Binding of antioxidant flavone isovitexin to human serum albumin investigated by experimental and computational assays

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Protein and lipid binding parameters in rainbow trout (Oncorhynchus mykiss) blood and liver fractions to extrapolate from an in vitro metabolic degradation assay to in vivo bioaccumulation potential of hydrophobic organic chemicals

Binding of hydrophobic chemicals to colloids such as proteins or lipids is difficult to measure using classical microdialysis methods due to low aqueous concentrations, adsorption to dialysis membranes and test vessels, and slow kinetics of equilibration. Here, we employed a three-phase partitioning system where silicone (polydimethylsiloxane, PDMS) serves as a third phase to determine partitioning between water and colloids and acts at the same time as a dosing device for hydrophobic chemicals. The applicability of this method was demonstrated with bovine serum albumin (BSA). Measured binding constants (K(BSAw)) for chlorpyrifos, methoxychlor, nonylphenol, and pyrene were in good agreement with an established quantitative structure-activity relationship (QSAR). A fifth compound, fluoxypyr-methyl-heptyl ester, was excluded from the analysis because of apparent abiotic degradation. The PDMS depletion method was then used to determine partition coefficients for test chemicals in rainbow trout (Oncorhynchus mykiss) liver S9 fractions (K(S9w)) and blood plasma (K(bloodw)). Measured K(S9w) and K(bloodw) values were consistent with predictions obtained using a mass-balance model that employs the octanol-water partition coefficient (K(ow)) as a surrogate for lipid partitioning and K(BSAw) to represent protein binding. For each compound, K(bloodw) was substantially greater than K(S9w), primarily because blood contains more lipid than liver S9 fractions (1.84% of wet weight vs 0.051%). Measured liver S9 and blood plasma binding parameters were subsequently implemented in an in vitro to in vivo extrapolation model to link the in vitro liver S9 metabolic degradation assay to in vivo metabolism in fish. Apparent volumes of distribution (V(d)) calculated from the experimental data were similar to literature estimates. However, the calculated binding ratios (f(u)) used to relate in vitro metabolic clearance to clearance by the intact liver were 10 to 100 times lower than values used in previous modeling efforts. Bioconcentration factors (BCF) predicted using the experimental binding data were substantially higher than the predicted values obtained in earlier studies and correlated poorly with measured BCF values in fish. One possible explanation for this finding is that chemicals bound to proteins can desorb rapidly and thus contribute to metabolic turnover of the chemicals. This hypothesis remains to be investigated in future studies, ideally with chemicals of higher hydrophobicity.

Equilibrium constants and free energies in unfolding of proteins in urea solutions

A novel thermodynamic approach to the reversible unfolding of proteins in aqueous urea solutions has been developed based on the premise that urea ligands are bound cooperatively to the macromolecule. When successive stoichiometric binding constants have values larger than expected from statistical effects, an equation for moles of bound urea can be derived that contains imaginary terms. For a very steep unfolding curve, one can then show that the fraction of protein unfolded, B̄, depends on the square of the urea concentration, U, and is given by \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} \begin{equation*}\bar {B}=\frac{{\mathit{A}}^{{\mathit{2}}}_{{\mathit{1}}}{\mathit{e}}^{{\mathrm{{\lambda}}}n\bar {B}}{\mathit{U}}^{{\mathit{2}}}}{{\mathrm{1\hspace{.167em}+\hspace{.167em}}}{\mathit{A}}^{{\mathrm{2}}}_{{\mathrm{1}}}{\mathit{e}}^{{\mathrm{{\lambda}}}\bar {B}}{\mathit{U}}^{{\mathrm{2}}}}{\mathrm{.}}\end{equation*}\end{document} A12 is the binding constant as B̄→ 0, and λ is a parameter that reflects the augmentation in affinities of protein for urea as the moles bound increases to the saturation number, n. This equation provides an analytic expression that reproduces the unfolding curve with good precision, suggests a simple linear graphical procedure for evaluating A12 and λ, and leads to the appropriate standard free energy changes. The calculated ΔG° values reflect the coupling of urea binding with unfolding of the protein. Some possible implications of this analysis to protein folding in vivo are described.

The use of mRNA display to select high-affinity protein-binding peptides

We report the use of “mRNA display,” an in vitro selection technique, to identify peptide aptamers to a protein target. mRNA display allows for the preparation of polypeptide libraries with far greater complexity than is possible with phage display. Starting with a library of ≈1013 random peptides, 20 different aptamers to streptavidin were obtained, with dissociation constants as low as 5 nM. These aptamers function without the aid of disulfide bridges or engineered scaffolds, yet possess affinities comparable to those for monoclonal antibody–antigen complexes. The aptamers bind streptavidin with three to four orders of magnitude higher affinity than those isolated previously by phage display from lower complexity libraries of shorter random peptides. Like previously isolated peptides, they contain an HPQ consensus motif. This study shows that, given sufficient length and diversity, high-affinity aptamers can be obtained even from random nonconstrained peptide libraries. By engineering structural constraints into these ultrahigh complexity peptide libraries, it may be possible to produce binding agents with subnanomolar binding constants.

Direct measurement of oligonucleotide binding stoichiometry of gene V protein by mass spectrometry.

The binding stoichiometry of gene V protein from bacteriophage f1 to several oligonucleotides was studied using electrospray ionization-mass spectrometry (ESI-MS). Using mild mass spectrometer interface conditions that preserve noncovalent associations in solution, gene V protein was observed as dimer ions from a 10 mM NH4OAc solution. Addition of oligonucleotides resulted in formation of protein-oligonucleotide complexes with stoichiometry of approximately four nucleotides (nt) per protein monomer. A 16-mer oligonucleotide gave predominantly a 4:1 (protein monomer: oligonucleotide) complex while oligonucleotides shorter than 15 nt showed stoichiometries of 2:1. Stoichiometries and relative binding constants for a mixture of oligonucleotides were readily measured using mass spectrometry. The binding stoichiometry of the protein with the 16-mer oligonucleotide was measured independently using size-exclusion chromatography and the results were consistent with the mass spectrometric data. These results demonstrate, for the first time, the observation and stoichiometric measurement of protein-oligonucleotide complexes using ESI-MS. The sensitivity and high resolution of ESI-MS should make it a useful too] in the study of protein-DNA interactions.

Transport in the blood of an anti-tumor water-soluble rutheniun cyclopentadienyl complex: a fluorescence study on albumin binding

Dissertação de mestrado, Qualidade em Análises, Faculdade de Ciências e Tecnologia, Universidade do Algarve, 2014

Mg induced Ca deficiency under alkaline conditions

Little is known about Mg induced Ca deficiency in alkaline conditions, and the relationship between Mg induced Ca deficiency and Na induced Ca deficiency. Dilute nutrient solutions (dominated by Mg) were used to investigate the effect of Ca activity ratio (CAR) on the growth of mungbeans (Vigna radiata (L.) Wilczek cv. Emerald). At pH 9.0, root growth was reduced below a critical CAR of 0.050 (corresponding to 90 % relative root length). Root growth was found to be limited more in Mg solutions than had been previously observed for Na solutions. Using a CAR equation modified with plasma membrane binding constants (to incorporate the differing antagonistic effects of Mg and Na), new critical CAR values were calculated for both Na (0.56) and Mg (0.44) dominated solutions. This modified CAR equation permits the calculation of CAR irrespective of the dominant salt present.

Interaction of zinc(II) with the cyclic octapeptides, cyclo[Ile(Oxn)-D-Val(Thz)](2) and ascidiacyclamide, a cyclic peptide from Lissoclinum patella

The interactions between zinc salts and the naturally occurring cyclic octapeptide ascidiacyclamide in methanol, as well as a synthetic analogue cyclo[Ile(Oxn)-D-Val(Thz)](2), were monitored by H-1 NMR and CD spectroscopy. Three zinc complexes were identified, their relative amounts depending on the nature of the anion (perchlorate, triflate or chloride) and the presence or absence of base. Binding constants for two of the zinc species were calculated from CD or H-1 NMR spectra, [Zn(L - H)](+) (KZn(L-H) = [Zn(L - H)(+)]/[Zn2+][(L - H)(-)] = 10(7 +/- 2) M-1; 95% methanol/5% water, 298.0 K, NEt3/HClO4 buffer 0.04 M) and [ZnLCl](+) (K-ZnCIL = [ZnCIL+]/[Zn2+][Cl-][L] = 10(7.2) (+/-) (0.1) M-2; d(3)-methanol, 301 K).

Quantitative affinity chromatography

The objective of this review is to summarize developments in the use of quantitative affinity chromatography to determine equilibrium constants for solute interactions of biological interest. Affinity chromatography is an extremely versatile method for characterizing interactions between dissimilar reactants because the biospecificity incorporated into the design of the affinity matrix ensures applicability of the method regardless of the relative sizes of the two reacting solutes. Adoption of different experimental strategies, such as column chromatography, simple partition equilibrium experiments, solid-phase immunoassay, and biosensor technology, has led to a situation whereby affinity chromatography affords a means of characterizing interactions governed by an extremely broad range of binding affinities-relatively weak interactions (binding constants below 10(3) M-1) through to interactions with binding constants in excess of 10(9) M-1. In addition to its important role in solute separation and purification, affinity chromatography thus also possesses considerable potential for investigating the functional roles of the reactants thereby purified. (C) 2001 Elsevier Science B.V. All rights reserved.

The development of chromatography for the characterization of protein interactions: a personal perspective

This article reviews the progress of a personal endeavour to develop chromatography as a quantitative procedure for the determination of reaction stoichiometries and equilibrium constants governing protein interactions. As well as affording insight into an aspect of chromatography with which many protein chemists are unfamiliar, it shows the way in which minor adaptations of conventional chromatographic practices have rendered the technique one of the most powerful methods available for the characterization of interactions. That pathway towards quantification is followed from the introduction of frontal gel filtration for the study of protein self-association to the characterization of ligand binding by the biosensor variant of quantitative affinity chromatography.

Solubilization of human erythrocyte membranes by ASB detergents

Understanding the membrane solubilization process and finding effective solubilizing agents are crucial challenges in biochemical research. Here we report results on the interaction of the novel linear alkylamido propyl dimethyl amino propanosulfonate detergents, ASB-14 and ASB-16, with human erythrocyte membranes. An estimation of the critical micelle concentration of these zwitterionic detergents (ASB-14 = 100 µM and ASB-16 = 10 µM) was obtained using electron paramagnetic resonance. The amount of proteins and cholesterol solubilized from erythrocytes by these detergents was then determined. The hemolytic activities of the ASB detergents were assayed and the detergent/lipid molar ratios for the onset of hemolysis (Re sat) and total lysis (Re sol) were calculated, allowing the determination of the membrane binding constants (Kb). ASB-14 presented lower membrane affinity (Kb = 7050 M-1) than ASB-16 (Kb = 15610 M-1). The amount of proteins and cholesterol solubilized by both ASB detergents was higher while Re sat values (0.22 and 0.08 detergent/lipid for ASB-14 and ASB-16, respectively) were smaller than those observed with the classic detergents CHAPS and Triton X-100. These results reveal that, besides their well-known use as membrane protein solubilizers to enhance the resolution of two dimensional electrophoresis/mass spectrometry, ASB-14 and ASB-16 are strong hemolytic agents. We propose that the physicochemical properties of ASB detergents determine their membrane disruption efficiency and can help to explain the improvement in the solubilization of membrane proteins, as reported in the literature.

Neurochondrin und Rack1 vermitteln die Signalintegration der Proteinkinase A

Die Spezifität und Effizienz zellulärer Signalprozesse wird durch die intrazelluläre Kompartimentierung von Signalmolekülen erreicht. A-Kinase-Ankerproteine (AKAPs) bilden eine Familie aus Gerüstproteinen, die zeitliche und räumliche Lokalisation der cAMP-abhängigen Proteinkinase (PKA) übernehmen. Die direkte Interaktion wird dabei über die Dimerisierungs- und Dockingdomäne (DD-Domäne) der regulatorischen Untereinheiten von PKA vermittelt. Das charakteristische strukturelle Merkmal bei kanonischen AKAPs ist eine amphipathische Helix. Es existiert allerdings auch eine kleine Gruppe von nicht-kanonischen AKAPs, deren Bindung an die DD-Domäne nicht über eine amphipathische Helix vermittelt wird. In dieser Arbeit wurden die zwei potentiellen nicht-kanonischen AKAPs Neurochondrin (neurite-outgrowth promoting protein) und Rack1 (receptor of activated C-kinase 1) charakterisiert. Neurochondrin, dessen Expression mit dem Neuriten-Wachstum in jungen Neuronen korreliert ist und das vermutlich eine entscheidende Funktion bei der Langzeitpotenzierung im Hippocampus übernimmt, zeigt in SPR-Bindungsstudien eine hochaffine, nanomolare Interaktion mit der R-Untereinheit Typ IIalpha von PKA. Kompetitionsanalysen mit dem AKAP-Disruptor-Peptid Ht 31 und Untersuchungen mit der isolierten DD-Domäne von RIIalpha bestätigen eine spezifische Interaktion. Das nicht-kanonische RII-Bindemotiv von Neurochondrin ist aus zwei Domänen aufgebaut, die einen hohen alpha-helikalen Anteil besitzen, aber keine amphipathische Helix bilden. Peptidbasierte Interaktionsstudien der einzelnen Domänen zeigen dennoch ebenfalls nanomolare Affinitäten zu RIIalpha. Rack1 ist ein etabliertes Gerüstprotein mit einer propellerartigen beta-Faltblattstruktur, für das bereits über 100 verschiedene Interaktionspartner beschrieben werden konnten. Die Integration von Rack1 in unterschiedliche Signalprozesse ist äußerst vielfältig. Um dabei die Spezifität jeder einzelnen Interaktion zu gewährleisten, sind individuelle Bindungsstrategien nötig. Die niedrigaffine Interaktion zur RIbeta-Untereinheit von PKA wird daher über multiple Bindestellen vermittelt. Die DD-Domäne von RIbeta übernimmt dabei eine spezifische Funktion, wie unter anderem durch Kompetitionsanalysen mit dem RI-spezifischen AKAP-Disruptor-Peptid RIAD gezeigt werden konnte. Die einzigartige Struktur der DD-Domäne generiert zudem ein Bindemotiv für Rack1, das Ähnlichkeiten mit der „Rack1 interacting-Domäne“ (RAID) von PDE4D5 aufweist. Sowohl Neurochondrin als auch Rack1 besitzen essenzielle neuronale Funktionen. Daher erweitert die Identifizierung der beiden neuen nicht-kanonischen AKAPs nicht nur die strukturelle Diversität der AKAP-Familie, sondern trägt zudem zum Verständnis der neuronalen Signalintegration von PKA bei.

Interactions of tea tannins and condensed tannins with proteins

Binding parameters for the interactions of four types of tannins: tea catechins, grape seed proanthocyanidins, mimosa 5-deoxy proanthocyanidins,and sorghum procyanidins (mDP=17), with gelatin and bovine serum albumin (BSA) have been determined from isothermal titration calorimetry data. Equilibrium binding constants determined for the interaction with gelatin were in the range 10(4) to 10(6) M-1 and in the order: sorghum procyanidins > grape seed proanthocyanidins > mimosa 5-deoxy proanthocyanidins > tea catechins. Interaction with BSA was generally weaker, with equilibrium binding constants of <= 10(3) M-1 for grape seed proanthocyanidins, mimosa 5-deoxy proanthocyanidins and tea catechins, and 10(4) M-1 for the sorghum procyanidins. In all cases the interactions with proteins were exothermic and involved multiple binding sites on the protein. The data are discussed in relation to the structures and the known nutritional effects of the condensed tannins.

Cascade dicopper architectures of a dibenzodioxatetraazamacrocycle

The dibenzodioxatetraazamacrocycle [26]pbz(2)N(4)O(2) was characterised by single crystal X-ray diffraction and the protonation constants of this compound and the stability constants of its copper(II) and lead(II) complexes were determined by potentiometry in water at 298.2 K in 0.10 mol dm(-3) in KNO3. Mono- and dinuclear complexes were found for both metal ions, the dinuclear complexes being the main species in the 5-7.5 pH range for copper(II) and 7.5-8.5 for lead(II). As expected the values of the stability constants for the copper(II) complexes are lower than those for related macrocycles containing only nitrogen atoms. The presence of mono- and dinuclear copper complexes was also confirmed by electrospray ionization mass spectrometry. These results suggest that the symmetric macrocyclic cavity of [26]pbZ(2)N(4)O(2) has enough space for the coordination of two metal ions. Additionally, NMR spectroscopy showed that the dinuclear complex of lead(II) has high symmetry. The equilibrium constants of the dinuclear copper(II) complexes and dicarboxylate anions (oxalate, malonate and succinate) were also determined in 0.10 mol dm-3 aqueous KNO3 solution. Only species containing one anion, Cu(2)H(h)LA((2+h)), were found, strongly suggesting that the anion bridges the two copper(II) ions. The binding constants of the cascade species formed by [Cu-2[26]pbZ(2)N(4)O(2)(H2O)(4+) with dicarboxylate anions decrease with the increase in length of the alkyl chain of the anion, a fact which was attributed to a higher conformational energy necessary for the rearrangement of the macrocycle to accommodate the larger anions bridging the two copper(II) centres. The variation of the magnetic susceptibility with temperature Of [Cu-2(H-2[26]pbz(2)N(4)O(2))(oxa)(3)]-4H(2)O and [Cu-2([26]pbz(2)N(4)O(2))(suc)Cl-2] were measured and the two complexes showed different behaviour. (c) 2007 Elsevier Ltd. All rights reserved.

pH-mediated interactions between poly(acrylic acid) and methylcellulose in the formation of ultrathin multilayered hydrogels and spherical nanoparticles

Poly(acrylic acid) forms insoluble hydrogen-bonded interpolymer complexes with methylcellulose in aqueous solutions under acidic conditions. In this work the reaction heats and binding constants were determined for the complexation between poly(acrylic acid) and methylcellulose by isothermal titration calorimetry at different pH and findings are correlated with the aggregation processes occurring in this system. The principal contribution to the complexation heat results from primary polycomplex particle aggregation. Transmission electron microscopy of nanoparticles produced at pH 1.4 and 2.4 demonstrated that they are spherical and dense structures. The nanoparticles ranged from 80 to 200 nm, whereas particles formed at pH 3.2 were 20-30 nm and were stabilized against aggregation by a network of uncomplexed macromolecules. For the first time, multilayered materials were developed on the basis of hydrogen-bonded complexes of poly(acrylic acid) and methylcellulose using layer-by-layer deposition on a glass surface. The thickness of these films was a linear function of the number of deposition cycles. The materials were subsequently cross-linked by thermal treatment, resulting in ultrathin hydrogels which detached from the glass substrate upon swelling. The swelling capacity of ultrathin hydrogels differed from the swelling of the thicker films of a similar chemical composition.