Wyniki wyszukiwania dla: BINDING
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Molecular basis and quantitative assessment of TRF1 and TRF2 protein interactions with TIN2 and Apollo peptides
PublikacjaShelterin is a six-protein complex (TRF1, TRF2, POT1, RAP1, TIN2, and TPP1) that also functions in smaller subsets in regulation and protection of human telomeres. Two closely related proteins, TRF1 and TRF2, make high-affinity contact directly with double-stranded telomeric DNA and serve as a molecular platform. Protein TIN2 binds to TRF1 and TRF2 dimer-forming domains, whereas Apollo makes interaction only with TRF2. To elucidate...
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Optimization of Chemical Functionalities of Indole-2-carboxamides To Improve Allosteric Parameters for the Cannabinoid Receptor 1 (CB1)
Publikacja5-Chloro-3-ethyl-N-(4-(piperidin-1-yl)phenethyl)-1H-indole-2-carboxamide (1; ORG27569) is a prototypical allosteric modulator for the cannabinoid type 1 receptor (CB1). Here, we reveal key structural requirements of indole-2-carboxamides for allosteric modulation of CB1: a critical chain length at the C3-position, an electron withdrawing group at the C5-position, the length of the linker between the amide bond and the phenyl ring...
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In vitro affinity of Deinococcus radiodurans MutS towards mismatched DNA exceeds that of its orthologues from Escherichia coli and Thermus thermophilus
PublikacjaThe mismatch binding protein MutS is responsible for the recognition of mispaired and unpaired bases, which is the initial step in DNA repair. Among the MutS proteins most extensively studied in vitro are those derived from Thermus thermophilus, Thermus aquaticus and Escherichia coli. Here, we present the first report on the in vitro examination of DNA mismatch binding activity of MutS protein from Deinococcus radiodurans and confront...
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Towards β-selectivity in functional estrogen receptor antagonists
PublikacjaBased on the benzo[b]naphtho[1,2-d]furan and benzo[b]naphtho[1,2-d]thiophene frameworks, a series of ligands with different basic side chains (BSCs) has been synthesized and pharmacologically evaluated. Also, their binding modes have been modelled using docking techniques. It was found that the introduction of a BSC in these systems brings about a decrease of affinity for both estrogen receptors α and β in an in vitro competitive...
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Justification of quasi-stationary approximation in models of gene expression of a self-regulating protein
PublikacjaWe analyse a model of Hes1 gene transcription and protein synthesis with a negative feedback loop. The effect of multiple binding sites in the Hes1 promoter as well as the dimer formation process are taken into account. We consider three, possibly different, time scales connected with: (i) the process of binding to/dissolving from a binding site, (ii) formation and dissociation of dimers, (iii) production and degradation of Hes1...
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Determination of long-chain aldehydes using a novel quartz crystal microbalance sensor based on a biomimetic peptide
PublikacjaThere is an increasingly popular trend aimed at improvement of fundamental metrological parameters of sensors via implementation of materials mimicking biological olfactory systems. This study presents investigation on usefulness of the peptide mimicking HarmOBP7 region as a receptor element of the piezoelectric sensor for selective analysis of long-chain aldehydes. Identification of odorant binding proteins creates new possibilities...
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Collagen Type II—Chitosan Interactions as Dependent on Hydroxylation and Acetylation Inferred from Molecular Dynamics Simulations
PublikacjaChitosan–collagen blends have been widely applied in tissue engineering, joints diseases treatment, and many other biomedical fields. Understanding the affinity between chitosan and collagen type II is particularly relevant in the context of mechanical properties modulation, which is closely associated with designing biomaterials suitable for cartilage and synovial fluid regeneration. However, many structural features influence...
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The estrogenicity of wastewater samples.
Dane BadawczeThe principle of operation of the kit is based on the fact that the tested sample with endocrine activity (containing compounds capable of binding to the human estrogen receptor α, hERα) releases the fluorescently labeled ligand (FluormoneTM ES2) from the receptor-ligand complex, which results in a reduction of the polarization value fluorescence. The...
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Complex modulus of Cement Bitumen Treated Material Mixture (28 days of curing at 20C)
Dane BadawczeDataset presents data of complex modulus determined for cold recycled mixture – cement bitumen treated material mixture with 3 combinations of binding agents: 2% cement, 6% emulsion (C2E6), 6% cement, 6% emulsion (C6E6), 6% cement, 2% emulsion (C6E2). Mixture was designed according to Polish requirements for the base course of pavement. Mixture contains...
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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
PublikacjaEvolution 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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Evolution towards simplicity in bacterial small heat shock protein system
PublikacjaEvolution 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 two...
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Characterization of Bioactivity of Selective Molecules in Fruit Wines by FTIR and NMR Spectroscopies, Fluorescence and Docking Calculations
PublikacjaFourier transform infrared (FTIR) and proton nuclear magnetic resonance (1H NMR) spectroscopies were applied to characterize and compare the chemical shifts in the polyphenols’ regions of some fruit wines. The obtained results showed that FTIR spectra (1800–900 cm−1) and 1H NMR (δ 6.5–9.3 ppm) of different fruit wines can be used as main indices of the year of vintage and quality of fruit wines. In addition to the classical determination...
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Mechanochemical Energy Transduction during the Main Rotary Step in the Synthesis Cycle of F1-ATPase
PublikacjaF1-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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A mobile loop order–disorder transition modulates the speed of chaperonin cycling
PublikacjaMolecular machines order and disorder polypeptides as they form and dissolve large intermolecular interfaces, but the biological significance of coupled ordering and binding has been established in few, if any, macromolecular systems. The ordering and binding of GroES co-chaperonin mobile loops accompany an ATP-dependent conformational change in the GroEL chaperonin that promotes client protein folding. Following ATP hydrolysis,...
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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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Complex modulus of Cement Bitumen Treated Material Mixture C3E4 laboratory mixed/laboratory compacted (7-365 days of curing at 20C)
Dane BadawczeDataset presents data of complex modulus determined for cold recycled mixture – cement bitumen treated material mixture with following binding agents: 3% cement, 4% emulsion (C3E4). Mixture was designed according to Polish requirements for the base course of pavement. Mixture was mixed in laboratory conditions on the basis of materials obtained from...
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Complex modulus of Cement Bitumen Treated Material Mixture C3E4 field mixed/laboratory compacted (7-365 days of curing at 20C)
Dane BadawczeDataset presents data of complex modulus determined for cold recycled mixture – cement bitumen treated material mixture with following binding agents: 3% cement, 4% emulsion (C3E4). Mixture was designed according to Polish requirements for the base course of pavement. Mixture was mixed in the field conditions and later compacted in laboratory. Mixture...
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Deformation Sweep Test of Cement Bitumen Treated Material Mixture C3E5.5 (field obtained material; over 28 days of curing at 20C)
Dane BadawczeDataset presents data of results of deformation sweep test determined for cold recycled mixture – cement bitumen treated material mixture with following binding agents: 3% cement and 5.5% emulsion (C3E5.5). Mixture was designed according to Polish requirements for the base course of pavement. Mixture contains 60% of RAP material. Specimen size: f=100...
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Deformation Sweep Test of Cement Bitumen Treated Material Mixture C3E5.5 (field cores; field curing)
Dane BadawczeDataset presents data of results of deformation sweep test determined for cold recycled mixture – cement bitumen treated material mixture with following binding agents: 3% cement and 5.5% emulsion (C3E5.5). Mixture was designed according to Polish requirements for the base course of pavement. Mixture contains 60% of RAP material. Specimen size: f=100...
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Cation sensing by diphenyl-azobenzocrowns
PublikacjaMetal cations complexation and proton binding by 13- and 16-membered diphenyl-azobenzocrowns and diphenyl-hydroxyazobenzocrowns were studied in acetonitrile using spectroscopic methods: UV–vis spectroscopy, spectrofluorimetry, and 1H NMR spectroscopy. Phenyl moieties in benzene rings were found to affect binding strength alkali and alkaline earth metal cations and hydrogen ion, and affect tautomeric equilibrium of hydroxyazobenzocrowns....
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Telomere uncapping by common oxidative guanine lesions: Insights from atomistic models
PublikacjaOxidative damage to DNA is widely known to contribute to aging and disease. This relationship has been extensively studied for telomeres – structures that cap chromosome ends – due to their role in cell proliferation and senescence, and exceptional susceptibility to oxidation. Indeed, the repetitive telomeric DNA sequence contains the 5′-GGG-3′ motif that has the lowest ionization potential of all trinucleotides. Accordingly, experiments...
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Complex modulus of Cement Bitumen Treated Material Mixture C3E4 cores obtained from the field section (28-365 days of curing at the field and later in laboratory at 20C)
Dane BadawczeDataset presents data of complex modulus determined for cold recycled mixture – cement bitumen treated material mixture with following binding agents: 3% cement, 4% emulsion (C3E4). Mixture was designed according to Polish requirements for the base course of pavement. Specimen were obtained from the field at 28, 180, 270 and 365 days after compaction....
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Fatigue data of Cement Bitumen Treated Material Mixture C3E5.5 (over 28 days of curing at 20C)
Dane BadawczeFatigue data of Cement Bitumen Treated Material Mixture C3E5.5 (over 28 days of curing at 20C)
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Complex modulus of Cement Bitumen Treated Material Mixture C3E5.5 (over 28 days of curing at 20C)
Dane BadawczeDataset presents data of complex modulus determined for cold recycled mixture – cement bitumen treated material mixture with following binding agents: 3% cement and 5.5% emulsion (C3E5.5). Mixture was designed according to Polish requirements for the base course of pavement. Mixture contains 60% of RAP material. Specimen size: f=100 mm, h=130 mm. Specimen...
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Fatigue data of Cement Bitumen Treated Material Mixture C3E5.5 (over 28 days of curing at 20C, field cores)
Dane BadawczeDataset presents data of fatigue life determined for cold recycled mixture – cement bitumen treated material mixture with following binding agents: 3% cement and 5.5% emulsion (C3E5.5). Mixture was designed according to Polish requirements for the base course of pavement. Mixture contains 60% of RAP material. Specimen size: f=100 mm, h=48,4 - 70,9 mm.
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Chemical investigation of the Al2O3 ultra-thin films
Dane BadawczeUltra-thin layers of oluminum oxide (Al2O3) were deposited by ALD method. Atomic layer deposition provides precise thickness control down to a single atomic layer. The precursors used were trimethylaluminum (Sigma-Aldrich) and purified water. The deposition of the atomic layer was carried out at 200 °C. Samples with a thickness of 2 and 8 nm of alumina...
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High resolution XPS analysis of BDD electrode functionalization steps towards SARS-CoV-2 detection
Dane BadawczeThis dataset contains the results of the high-resolution XPS analyses of a set of boron-doped diamond (BDD) electrodes after consecutive functionalization steps toward anchoring of a receptor capable of SARS-CoV-2 virus detection. The analysis was carried out in the binding energy range of C1s, N1s, O1s, Ni2p3/2. The measurements were carried out on...
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Identification of 1H‐indene‐(1, 3, 5, 6)‐tetrol derivatives as potent pancreatic lipase inhibitors using molecular docking and molecular dynamics approach
PublikacjaPancreatic lipase is a potential therapeutic target to treat diet-induced obesity in humans, as obesity-related diseases continue to be a global problem. Despite intensive research on finding potential inhibitors, very few compounds have been introduced to clinical studies. In this work, new chemical scaffold 1H-indene-(1,3,5,6)-tetrol was proposed using knowledge-based approach, and 36 inhibitors were derived by modifying its...
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Unusual structural properties of water within the hydration shell of hyperactive antifreeze protein
PublikacjaMany hypotheses can be encountered explaining the mechanism of action of antifreeze proteins. One widespread theory postulates that the similarity of structural properties of solvation water of antifreeze proteins to ice is crucial to the antifreeze activity of these agents. In order to investigate this problem, the structural properties of solvation water of the hyperactive antifreeze protein from Choristoneura fumiferana were...
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The Impact of Long-Time Chemical Bonds in Mineral-Cement-Emulsion Mixtures on Stiffness Modulus
PublikacjaDeep cold in-place recycling is the most popular method of reuse of existing old and deteriorated asphalt layers of road pavements. In Poland, in most cases, the Mineral-Cement-Emulsion mixture technology is used, but there are also applications combining foamed bitumen and cement. Mineral-Cement-Emulsion mixtures contain two different binding agents – cement as well as asphalt from the asphalt emulsion. Asphalt creates asphalt...
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Why do G-quadruplexes dimerize through the 5’-ends? Driving forces for G4 DNA dimerization examined in atomic detail
PublikacjaG-quadruplexes (G4) are secondary structures formed by guanine-rich nucleic acid sequences and shown to exist in living cells where they participate in regulation of gene expression and chromosome maintenance. G-quadruplexes with solvent-exposed guanine tetrads show the tendency to associate together through cofacial stacking, which may be important for packaging of G4-forming sequences and allows for the design of higher-order...
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Texture or Linker? Competitive Patterning of Receptor Assembly toward Ultra-Sensitive Impedimetric Detection of Viral Species at Gold-Nanotextured Titanium Surfaces
PublikacjaIn this work, we study the electrodes with a periodic matrix of gold particles pattered by titanium dimples and modified by 3-mercaptopropionic acid (MPA) followed by CD147 receptor grafting for specific impedimetric detection of SARS-CoV-2 viral spike proteins. The synergistic DFT and MM/MD modeling revealed that MPA adsorption geometries on the Au–Ti surface have preferential and stronger binding patterns through the carboxyl...
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The interactions of monomeric acridines and unsymmetrical bisacridines (UAs) with DNA duplexes: an insight provided by NMR and MD studies
PublikacjaMembers of a novel class of anticancer compounds, exhibiting high antitumor activity, i.e. the unsymmetrical bisacridines (UAs), consist of two heteroaromatic ring systems. One of the ring systems is an imidazoacridinone moiety, with the skeleton identical to the structural base of Symadex. The second one is a 1-nitroacridine moiety, hence it may be regarded as Nitracrine’s structural basis. These monoacridine units are connected...
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Modification of quaternary structure of Candida albicans GlcN-6-P synthase and its desensitization to inhibition by UDP-GlcNAc by site-directed mutagenesis
PublikacjaSite-directed mutagenesis of the CaGFA1 gene encoding glucosamine-6-phosphate synthase from Candida albicans was performed. Desensitization of the enzyme to inhibition by UDPGlcNAc was achieved upon T487I and H492F substitutions at the UDP-GlcNAc binding site, exchange of D524, S525 and S527 for Ala at the dimer:dimer interface and construction of the tail-lock array (L434R and L460A) at the C-tail region. The first two sets if...
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Characterization of metabolites in different kiwifruit varieties by NMR and fluorescence spectroscopy
PublikacjaIt is known from our previous studies that kiwifruits, which are used in common human diet, have preventive properties of coronary artery disease. This study describes a combination of 1H NMR spectroscopy, multivariate data analyses and fluorescence measurements in differentiating of some kiwifruit varieties, their quenching and antioxidant properties. A total of 41 metabolites were identified by comparing with literature data...
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Bacteriophages as Factories for Eu2O3 Nanoparticle Synthesis
PublikacjaThe use of phage display to identify peptides with an ability to bind and synthesize Eu2O3 nanoparticles is demonstrated in this report. This is the first report of modified phages specifically binding a lanthanide. The peptides exposed on virions revealed very strong binding to Eu2O3 nanoparticles and the ability to catalyze Eu2O3 nanoparticles’ formation from Eu(OH)3 and Eu(NO3)3 solutions. The luminescence emission spectrum...
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Long-range, water-mediated interaction between a moderately active antifreeze protein molecule and the surface of ice
PublikacjaUsing molecular dynamics simulations, we show that a molecule of moderately active antifreeze protein (type III AFP, QAE HPLC-12 isoform) is able to interact with ice in an indirect manner. This interaction occurs between the ice binding site (IBS) of the AFP III molecule and the surface of ice, and it is mediated by liquid water which separates these surfaces. As a result, the AFP III molecule positions itself at a specific orientation...
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The long-term properties of mineral-cement-emulsion mixtures
PublikacjaThis publication presents evaluation of long-term behavior of mineral-cement-emulsion (MCE) mixtures. MCE mixtures are among the major products of cold recycling of old asphalt pavements. They are composed by binding of the old materials reclaimed from the pavement and new mineral aggregate using two different binding agents – cement and bituminous emulsion. While bituminous emulsion dissolutes and binds materials quite fast, it...
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Mapping the Transglycosylation Relevant Sites of Cold-Adapted β-D-Galactosidase from Arthrobacter sp. 32cB
PublikacjaB-Galactosidase from Arthrobacter sp. 32cB (ArthbetaDG) is a cold-adapted enzyme able to catalyze hydrolysis of beta-D-galactosides and transglycosylation reaction, where galactosyl moiety is being transferred onto an acceptor larger than a water molecule. Mutants of ArthbetaDG D207A and E517Q were designed to determine the significance of specific residues and to enable formation of complexes with lactulose and sucrose and to...
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Marek Zienkiewicz dr inż.
OsobyDoktor inżynier Marek Hubert dwojga imion Zienkiewicz jest absolwentem Wydziału Geodezji, Inżynierii Przestrzennej i Budownictwa Uniwersytetu Warmińsko-Mazurskiego w Olsztynie. Zainteresowania naukowe w okresie studiów inżynierskich, magisterskich i doktoranckich rozwijał pod opieką przedstawicieli olsztyńskiej szkoły geodezyjnego rachunku wyrównawczego. W roku 2011 uzyskał tytuł zawodowy magistra inżyniera w zakresie geodezji...
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Deflection measurement of field section with pavement with base course made of Cement Bitumen Treated Material Mixture C3E4 (28, 180, 270, 365 days after compaction)
Dane BadawczeDataset presents data of deflections determined for pavement with base course made of cold recycled mixture – cement bitumen treated material mixture with following binding agents: 3% cement, 4% emulsion (C3E4). Mixture was designed according to Polish requirements for the base course of pavement. Mixture was mixed in stationary plant and compacted...
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Fatigue data of Cement Bitumen Treated Material Mixture C3E5.5 (Direct tension, over 28 days of curing at 20C)
Dane BadawczeFatigue data of Cement Bitumen Treated Material Mixture C3E5.5 (Direct tension, over 28 days of curing at 20C)
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Depth profile of the composition of 8 nm Al2O3 thin film
Dane Badawcze8 nm layer of aluminum oxide (Al2O3) was deposited by ALD method on a s. Atomic layer deposition provides precise thickness control down to a single atomic layer. The precursors used were trimethylaluminum (Sigma-Aldrich) and purified water. The deposition of the atomic layer was carried out at 200 °C. To investigate the profile of concenration of...
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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
PublikacjaThe 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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Influence of different cultivation systems on bioactivity of asparagus
PublikacjaEvaluation of functional and bioactive compounds of Asparagus officinalis L. growing in conventional and organic greenhouse and conventional open –field farming was the aim of this research. Polyphenols in cladodes grown conventionally were higher than organic. Flavonoids and carotenoids were the highest in cladodes in open field. Organic spears were richer in total phenolics (+6.9% and +19.1%) and flavonoids (+4.7% and 16.8%)...
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Selective detection of F- by chromogenic tetrazole receptor
PublikacjaA chromogenic anion host 4, containing two amide functionalities linked to azo dye and tetrazole rings was synthesized and its complexes with various anions were investigated. The results show that receptor 4 can recognize selectively biologically important F- ion. The binding affinity for F- was investigated by naked-eye colour change, UV-Vis and 1H NMR spectroscopy. Addition F- ion in CH3CN and DMSO to receptor 4 cause a colour...
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Immunoanalityka – użyteczne podejście analityczne w badaniach środowiska
PublikacjaWażnym krokiem w rozwoju bezpośrednich metodyk analitycznych było opracowanie technik immunoanalitycznych. Początkowo znalazły one zastosowanie praktyczne w analityce medycznej a później także w analityce środowiskowej. Dzięki temu możliwe jest ilościowe oznaczenie stosunkowo szerokiego spektrum ksenobiotyków w próbkach charakteryzujących się złożonym składem matrycy bez praco- i czasochłonnego etapu przygotowania tych próbek do...
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Benzonaza(R): możliwości praktycznych zastosowań.
PublikacjaBenzonaza znajduje zastosowanie w efektywnym obniżaniu lepkości i usuwaniu kwasów nukleinowych z roztworów białkowych. Zbadano w praktyce jej możliwości aplikacyjne w oczyszczaniu białek rekombinantowych wiążących jednoniciowe DNA (ang. SSB - single stranded DNA binding protein).
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Role of the Solvation Water in Remote Interactions of Hyperactive Antifreeze Proteins with the Surface of Ice
PublikacjaMost 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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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...