Evaluation of solute binding to proteins and intra-protein distances from steady state fluorescence measurements

Interaction of normelinonine F and related N-methyl-β-carbolines derivatives with bovine serum albumin. Spectroscopic profiles, multivariate analysis and theoretical calculations

β-carbolines (βCs) represent a large family of bioactive alkaloids, including norharmane and normelinonine F, known for their diverse pharmacological activities. The effects of these alkaloids may depend, among other factors, on their delivery, accumulation in different subcellular compartments, and interactions with biomacromolecules such as serum albumins. In this study, we investigated the pH dependence of the interactions between bovine serum albumin (BSA) and four βCs (norharmane, normelinonine F, and their corresponding N(9)-methyl derivatives) using UV-vis and fluorescence spectroscopy, combined with multivariate analysis and molecular docking. This selected set of N-methyl derivatives provides valuable insights into molecular-level binding interactions, clarifying aspects observed in previous studies. The results reveal a distinct spectroscopic interaction pattern for quaternary βCs compared to derivatives with a free N(2)-pyridinic nitrogen. Specifically, normelinonine F and N(9)-methyl-normelinonine F exhibited weak interactions, likely with external sites (site 3, subdomain IB) and/or the protein surface. In contrast, for N(2)-unsubstituted derivatives such as norharmane and N(9)-methyl-norharmane, stronger interactions and internalization into less polar and/or hydrophobic BSA sites predominate across the investigated pH-range (4 < pH < 9), likely site 2 (subdomain IIIA). However, the interaction of the corresponding cationic species of norharmane and N(9)-methyl-norharmane with BSA remains unclear due to low interaction levels and similar UV-vis absorption and emission spectra between free and BSA-bound species.

Journey of micronanoplastics with blood components

The entry of micro- and nanoplastics (MNPs) into the human body is inevitable. They enter blood circulation through ingestion, inhalation, and dermal contact by crossing the gut-lung-skin barrier (the epithelium of the digestive tract, the respiratory tract, and the cutaneous layer). There are many reports on their toxicities to organs and tissues. This paper presents the first thorough assessment of MNP-driven bloodstream toxicity and the mechanism of toxicity from the viewpoint of both MNP and environmental co-pollutant complexes. Toxic impacts include plasma protein denaturation, hemolysis, reduced immunity, thrombosis, blood coagulation, and vascular endothelial damage, among others, which can lead to life-threatening diseases. Protein corona formation, oxidative stress, cytokine alterations, inflammation, and cyto- and genotoxicity are the key mechanisms involved in toxicity. MNPs change the secondary structure of plasma proteins, thereby preventing their transport functions (for nutrients, drugs, oxygen, etc.). MNPs inhibit erythropoiesis by influencing hematopoietic stem cell proliferation and differentiation. They cause red blood cell and platelet aggregation, as well as increased adherence to endothelial cells, which can lead to thrombosis and cardiovascular disease. White blood cells and immune cells phagocytose MNPs, provoking inflammation. However, research gaps still exist, including gaps regarding the combined toxicity of MNPs and co-pollutants, toxicological studies in human models, advanced methodologies for toxicity analysis, bioaccumulation studies, inflammation and immunological responses, dose-response relationships of MNPs, and the effect of different physiochemical characteristics of MNPs. Furthermore, most studies have analyzed toxicity using prepared MNPs; hence, studies must be undertaken using true-to-life MNPs to determine the real-world scenario. Additionally, nanoplastics may further degrade into monomers, whose toxic effects have not yet been explored. The research gaps highlighted in this review will inspire future studies on the toxicity of MNPs in the vascular/circulatory systems utilizing in vivo models to enable more reliable health risk assessment.

The interaction on HSA and the antibacterial activity from four polyoxometalate hybrids based on berberine

Four organic-polyoxometalate hybrids BR4[SiW12O40] (BR-SiW), BR3[PMo12O40] (BR-PMo), BR4K[EuSiW11O40]·2H2O (BR-EuSiW) and BR6Na3[EuW10O36] (BR-EuW) were fabricated by the polyoxometalates (POMs) anions and berberine cations (BR) noted for the alkaloids in traditional Chinese herbal medicine. These hybrids have been characterized and confirmed. The interaction between hybrids and human serum albumin (HSA) was investigated in a buffer solution (pH 7.4) using ultraviolet-visible light absorption and fluorescence techniques. The classical Stern-Volmer equation was used to analyze the fluorescence quenching at three temperatures (296, 303 and 310 K), and the static quenching mechanism for interaction was proposed. The Thermodynamic parameters, enthalpy, entropy change, and Gibbs free energy of hybrids interacting on HSA were calculated by Scatchard equation. The results indicated that therewas one binding site on the protein and BR-POMs all showed stronger binding force than that of raw materials. Synchronous fluorescence results showed that the binding sites of BR-POMs and HSA were not effectively affected the surrounding microenvironment. The following antibacterial experiments implied that inhibitory effect of hybrids were synergistic effect from organic active ingredient and POMs but the simple combination. All these data were prepared for further research on biology.

Detailing Protein-Bound Uremic Toxin Interaction Mechanisms with Human Serum Albumin in the Pursuit of Designing Competitive Binders

Chronic kidney disease is the gradual progression of kidney dysfunction and involves numerous co-morbidities, one of the leading causes of mortality. One of the primary complications of kidney dysfunction is the accumulation of toxins in the bloodstream, particularly protein-bound uremic toxins (PBUTs), which have a high affinity for plasma proteins. The buildup of PBUTs in the blood reduces the effectiveness of conventional treatments, such as hemodialysis. Moreover, PBUTs can bind to blood plasma proteins, such as human serum albumin, alter their conformational structure, block binding sites for other valuable endogenous or exogenous substances, and exacerbate the co-existing medical conditions associated with kidney disease. The inadequacy of hemodialysis in clearing PBUTs underscores the significance of researching the binding mechanisms of these toxins with blood proteins, with a critical analysis of the methods used to obtain this information. Here, we gathered the available data on the binding of indoxyl sulfate, p-cresyl sulfate, indole 3-acetic acid, hippuric acid, 3-carboxyl-4-methyl-5-propyl-2-furan propanoic acid, and phenylacetic acid to human serum albumin and reviewed the common techniques used to investigate the thermodynamics and structure of the PBUT-albumin interaction. These findings can be critical in investigating molecules that can displace toxins on HSA and improve their clearance by standard dialysis or designing adsorbents with greater affinity for PBUTs than HSA.

Binding of toluidine blue-myristic acid derivative to cucurbit[7]uril and human serum albumin: computational and biophysical insights towards a biosupramolecular assembly

A new toluidine blue-myristic acid photosensitizer derivate (TBOMyr) was investigated as a design molecule to bind simultaneously to cucurbit[7]uril (CB[7]) and human serum albumin (HSA) with the aim of constructing a biosupramolecular assembly. Molecular docking and dynamics calculations revealed the main supramolecular and bio-molecular interactions of TBOMyr with the macrocycle or the protein, respectively. The addition of the negatively charged myristic acid-like tail resulted in a unique conformation of the CB[7] complex where the phenothiazine core was included in the cavity of CB[7], leaving the fatty acid portion free to interact with the protein. A favorable ternary interaction between TBOMyr, CB[7] and HSA was suggested by the calculations, and an experimental binding affinity in the order of 10⁵ M^-1 was determined for the TBOMyr@CB[7] complex with HSA. The new TBOMyr derivative could find applications in photodynamic therapy benefiting from the biosupramolecular interactions as a transport system.

Riboflavin-Mediated Photooxidation of Gold Nanoparticles and Its Effect on the Inactivation of Bacteria

Photodynamic inactivation (PDI) of microorganisms, based on the ability of photosensitizers to produce reactive oxygen species (ROS) under adequate irradiation, emerges as a promising technique to face the increasing bacterial resistance to conventional antimicrobials. In this work, we analyze the combined action of Riboflavin (Rf) and pectin-coated gold nanoparticles (PecAuNP) on Staphylococcus aureus (S. aureus) and Pseudomonas aeruginosa (P. aeruginosa) as suitable PDI strategy. We demonstrate that gold ions can be generated upon Rf-photosensitized oxidation of PecAuNP. Transient absorption spectroscopy shows that the Rf cationic radical can accept an electron from the nanoparticles to yield Au(I) ions, which in aqueous medium is disproportionate to yield Au⁰ and Au(III). Microbiological assays showed that the presence of PecAuNP enhanced the antibacterial activity of photoirradiated Rf toward S. aureus and P. aeruginosa, in line with the well-known antibacterial activity of gold ions. Moreover, the irradiation of Rf solutions containing about 100 μM PecAuNP enabled the solutions to be bactericidal against both bacteria.

Interactions between Imidacloprid and Thiamethoxam and Dissolved Organic Matter Characterized by Two-Dimensional Correlation Spectroscopy Analysis, Molecular Modeling, and Density Functional Theory Calculations

The heavy application of neonicotinoid insecticides in agricultural production has burdened the environment. In the present study, interactions of two neonicotinoid insecticides imidacloprid and thiamethoxam with dissolved organic matter (DOM) were investigated by spectroscopic techniques, molecular modeling, and density functional theory (DFT) calculations. The static mechanism of imidacloprid and thiamethoxam quenching the endogenous fluorescence of DOM was assessed through time-resolved analyses. During the binding process, a protein-like substance binds imidacloprid and thiamethoxam later than a humic-like substance, as analyzed by two-dimensional correlation spectroscopy, but more strongly than the humic-like substance, as suggested by molecular modeling and DFT calculations. The conformational changes of DOM are attributed to imidacloprid and thiamethoxam, as assessed with three-dimensional spectra. Fourier transform infrared spectroscopy indicated that DOM binds imidacloprid and thiamethoxam by hydroxyl, aliphatic C-H, amide I, and carboxyl to form stable DOM-imidacloprid and DOM-thiamethoxam complexes. Understanding the changes in the structural conformation of humic-like and protein-like substances with imidacloprid and thiamethoxam helps further understand the fate of the neonicotinoids in the environment.

Phytoestrogen coumestrol: Antioxidant capacity and its loading in albumin nanoparticles

Coumestrol is a polyphenol with promising therapeutic applications as phytoestrogen, antioxidant and potential cancer chemoprevention agent. The presence of two hydroxyl groups on its chemical structure, with orientation analogous to estradiol, is responsible of both, its antioxidant capacity and its estrogenic activity. However, several studies show that the interaction of polyphenols with food and plasma proteins reduces their antioxidant efficacy. We studied the interaction of coumestrol with bovine serum albumin protein (BSA) by fluorescence spectroscopy and circular dichroism techniques, and the effect of this interaction on its antioxidant activity as a hydroxyl radical scavenger. In addition, coumestrol antioxidant capacity profile using different assays (DPPH, ORAC-FL and ORAC-EPR) was studied. To explain its reactivity we used several methodologies, including DFT calculations, to define its antioxidant mechanism. Coumestrol antioxidant activity unveiled interesting antioxidant properties. BSA interaction with coumestrol reduces significantly photolytic degradation in several media thus preserving its antioxidant properties. Results suggest no significant changes in BSA structure and activity when interacting with coumestrol. Furthermore, this interaction is stronger than for other phytoestrogens such as daidzein and genistein. Considering our promising results, we reported for the first time the fabrication and characterization of coumestrol-loaded albumin nanoparticles. The resulting spherical and homogeneous nanoparticles showed a diameter close to 96 nm. The coumestrol incorporation efficiency in BSA NPs was 22.4%, which is equivalent to 3 molecules of coumestrol for every 10 molecules of BSA.

The interaction of the excited states of safranine-O with low generation carboxyl terminated PAMAM dendrimers in an aqueous medium

The interaction of the singlet and triplet excited states of the synthetic dye safranine-O with carboxyl-terminated poly(amidoamine) (PAMAM) dendrimers was investigated in a buffer solution at pH 8. Low half-generation PAMAM dendrimers (G -0.5; G +0.5: G 1.5) were employed. The UV-vis absorption spectrum of the dye presents only a very small red shift in the presence of dendrimers. Fluorescence quenching was detected and it was interpreted by a static mechanism in terms of the association of the dye with the dendrimer. Laser flash photolysis experiments were carried out and transient absorption spectra of the triplet and radicals were obtained. The triplet state is quenched by the dendrimers with rate constants well below the diffusional limit. The quenching process was characterized as an electron transfer process and the quantum yield of radicals was estimated. It was found that radicals are formed with a high efficiency in the triplet quenching reaction.

NANoPoLC algorithm for correcting nanoparticle concentration by sample polydispersity

Variability in the polydispersity of colloidal nanoparticles results in significant differences in the total number of nanoparticles available for the determination of their concentration, which ultimately affects their bioavailability and biodistribution. In the current work, we developed a novel algorithm, named Nanoparticle Polydispersity Corrector (NANoPoLC), which was shown to render a more realistic calculation of the actual nanoparticle concentration in solution.

Electroconductive nanoengineered biomimetic hybrid fibers for cardiac tissue engineering

We report for the first time the preparation of a fibrous material composed of surface grafted spherical nanosilver and collagen using one-step electrospinning. The resulting composite showed comparable morphology to the control without nanosilver, but had improved electrical conductivity. Under electrical stimulation, fibrous materials containing nanosilver increased connexin-43 expression and proliferation of neonatal cardiomyocytes. Furthermore, composites containing nanosilver prevented biofilm formation but did not activate macrophages.

Association models for binding of molecules to nanostructures

The interaction between nanoparticles and molecules determines the activity of nanostructures.

Riboflavin photosensitized oxidation of myoglobin

The reaction of the fresh meat pigment oxymyoglobin, MbFe(II)O₂, and its oxidized form metmyoglobin, MbFe(III), with triplet-state riboflavin involves the pigment protein, which is oxidatively cleaved or dimerized as shown by SDS-PAGE and Western blotting. The overall rate constant for oxidation of MbFe(II)O₂ by ³Rib is (3.0 ± 0.5) × 10⁹ L·mol⁻¹·s⁻¹ and (3.1 ± 0.4) × 10⁹ L·mol⁻¹·s⁻¹ for MbFe(III) in phosphate buffer of pH 7.4 at 25 °C as determined by laser flash photolysis. The high rates are rationalized by ground state hydrophobic interactions as detected as static quenching of fluorescence from singlet-excited state riboflavin by myoglobins using time-resolved fluorescence spectroscopy and a Stern-Volmer approach. Binding of riboflavin to MbFe(III) has K(a) = (1.2 ± 0.2) × 10⁴ mol·L⁻¹ with ΔH° = -112 ± 22 kJ·mol⁻¹ and ΔS° = -296 ± 75 J·mol⁻¹·K⁻¹. For meat, riboflavin is concluded to be a photosensitizer for protein oxidation but not for discoloration.

FAD binding properties of a cytosolic version of Escherichia coli NADH dehydrogenase-2

Respiratory NADH dehydrogenase-2 (NDH-2) of Escherichia coli is a peripheral membrane-bound flavoprotein. By eliminating its C-terminal region, a water soluble truncated version was obtained in our laboratory. Overall conformation of the mutant version resembles the wild-type protein. Considering these data and the fact that the mutant was obtained as an apo-protein, the truncated version is an ideal model to study the interaction between the enzyme and its cofactor. Here, the FAD binding properties of this version were characterized using far-UV circular dichroism (CD), differential scanning calorimetry (DSC), limited proteolysis, and steady-state and dynamic fluorescence spectroscopy. CD spectra, thermal unfolding and DSC profiles did not reveal any major difference in secondary structure between apo- and holo-protein. In addition, digestion site accessibility and tertiary conformation were similar for both proteins, as seen by comparable chymotryptic cleavage patterns. FAD binding to the apo-protein produced a parallel increment of both FAD fluorescence quantum yield and steady-state emission anisotropy. On the other hand, addition of FAD quenched the intrinsic fluorescence emission of the truncated protein, indicating that the flavin cofactor should be closely located to the protein Trp residues. Analysis of the steady-state and dynamic fluorescence data confirms the formation of the holo-protein with a 1:1 binding stoichiometry and an association constant KA=7.0(±0.8)×10(4)M(-1). Taken together, the FAD-protein interaction is energetically favorable and the addition of FAD is not necessary to induce the enzyme folded state. For the first time, a detailed characterization of the flavin:protein interaction was performed among alternative NADH dehydrogenases.

Evaluation of the number of binding sites in proteins from their intrinsic fluorescence: limitations and pitfalls

Changes in the intrinsic protein fluorescence with the additive concentration provide one of the most employed methodologies for the evaluation of the binding constant and the number of binding sites. In the last years, more than 175 studies have been published where the double logarithmic plot shown below is used toward determining the number of equivalent binding sites (n). Log [(F° - F)/F] = log K + n log [Q0 ]. However, the value of n evaluated by this procedure is unrelated to the number of equivalent binding sites; rather it represents the stoichiometry of the binding step. The confusion on the meaning of n arises upon assuming that the binding process is represented by the forward and backward elementary steps shown below, implying that binding of the n solutes takes place simultaneously, i.e. there are no intermediate species. nQ + P ⇆ Qn P. The conclusion that n is unrelated to the number of equivalent binding sites is supported by the fact that in all the systems considered (99% of them) n values are close to one and much smaller than those obtained by ultrafiltration. It is then remarkable, the profusion of publications in peer-reviewed, specialized journals including a conceptual error that confuses Hill's coefficient and/or the stoichiometry of the binding step with the number of independent binding sites. Here, we discuss the origin of this common misconception and provide alternative methods to determine the number of binding sites.

Ostreopexin: a hemopexin fold protein from the oyster mushroom, Pleurotus ostreatus

Proteins with hemopexin repeats are widespread in viruses, prokaryotes and eukaryotes. We report here for the first time the existence of a protein in fungi with the four-bladed β-propeller fold that is typical for hemopexin-like proteins. This protein was isolated from the edible basidiomycetous fungus Pleurotus ostreatus and is named ostreopexin. It binds to Ni(2+)-NTA-agarose, and is structurally and functionally very similar to PA2 albumins isolated from legume seeds and the hemopexin fold protein from rice. Like these plant proteins, ostreopexin shows reversible binding to hemin with moderate affinity, but does not bind to polyamines. We suggest that ostreopexin participates in intracellular management of metal (II or III)-chelates.

Design of near-infrared fluorescent bioactive conjugated functional iron oxide nanoparticles for optical detection of colon cancer

Background

Colon cancer is one of the major causes of death in the Western world. Early detection significantly improves long-term survival for patients with the disease. Near- infrared (NIR) fluorescent nanoparticles hold great promise as contrast agents for tumor detection. NIR offers several advantages for bioimaging compared with fluorescence in the visible spectrum, ie, lower autofluorescence of biological tissues, lower absorbance, and consequently deeper penetration into biomatrices.

Methods and results

NIR fluorescent iron oxide nanoparticles with a narrow size distribution were prepared by nucleation, followed by controlled growth of thin iron oxide films onto cyanine NIR dye conjugated gelatin-iron oxide nuclei. For functionalization, and in order to increase the NIR fluorescence intensity, the NIR fluorescent iron oxide nanoparticles obtained were coated with human serum albumin containing cyanine NIR dye. Leakage of the NIR dye from these nanoparticles into phosphate-buffered saline solution containing 4% albumin was not detected. The work presented here is a feasibility study to test the suitability of iron oxide-human serum albumin NIR fluorescent nanoparticles for optical detection of colon cancer. It demonstrates that encapsulation of NIR fluorescent dye within these nanoparticles significantly reduces photobleaching of the dye. Tumor-targeting ligands, peanut agglutinin and anticarcinoembryonic antigen antibodies (αCEA), were covalently conjugated with the NIR fluorescent iron oxide-human serum albumin nanoparticles via a poly(ethylene glycol) spacer. Specific colon tumor detection was demonstrated in chicken embryo and mouse models for both nonconjugated and the peanut agglutinin-conjugated or αCEA-conjugated NIR fluorescent iron oxide-human serum albumin nanoparticles.

Conclusion

Conjugation of peanut agglutinin or αCEA to the nanoparticles significantly increased the fluorescence intensity of the tagged colon tumor tissues relative to the nonconjugated nanoparticles.

Speciation analysis of aqueous nanoparticulate diclofenac complexes by solid-phase microextraction

The dynamic sorption of an organic compound by nanoparticles (NPs) is analyzed by solid-phase microextraction (SPME) for the example case of the pharmaceutical diclofenac in dispersions of impermeable (silica, SiO(2)) and permeable (bovine serum albumin, BSA) NPs. It is shown that only the protonated neutral form of diclofenac is accumulated in the solid phase, and hence this species governs the eventual partition equilibrium. On the other hand, the rate of the solid/water partition equilibration is enhanced in the presence of the sorbing nanoparticles of SiO(2) and BSA. This feature demonstrates that the NPs themselves do not enter the solid phase to any appreciable extent. The enhanced rate of attainment of equilibrium is due to a shuttle-type of contribution from the NP-species to the diffusive supply of diclofenac to the water/solid interface. For both types of nanoparticulate complexes, the rate constant for desorption (k(des)) of bound diclofenac was derived from the measured thermodynamic affinity constant and a diffusion-limited rate of adsorption. The computed k(des) values were found to be sufficiently high to render the NP-bound species labile on the effective time scale of SPME. In agreement with theoretical prediction, the experimental results are quantitatively described by fully labile behavior of the diclofenac/nanoparticle system and an ensuing accumulation rate controlled by the coupled diffusion of neutral, deprotonated, and NP-bound diclofenac species.

Human serum albumin stability and toxicity of anthraquinone dye alizarin complexone: an albumin-dye model

The complexation between the primary vector of ligands in blood plasma, human serum albumin (HSA) and a toxic anthraquinone dye alizarin complexone, was unmasked by means of circular dichroism (CD), molecular modeling, steady state and time-resolved fluorescence, and UV/vis absorption measurements. The structural investigation of the complexed HSA through far-UV CD, three-dimensional and synchronous fluorescence shown the polypeptide chain of HSA partially destabilizing with a reduction of α-helix upon conjugation. From molecular modeling and competitive ligand binding results, Sudlow's site I, which was the same as that of warfarin-azapropazone site, was appointed to retain high-affinity for alizarin complexone. Moreover, steady state fluorescence displayed that static type and Förster energy transfer is the operational mechanism for the vanish in the tryptophan (Trp)-214 fluorescence, this corroborates time-resolved fluorescence that HSA-alizarin complexone adduct formation has an affinity of 10(5) M(-1), and the driving forces were found to be chiefly π-π, hydrophobic, and hydrogen bonds, associated with an exothermic free energy change. These data should be utilized to illustrate the mechanism by which the toxicological action of anthraquinone dyes is mitigated by transporter HSA.