empirycznymi, którymi posługuje się tradycyjna dynamika molekularna. W niniejszej pracy przedstawiono szczegółowo sposób obliczenia pochodnych elementów macierzy Hamiltona i macierzy nakładania...
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Metals and metal-binding ligands in wine: Analytical challenges in identification.
PublikacjaBackground Due to important role of metals in the vinification process as well as their impact on the human health, their content in this alcoholic beverage has been extensively studied by many researchers. It is already known that speciation of metals determines their toxicity and bioavailability as well as influences their activity. Understanding the chemistry and knowing the structures of metal complexes could have relevant...
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DNAffinity: a machine-learning approach to predict DNA binding affinities of transcription factors
PublikacjaWe present a physics-based machine learning approach to predict in vitro transcription factor binding affinities from structural and mechanical DNA properties directly derived from atomistic molecular dynamics simulations. The method is able to predict affinities obtained with techniques as different as uPBM, gcPBM and HT-SELEX with an excellent performance, much better than existing algorithms. Due to its nature, the method can...
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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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Geometry optimization of steroid sulfatase inhibitors - the influence on the free binding energy with STS
PublikacjaIn the paper we review the application of two techniques (molecular mechanics and quantum mechanics) to study the influence of geometry optimization of the steroid sulfatase inhibitors on the values of descriptors coded their chemical structure and their free binding energy with the STS protein. We selected 22 STS-inhibitors and compared their structures optimized with MM+, PM7 and DFT B3LYP/6–31++G* approaches considering separately...
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Naphthyl-vs. anthrylpyridine-2,6-dicarboxamides in cation binding studies. Synthesis and spectroscopic properties
PublikacjaPyridine-2,6-carboxamides bearing - or -naphthyl- and - or -anthryl- residues were prepared using simple method from pyridine-2,6-carboxylic acid dichloride and the respective aromatic amines. For the obtained receptors selective binding of lead(II), and copper(II) was found. Ion-receptor interactions were studied using UV-vis spectroscopy, spectrofluorimetry, 1H NMR, and FTIR spectroscopy. The reversible lead(II) and copper(II)...
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Common functionally important motions of the nucleotide‐binding domain of H sp70
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Riboflavin binding protein—Chiral stationary phase: Investigation of retention mechanism
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