Search results for "binding"
showing 10 items of 3896 documents
Noroviral P-Particles as an In Vitro Model to Assess the Interactions of Noroviruses with Probiotics
2014
Noroviruses (NoVs) are the main etiologic agents of acute epidemic gastroenteritis and probiotic bacteria have been reported to exert a positive effect on viral diarrhea. The protruding (P) domain from NoVs VP1 capsid protein has the ability to assemble into the so-called P-particles, which retain the binding ability to host receptors. We purified the P-domains from NoVs genotypes GI.1 and GII.4 as 6X(His)-tagged proteins and determined that, similar to native domains, they were structured into P-particles that were functional in the recognition of the specific glycoconjugated receptors, as established by surface plasmon resonance experiments. We showed that several lactic acid bacteria (pr…
Computational approach to design of aptamers to the receptor binding domain of SARS-CoV-2
2021
The aim of the research. In this work, in silico selection of DNA-aptamers to the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein was performed using molecular modeling methods. Material and methods. A new computational approach to aptamer in silico selection is based on a cycle of simulations, including the stages of molecular modeling, molecular docking, molecular dynamic simulations, and quantum chemical calculations. To verify the obtained calculated results flow cytometry, fluorescence polarization, and small-angle X-ray scattering methods were applied. Results. An initial library consisted of 256 16-mer oligonucleotides was modeled. Based on molecular docking results, th…
Towards the understanding at the molecular level of the structured-water absorption and fluorescence spectra: a fingerprint of π-stacked water
2013
An intriguing absorption peak around ∼270 nm (4.59 eV) has been recurrently recorded in aqueous solutions of salts, sugars, amino acids, in the free-solute zone (exclusion zone) adjacent to various hydrophilic surfaces, as well as a transient in the conversion process of ice to water. The corresponding associated fluorescence has been observed in the interval 480–490 nm (2.58–2.53 eV). The spectroscopic features have been related to the presence of structured water but its nature remains incompletely understood. On the basis of high-level ab initio computations, the main absorption feature of structured water is assigned to the presence of two π-stacked ground-state water molecules, prefera…
DNA fluorescence induced by polymethine cation pyrvinium binding
1991
Pyrvinium is a polymethine cation which shows interesting fluorescence emission and DNA binding properties. In diluted aqueous solution, pyrvinium pamoate induced a bright yellow fluorescence in kinetoplast DNA from Trypanosoma cruzi epimastigotes as well as in chicken erythrocyte nuclei under a wide range of excitations. No fading was observed after mounting in suitable media. Spectroscopic studies on pyrvinium solutions revealed bathochromic and hypochromic shifts in the absorption spectrum of its complex with DNA. A striking enhancement of pyrvinium fluorescence was found in solvents of high viscosity or after binding to DNA. Experimental results and the chemical structure of pyrvinium a…
Water and oxoanion encapsulation chemistry in a 1H-pyrazole azacryptand
2019
Anion complexes of the cryptand built with the tripodal amine tris(2-aminoethyl)amine, known as tren, with water and several oxoanions of biological and environmental interest (nitrate, sulfate, phosphate, perchlorate and arsenate) have been crystallized from aqueous solution and resolved with single-crystal X-ray diffraction. All crystals show guest species encapsulated in the interior of the cavity as well as, in some cases, sitting in the grooves defined by the arms of the macrocycle. Hydrogen bonding and electrostatic interactions play a major role in anion binding to the host. The macrocycle is able to encapsulate anions in a wide range of protonation degrees. Solution studies have bee…
Application of the Generalized Molar-Ratio Method to the Determination of the Stoichiometry and Apparent Binding Constant of Nanoparticle-Organic Cap…
2015
A generalization of the molar-ratio method is applied to the determination of the stoichiometry and apparent binding constant of metal nanoparticle-organic capping complexes (MmLx) using voltammetric data for the oxygen reduction reaction (ORR) in air-saturated aqueous phosphate buffer solutions. The method is applied to the formation of binary nanohybrids consisting of gold nanoparticles (AuNPs) capped with a rigid spacer, cucurbit[7]uril (CB), termed AuNP@CB, as well as to the formation of their ternary complexes (MmLxBz) with methylene blue (MB), termed AuNP@CB@MB. The obtained stoichiometries correspond to binding of four Au surface atoms for each CB unit.
Exploring new water soluble bridged dicopper(II) assemblies: Synthesis, structure, spectroscopic characterization, properties, and their interactions…
2021
Abstract Three new water soluble dimetallic copper(II) complexes, [Cu(H2O)5][Cu2(cpdp)(µ-O2As(CH3)2)]2Br2·13.83H2O·0.67CH3OH (1), [Cu2(Hcpdp)(µ-SO4)]·5H2O (2) and [Cu2(cpdp)(µ-pz)]·16H2O (3) (H3cpdp = N,N′-Bis[2-carboxybenzomethyl]-N,N′-Bis[2-pyridylmethyl]-1,3-diaminopropan-2-ol; (CH3)2AsO2− = cacodylate; SO42− = sulfate; pz− = pyrazolate) have been successfully synthesized and characterized for the investigation of coordination/binding aspects with biologically significant monosaccharide, d -glucosamine. Preparation of 1, 2 and 3 has been achieved by carrying out reaction of H3cpdp with stoichiometric quantities of CuCl2·2H2O/NaO2As(CH3)2·3H2O, CuSO4·5H2O and CuCl2·2H2O/1H-pyrazole, respe…
Binding between (Ethylene Oxide)13−(Propylene Oxide)30−(Ethylene Oxide)13 and Sodium Decanoate. Volume, Enthalpy, and Heat Capacity Studies
2002
Volume, enthalpy, and heat capacity of transfer (ΔYt) of (ethylene oxide)13−(propylene oxide)30−(ethylene oxide)13 (L64), at some concentrations, from water to the aqueous sodium decanoate (NaDec) solutions as functions of the surfactant concentration (mS) were determined at 298 K. The copolymer was studied in both the unassociated and associated forms. For a given L64 concentration (mC), the ΔYt vs mS profiles for the volume and the enthalpy are equal but different from that of the heat capacity because the latter contains also the relaxation terms. The experimental data were analyzed by assuming the distribution of L64 between the aqueous and the micellar phases and the shift of micelliza…
Selective recognition of fluoride anion in water by a copper(II) center embedded in a hydrophobic cavity
2014
The ability of a water-soluble pentacationic calix[6]arene-based CuII complex to bind anions in water has been explored. Quite remarkably, the complex exhibits strong and selective fluoride binding in the pH range of 6–7. The binding constant at pH 5.9 was evaluated to be 85 000 M−1, which is one of the highest values ever reported for a fluoride probe in water and at this pH. The complex also binds chloride ions, but 1000 times less efficiently. The combination of the calix[6]arene hydrophobic cavity with the CuII complex, presenting its labile site in the endo position, is the reason for the selective recognition process. The single crystal X-ray structure of the organo-soluble parent com…
Diversification of CYCLOIDEA-like TCP genes in the basal eudicot families Fumariaceae and Papaveraceae s.str.
2006
CYCLOIDEA-like genes belong to the TCP family of transcriptional regulators and have been shown to control different aspects of shoot development in various angiosperm lineages, including flower monosymmetry in asterids and axillary meristem growth in monocots. Genes related to the CYC gene from ANTIRRHINUM show independent duplications in both asterids and rosids. However, it remains unclear to what extent this affected the evolution of flower symmetry and shoot branching in these and other eudicot lineages. Here, we show that CYC-like genes have also undergone duplications in two related Ranunculales families, Fumariaceae and Papaveraceae s.str. These families exhibit morphological divers…