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Wyniki wyszukiwania dla: BINDING ANALYSIS
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Similarities and differences in affinity and binding modes of tricyclic pyrimido- and pyrazinoxanthines at human and rat adenosine receptors
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Novel thermostable ssDNA-binding proteins from Thermus thermophilus and T. aquaticus - expression and purification
PublikacjaBiałka SSB są niezbędne do życia każdemu organizmowi. W tej pracy prezentujemy wyniki otrzymania i oczyszczania białek SSB Thermus thermophilus i T. aquaticus. Dotąd były znane białka SSB jedynie o budowie homotetrameru lub heterotrimeru. Białka SSB Thermus thermophilus i T. aquaticus stanowią nową klasę białek SSB - białek homodimerycznych. Ponadto dowiedziono, iż białka te są użyteczne w reakcji PCR.
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Novel thermostable ssDNA-binding proteins from Thermus thermophilus and T. aquaticus-expression and purification
PublikacjaSklonowano w system ekspresyjny pET-30LIC Escherichia coli gen kodujący białka SSB-podobne Thermus thermophilus i T. aquaticus. Oczyszczono do homogenności białka SSB-podobne, a uzyskane preparaty umożliwiają wykonanie badań strukturalnych w/w białek.
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Irreversible alterations in the hemoglobin structure affect oxygen binding in human packed red blood cells
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Fusion of Taq DNA polymerase with single-stranded DNA binding-like protein of Nanoarchaeum equitans—Expression and characterization
PublikacjaDNA polymerases are present in all organisms and are important enzymes that synthesise DNA molecules. They are used in various fields of science, predominantly as essential components for in vitro DNA syntheses, known as PCR. Modern diagnostics, molecular biology and genetic engineering need DNA polymerases which demonstrate improved performance. This study was aimed at obtaining a new NeqSSB-TaqS fusion DNA polymerase from the...
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Analysis of IPv6 handovers in IEEE 802.16 environment
PublikacjaThe second generation of WiMAX solutions, based on IEEE 802.16-2005 standard, offers limited mobility support. Unfortunately, after quickly changing the point of attachment on the WiMAX data link layer (DLL), very slow and inefficient IPv6 reconfiguration takes place. Delays introduced by automatic configuration (DHCPv6 and IPv6 protocols) and Mobile IPv6 can easily diminish or even render useless all benefits gained using the...
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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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Predicting Value of Binding Constants of Organic Ligands to Beta-Cyclodextrin: Application of MARSplines and Descriptors Encoded in SMILES String
PublikacjaThe 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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Design of new cholinesterase inhibitors based on phosphorus analogs of tacrine as potential anti-Alzheimer’s disease agents
PublikacjaBased on the analysis of the determined free binding energy (using the AutoDock Vina 1.1.2 docking program), the most potent cholinesterase inhibitors were selected. Moreover, studies of 3D visualization of the results of molecular modeling led to the identification of potential sites for the interaction of new potential inhibitors with amino acid residues building active sites of investigated cholinesterases.
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The influence of combination of binding agents on fatigue properties of deep cold in-place recycled mixtures in Indirect Tensile Fatigue Test (ITFT)
PublikacjaThe publication presents fatigue properties of cold recycled mixtures for eight combinations of binding agents (cement and bituminous emulsion). Cold recycled mixtures were evaluated in Indirect Tensile Fatigue Test (ITFT) at the temperature of 20 C in controlled stress mode. As a function of horizontal stress, fatigue life is strongly influenced by combination of the binding agents. When fatigue life is analyzed as a function...
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Insights into the Effects of Cancer Associated Mutations at the UPF2 and ATP-Binding Sites of NMD Master Regulator: UPF1
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Highly Conserved Homotrimer Cavity Formed by the SARS-CoV-2 Spike Glycoprotein: A Novel Binding Site
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Synthesis and SAR Studies of Antibacterial Peptidyl Derivatives Based upon the Binding Site of Human Cystatin C
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Molecular dynamics study of a gelsolin-derived peptide binding to a lipid bilayer containing phosphatidylinositol 4,5-bisphosphate
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Liver fatty acid-binding protein might be a predictive marker of clinical response to systemic treatment in psoriasis
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Structure-activity relationship study of tetrapeptide inhibitors of the Vascular Endothelial Growth Factor A binding to Neuropilin-1
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Pharmacological characterization and binding modes of novel racemic and optically active phenylalanine-based antagonists of AMPA receptors
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Binding of anionic Pt(ii) complexes in a dedicated organic matrix: towards new binary crystalline composites
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Electron Binding Capabilities of Some Silylenes Having Small Singlet−Triplet Splittings or Triplet Ground States
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Strength of the Lewis–Brønsted Superacids Containing In, Sn, and Sb and the Electron Binding Energies of Their Corresponding Superhalogen Anions
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Fibronectin-, vitronectin- and laminin-binding proteins at the cell walls of Candida parapsilosis and Candida tropicalis pathogenic yeasts
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Molecular simulations study of ligand-release mechanism in an odorant-binding protein from the southern house mosquito
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Fusion of DNA-binding domain of Pyrococcus furiosus ligase with TaqStoffel DNA polymerase as a useful tool in PCR with difficult targets
PublikacjaThe DNA coding sequence of TaqStoffel polymer- ase was fused with the DNA-binding domain of Pyrococcus furiosus ligase. The resulting novel recombinant gene was cloned and expressed in E. coli. The recombinant enzyme was purified and its enzymatic features were studied. The fusion protein (PfuDBDlig-TaqS) was found to have enhanced processivity as a result of the conversion of the Taq DNA polymerase from a relatively low processive...
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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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Structural analysis and physico-chemical characterization of mononuclear manganese(II) and polynuclear copper(II) complexes with pyridine-based alcohol
PublikacjaTwo novel manganese(II) and copper(II) complexes, mononuclear [Mn(H2O)2(2-(CH2)2OHpy)2](NO3)2 (1) and polynuclear [Cu(SO4)(2-(CH2)2OHpy)2]n (2), based on 2-(hydroxyethyl)pyridine (2-(CH2)2OHpy) were synthesised and fully characterised using X-ray structure analysis as well as spectroscopic, magnetic and thermal methods. Both central metal ions Mn(1) and Cu(1) are coordinated by two N,O-donor 2-(CH2)2OHpy ligands and possess an...
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Analysis of Reconstituted Tripartite Complex Supports Avidity-based Recruitment of Hsp70 by Substrate Bound J-domain Protein
PublikacjaHsp70 are ubiquitous, versatile molecular chaperones that cyclically interact with substrate protein(s). The initial step requires synergistic interaction of a substrate and a J-domain protein (JDP) cochaperone, via its J-domain, with Hsp70 to stimulate hydrolysis of its bound ATP. This hydrolysis drives conformational changes in Hsp70 that stabilize substrate binding. However, because of the transient nature of substrate and JDP...
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Analysis of IPv6 Handovers in IEEE 802.16 environment
PublikacjaZaprezentowano pełną analizę wpływu poszczególnych faz procesu przełączania w warstwie drugiej i trzeciej na przerwy w transmisji wynikające ze zmiany stacji bazowej BS przez przemieszczający się węzeł ruchomy MN. Zaproponowano i przebadano symulacyjnie 10 scenariuszy przełączania, w tym 8 różnych algorytmów stanowej autokonfiguracji węzłów MN, wspierających protokół IPv6 w środowiskach sieci WiMAX. W badaniach wskazano na możliwości...
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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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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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Photoresponsive, amide-based derivative of embonic acid for anion recognition
PublikacjaThe synthesis and ion-binding properties of amide-based derivative of embonic acid andp-aminoazobenzenewere described. The new compound was characterized by X-ray structural analysis and spectroscopic methods.Ligand interacts in acetonitrile with Y-shaped anions (benzoates and acetates) and dihydrogen phosphatesforming complexes of 1:1 stoichiometry. In more polar DMSO the complexes stoichiometry changes to 2:1(L:anion). Light-inducedtranstocisisomerization...
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Studies of the Interaction Dynamics in Albumin-Chondroitin Sulfate Systems by Recurrence Method
PublikacjaThe physicochemical basis of lubrication of articular cartilage is still not fully understood. However, the synergy between components of the synovial fluid can be a crucial factor that could explain this phenomenon. This work presents a nonlinear data analysis technique named the recurrence method, applied to the system involving two components of synovial fluid: albumin and chondroitin sulfate (CS) immersed in a water environment....
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Structural and dynamic insights on the EmrE protein with TPP+ and related substrates through molecular dynamics simulations
PublikacjaEmrE is a bacterial transporter protein that forms an anti-parallel homodimer with four transmembrane helices in each monomer. EmrE transports positively charged aromatic compounds, such as TPP+ and its derivatives. We performed molecular dynamics (MD) simulations of EmrE in complex with TPP+, MeTPP+, and MBTPP+ embedded in a membrane. The detailed molecular properties and interactions were analysed for all EmrE-ligand complexes....
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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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Identification, cloning, expression, and characterizationof a highly thermostable single-stranded-DNA-binding protein (SSB) from Deinococcus murrayi
PublikacjaZidentyfikowano i scharakteryzowano białko SSB-podobne, pochodzące z Deinococcus murrayi (DmuSSB). Otrzymany w reakcji PCR fragment zawierający kompletny gen ssb sklonowano w systemie ekspresyjnym Escherichia coli. Gen składa się z 826 nt, kodujących 276 reszt aminokwasowych z wyliczoną teoretycznie masą cząsteczkową monomeru równą 30,14 kDa. DmuSSB zawiera dwie domeny wiążące jednoniciowe DNA OBna monomer I funkcjonuje jako homodimer....
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Structure and function of the Ts2631 endolysin of Thermus scotoductus phage vB_Tsc2631 with unique N-terminal extension used for peptidoglycan binding
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Physicochemical profile of Os (III) complexes with pyrazine derivatives: From solution behavior to DNA binding studies and biological assay
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Prenatal stress leads to changes in IGF-1 binding proteins network in the hippocampus and frontal cortex of adult male rat
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A Cu/Zn heterometallic complex with solvent-binding cavity, catalytic activity for the oxidation of 1-phenylethanol and unusual magnetic properties
PublikacjaMononuclear and polymeric complexes of zinc(II) and copper(II) have been synthesized using two isomers of the hemi-salen ligand with a different mutual orientation of donor atoms. The heterometallic Cu/Zn metallocycle features a catalytic niche filled with the molecule of water and molecules of methanol. This unusual compound exhibits both pronounced catalytic activity in the reaction of oxidation of a secondary alcohol to ketone...
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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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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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Mechanism of Binding of Antifungal Antibiotic Amphotericin B to Lipid Membranes: An Insight from Combined Single-Membrane Imaging, Microspectroscopy, and Molecular Dynamics
PublikacjaAmphotericin B is a lifesaving polyene antibiotic used in the treatment of systemic mycoses. Unfortunately, the pharmacological applicability of this drug is limited because of its severe toxic side effects. At the same time, the lack of a well-defined mechanism of selectivity hampers the efforts to rationally design safer derivatives. As the drug primarily targets the biomembranes of both fungi and humans, new insights into the...
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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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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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Corrigendum to “Binding energies of Eu2+ and Eu3+ ions in β-Ca2SiO4 doped with europium” [Opt. Mater. 35 (2013) 2107–2114]
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How do sterols determine the antufungal activitiy of amphotericin B? Free energy of binding between the drug and its membrane targets.
PublikacjaAmphotericin B (AmB) is a well-known polyene antibiotic used to treat systemic fungal infections. It is commonly accepted that the presence of sterols in the membrane is essential for the AmB biological activity, that is, for the formation of transmembrane ion channels. The selective toxicity of AmB for fungal cells is attributed to the fact that it is more potent against fungal cell membranes containing ergosterol than against...
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Design, synthesis and in vitro biological evaluation of a small cyclic peptide as inhibitor of vascular endothelial growth factor binding to neuropilin-1
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Branched pentapeptides as potent inhibitors of the vascular endothelial growth factor 165 binding to Neuropilin-1: Design, synthesis and biological activity
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Chemical composition of tellurium oxides thin films deposited by magnetron sputtering method
Dane BadawczeThin films were prepared by radio frequency reactive magnetron sputtering technique. Metallic Te target was sputtered for about 45 min in argon-oxygen atmosphere what resulted in 300 nm film thickness deposition. The pressure in the chamber was below 0.2 Pa and substrate was heated at 200 °C. The distance between sputtered target and the Corning 1737...
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Chemical, Aroma and Pro-Health Characteristics of Kaffir Lime Juice—The Approach Using Optimized HS-SPME-GC-TOFMS, MP-OES, 3D-FL and Physiochemical Analysis
PublikacjaThe study aimed to provide the chemical, aroma and prohealth characteristics of the kaffir lime juice. A procedure using solid-phase microextraction with gas chromatography (SPME-GC-TOFMS) was optimized and validated for the determination of terpenes of kaffir lime. Main physicochemical parameters: pH, vitamin C, citric acid and °Brix were evaluated. Micro- and macro elements were determined using microwave plasma optic emission...