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Search results for: ENERGY OF BINDING
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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
PublicationLeather 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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Mechanochemical Energy Transduction during the Main Rotary Step in the Synthesis Cycle of F1-ATPase
PublicationF1-ATPase is a highly efficient molecular motor that can synthesize ATP driven by a mechanical torque. Its ability to function reversibly in either direction requires tight mechanochemical coupling between the catalytic domain and the rotating central shaft, as well as temporal control of substrate binding and product release. Despite great efforts and significant progress, the molecular details of this synchronized and fine-tuned...
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Comparison of Cadmium Cd2+ and Lead Pb2+ Binding by Fe2O3@SiO2‐EDTA Nanoparticles – Binding Stability and Kinetic Studies
PublicationThis 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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Quantitative chirality in the binding of androgens to their receptor
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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
PublicationBackground 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
Publicationhas 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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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
PublicationOkreślono 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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DAF - and collagen-binding properties of chimeric Dr fimbriae
PublicationEkspozycja 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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Recycling of waste tires in the light of binding law in Poland
PublicationA 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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Low-energy positron scattering from gas-phase benzene
PublicationIn this paper we are presenting calculations of the elastic cross section of positrons with gas-phase benzene for the energy range from 0.25 eV to 9.0 eV. The calculations are done with the molecular R-matrix method for positron-scattering from poly-atomic molecules using a scaling factor to scale the electron-positron interaction. The scaling factor influences the position of the poles of the R-matrix. We adjust the scaling factor...
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Characterization of single-stranded DNA-binding proteins from the psychrophilic bacteria
PublicationSingle-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
PublicationSingle-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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In vitro antioxidative and binding properties of phenolics in traditional, citrus and exotic fruits
PublicationMany 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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Effect of Ion and Binding Site on the Conformation of Chosen Glycosaminoglycans at the Albumin Surface
PublicationAlbumin 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
PublicationNew 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
PublicationPraca 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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A Colorimetric Microplate Assay for DNA-Binding Activity of His-Tagged MutS Protein
PublicationA 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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Optimising DNA binding to carbon nanotubes by non-covalent methods
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Carotenoid binding to proteins: Modeling pigment transport to lipid membranes
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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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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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Metals and metal-binding ligands in wine: Analytical challenges in identification.
PublicationBackground 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
PublicationWe 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
PublicationThe 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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Naphthyl-vs. anthrylpyridine-2,6-dicarboxamides in cation binding studies. Synthesis and spectroscopic properties
PublicationPyridine-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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Serum Fatty Acid-Binding Protein 4 is Increased in Patients with Psoriasis
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Induced circularly polarized luminescence for revealing DNA binding with fluorescent dyes
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Maintenance and stabilization of mtDNA can be facilitated by the DNA-binding activity of Ilv5p
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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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Binding energies of Eu2+ and Eu3+ ions in β-Ca2SiO4 doped with europium
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Novel single-stranded DNA-binding protein from psyvhrophilic bacterium Psychrobacter arcticus
PublicationTo 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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Role of cholesterol in substrate recognition by -secretase
Publication-Secretase is an enzyme known to cleave multiple substrates within their transmembrane domains, with the amyloid precursor protein of Alzheimer’s Disease among the most prominent examples. The activity of -secretase strictly depends on the membrane cholesterol content, yet the mechanistic role of cholesterol in the substrate binding and cleavage remains unclear. In this work, we used all-atom molecular dynamics simulations to examine...
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Identification and properties of the psychrophilic bacterium Desulfolatea psychrophila single-stranded DNA binding proteins
PublicationTo 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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Thermodynamic, Anticoagulant, and Antiproliferative Properties of Thrombin Binding Aptamer Containing Novel UNA Derivative
PublicationThrombin is a serine protease that plays a crucial role in hemostasis, fibrinolysis, cell proliferation, and migration. Thrombin binding aptamer (TBA) is able to inhibit the activity of thrombin molecule via binding to its exosite I. This 15-nt DNA oligonucleotide forms an intramolecular, antiparallel G-quadruplex structure with a chair-like conformation. In this paper, we report on our investigations on the influence of certain...
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A Highly Selective Biosensor Based on Peptide Directly Derived from the HarmOBP7 Aldehyde Binding Site
PublicationThis paper presents the results of research on determining the optimal length of a peptide chain to eectively bind octanal molecules. Peptides that map the aldehyde binding site in HarmOBP7 were immobilized on piezoelectric transducers. Based on computational studies, four Odorant Binding Protein-derived Peptides (OBPPs) with dierent sequences were selected. Molecular modelling results of ligand docking with selected peptides were...
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Induced-fit binding of laccase to gold and carbon electrodes for the biological fuel cell applications
PublicationAnalogues of laccase natural substrates (syringic, veratric, ferulic, vanillic, isovanillic, 3,5-dimethoxybenzoic aldehydes) were employed to bind and orient laccase molecules in a way which facilitates adsorption of the catalyst molecules and their electrical connection with the conductive support. Laccase was bound efficiently to these substrates both on gold and carbon electrodes forming, respectively, 2D and 3D films sensitive...
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The Ellenbogen's "Matter as Software" Concept for Quantum Computer Implementation: II Bonding Between the C60 and X@C60 Molecules as Available Molecular Building Blocks (MBBs) for Tip-Based Nanofabrication (TBN) of Quantum Computing Devices
PublicationThe binding energy, BE of the X@C60-X@C60 homodimer and the X@C60-Y@C60 heterodimer resulting from the bond formation between the occupied X@C60 MBB and the C60 molecule was studied by means of semiempirical PM7 calculations, where X and Y denote atoms from H to Bi, excluding Tc and lanthanides. All possible combinations of N = 68 guest atoms were considered, which resulted in K = 2346 of different calculated dimers of (X@C60-Y@C60)...
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A highly thermostable, homodimeric single-stranded DNA-binding protein from Deinococcus radiopugnans
PublicationWe report the identification and characterization of the single-stranded DNA-binding protein (SSB) from the mesophile and highly radiation-resistant Deinococcus radiopugnans (DrpSSB). PCR-derived DNA fragment containing the complete structural gene for DrpSSB protein was cloned and expressed in Escherichia coli. The gene consisting of an open reading frame of 900 nucleotides encodes a protein of 300 amino acids with a calculated...
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Synthesis, structure, DNA binding and anticancer activity of mixed ligand ruthenium(II) complex
PublicationIn 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 cryptic ribosome binding site, false signals in reporter systems and avoidance of protein translation chaos
PublicationThe expression of reporter gene may be induced by activation of cryptic signalling sequences, as we found while constructing the mutS-lacZ fusion gene. We cloned the Escherichia coli lacZ gene encoding beta-galactosidase into a plasmid vector carrying the Thermus thermophilus mutS gene. The clones expected to produce beta-galactosidase as the C-terminal fusion were selected for the complementation of beta-galactosidase activity...
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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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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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Hybrid materials comprising trimethylglycinamide groups: immobilization consequences for anion binding affinities
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Assessment of Adjustment of GNSS Railway Measurements with Parameter-Binding Conditions in a Stationary Scenario
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