Search results for "binding site"
showing 10 items of 856 documents
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…
The biomaterial polyphosphate blocks stoichiometric binding of the SARS-CoV-2 S-protein to the cellular ACE2 receptor
2020
The effect of the polyanionic polymer of inorganic polyphosphate (polyP) involved in innate immunity on the binding of the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein to the cellular ACE2 receptor was studied. The RBD surface comprises a basic amino acid stretch of four arginine residues which interact with the physiological polyP (polyP40) and polyP3. Subsequently, the interaction of RBD with ACE2 is sensitively inhibited. After the chemical modification of arginine, an increased inhibition by polyP, at a 1 : 1 molar ratio (polyP : RBP), is measured already at 0.1 μg mL−1. Heparin was ineffective. The results suggest a potential therapeutic benefit of polyP against SARS-C…
Arginine-rich peptides are blockers of VR-1 channels with analgesic activity
2000
Vanilloid receptors (VRs) play a fundamental role in the transduction of peripheral tissue injury and/or inflammation responses. Molecules that antagonize VR channel activity may act as selective and potent analgesics. We report that synthetic arginine-rich hexapeptides block heterologously expressed VR-1 channels with submicromolar efficacy in a weak voltage-dependent manner, consistent with a binding site located near/at the entryway of the aqueous pore. Dynorphins, natural arginine-rich peptides, also blocked VR-1 activity with micromolar affinity. Notably, synthetic and natural arginine-rich peptides attenuated the ocular irritation produced by topical capsaicin application onto the eye…
Integrating genomic binding site predictions using real-valued meta classifiers
2008
Currently the best algorithms for predicting transcription factor binding sites in DNA sequences are severely limited in accuracy. There is good reason to believe that predictions from different classes of algorithms could be used in conjunction to improve the quality of predictions. In this paper, we apply single layer networks, rules sets, support vector machines and the Adaboost algorithm to predictions from 12 key real valued algorithms. Furthermore, we use a ‘window’ of consecutive results as the input vector in order to contextualise the neighbouring results. We improve the classification result with the aid of under- and over-sampling techniques. We find that support vector machines …
Deconvolution procedure of the UV-vis spectra. A powerful tool for the estimation of the binding of a model drug to specific solubilisation loci of b…
2015
UV-vis-spectra evolution of Nile Red loaded into Tween 20 micelles with pH and [Tween 20] have been analysed in a non-conventional manner by exploiting the deconvolution method. The number of buried sub-bands has been found to depend on both pH and bio-surfactant concentration, whose positions have been associated to Nile Red confined in aqueous solution and in the three micellar solubilisation sites. For the first time, by using an extended classical two-pseudo-phases-model, the robust treatment of the spectrophotometric data allows the estimation of Nile Red binding constant to the available loci. Hosting capability towards Nile Red is exalted by the pH enhancement. Comparison between bin…
The size of aryl linker between two polyaza-cyclophane moieties controls the binding selectivity to ds-RNA vs ds-DNA
2013
Aryl-linked (pyridine- vs. phenanthroline-) bis-polyaza pyridinophane scorpiands PYPOD and PHENPOD strongly bind to the double stranded DNA and RNA, whereby very intriguing RNA over DNA selectivity is finely tuned by aryl-linker length and aromatic surface. Moreover, PYPOD and PHENPOD dimer formation at high compound/polynucleotide ratios is highly sensitive to the fine interplay between the steric and binding properties of compound-dimers and the DNA minor groove/RNA major groove. That is demonstrated by significantly different induced CD spectra, which allow spectroscopic differentiation between various DNA/RNA secondary structures. A significantly higher (micromolar) antiproliferative ef…
The Low-Affinity ATP Binding Site of the Escherichia coli SecA Dimer Is Localized at the Subunit Interface
1997
The homodimeric SecA protein is the ATP-dependent force generator in the Escherichia coli precursor protein translocation cascade. SecA contains two essential nucleotide binding sites (NBSs), i.e., NBS1 and NBS2 that hind ATP with high and low affinity, respectively. The photoactivatable bifunctional cross-linking agent 3'-arylazido-8-azidoadenosine 5'-triphosphate (diN(3)ATP) was used to investigate the spatial arrangement of the nucleotide binding sites of SecA, DiN(3)ATP is an authentic ATP analogue as it supports SecA-dependent precursor protein translocation and translocation ATPase, UV-induced photo-cross-linking of the diN(3)ATP-bound SecA results in the formation of stable dimeric s…
Integrative Model for Binding of Bacillus thuringiensis Toxins in Susceptible and Resistant Larvae of the Diamondback Moth (Plutella xylostella)
1999
ABSTRACT Insecticidal crystal proteins from Bacillus thuringiensis in sprays and transgenic crops are extremely useful for environmentally sound pest management, but their long-term efficacy is threatened by evolution of resistance by target pests. The diamondback moth ( Plutella xylostella ) is the first insect to evolve resistance to B. thuringiensis in open-field populations. The only known mechanism of resistance to B. thuringiensis in the diamondback moth is reduced binding of toxin to midgut binding sites. In the present work we analyzed competitive binding of B. thuringiensis toxins Cry1Aa, Cry1Ab, Cry1Ac, and Cry1F to brush border membrane vesicles from larval midguts in a susceptib…
Occurrence of a common binding site in Mamestra brassicae, Phthorimaea operculella, and Spodoptera exigua for the insecticidal crystal proteins CryIA…
1997
Specific binding to midgut membrane proteins is required for the toxicity of insecticidal crystal proteins (ICP) from Bacillus thuringiensis. A direct relationship between toxicity and binding has been proposed. It has been hypothesized that sharing of a single receptor by more than one ICP could lead to the occurrence of multiple resistance in the event of an alteration in the common receptor. Binding of CryIA(a), CryIA(b) and CryIA(c), three structurally related ICPs, has been studied in Phthorimaea operculella, Mamestra brassicae and, Spodoptera exigua using brush border membrane vesicles (BBMV) from the midgut tissue. Using iodinated CryIA(b), the three insects showed similar results: o…
Common receptor for Bacillus thuringiensis toxins Cry1Ac, Cry1Fa, and Cry1Ja in Helicoverpa armigera, Helicoverpa zea and Spodoptera exigua
2005
ABSTRACT Binding studies using 125 I-Cry1Ac and biotinylated Cry1Fa toxins indicate the occurrence of a common receptor for Cry1Ac, Cry1Fa, and Cry1Ja in Helicoverpa armigera , Helicoverpa zea , and Spodoptera exigua . Our results, along with previous binding data and the observed cases of cross-resistance, suggest that this pattern seems to be widespread among lepidopteran species.