Study on the Interaction Mechanism of Lysozyme and Bromophenol Blue by Fluorescence Spectroscopy

Unraveling the Compositional and Molecular Features Involved in Lysozyme-Benzothiazole Derivative Interactions

In this work we present a computational analysis together with experimental studies, focusing on the interaction between a benzothiazole (BTS) and lysozyme. Results obtained from isothermal titration calorimetry, UV-vis, and fluorescence were contrasted and complemented with molecular docking and machine learning techniques. The free energy values obtained both experimentally and theoretically showed excellent similarity. Calorimetry, UV-vis, and 3D/2D-lig-plot analysis revealed that the most relevant interactions between BTS and lysozyme are based on a predominance of aromatic, hydrophobic Van der Waals interactions, mainly aromatic edge-to-face (T-shaped) π-π stacking interactions between the benzene ring belonging to the 2-(methylthio)-benzothiazole moiety of BTS and the aromatic amino acid residue TRP108 of the lysozyme receptor. Next, conventional hydrogen bonding interactions contribute to the stability of the BTS-lysozyme coupling complex. In addition, mechanistic approaches performed using elastic network models revealed that the BTS ligand theoretically induces propagation of allosteric signals, suggesting non-physiological conformational flexing in large blocks of lysozyme affecting α-helices. Likewise, the BTS ligand interacts directly with allosteric residues, inducing perturbations in the conformational dynamics expressed as a moderate conformational softening in the α-helices H1, H2, and their corresponding β-loop in the lysozyme receptor, in contrast to the unbound state of lysozyme.

Lysozyme crystals dyed with bromophenol blue: where has the dye gone?

Protein crystals can easily be coloured by adding dyes to their mother liquor, but most structures of these protein-dye complexes remain unsolved. Here, structures of lysozyme in complex with bromophenol blue obtained by soaking orthorhombic and tetragonal crystals in a saturated solution of the dye at different pH values from 5.0 to 7.5 are reported. Two different binding sites can be found in the lysozyme-bromophenol blue crystals: binding site I is located near the amino- and carboxyl-termini, while binding site II is located adjacent to helices α1 (residues 4-15) and α3 (residues 88-100). In the orthorhombic crystals soaked at pH 7.0, binding of the dye takes place in both sites without significant changes in the unit cell. However, soaking tetragonal crystals with bromophenol blue results in two different complexes. Crystals soaked at pH 5.5 (HEWL-T1) show a single dye molecule bound to site II, and the crystals belong to space group P4₃2₁2 without significant changes in the unit cell (a = b = 78.50, c = 37.34 Å). On the other hand, crystals soaked at pH 6.5 in the presence of imidazole (HEWL-T2) show up to eight molecules of the dye bound to site II, and display changes in space group (P2₁2₁2₁) and unit cell (a = 38.00, b = 76.65, c = 84.86 Å). In all of the structures, the dye molecules are placed at the surface of the protein near to positively charged residues accessible through the main solvent channels of the crystal. Differences in the arrangement of the dye molecules at the surface of the protein suggest that the binding is not specific and is mainly driven by electrostatic interactions.

Extraction of Thermodynamic Parameters of Protein Unfolding Using Parallelized Differential Scanning Fluorimetry

Thermodynamic properties of protein unfolding have been extensively studied; however, the methods used have typically required significant preparation time and high protein concentrations. Here we present a facile, simple, and parallelized differential scanning fluorimetry (DSF) method that enables thermodynamic parameters of protein unfolding to be extracted. This method assumes a two-state, reversible protein unfolding mechanism and provides the capacity to quickly analyze the biophysical mechanisms of changes in protein stability and to more thoroughly characterize the effect of mutations, additives, inhibitors, or pH. We show the utility of the DSF method by analyzing the thermal denaturation of lysozyme, carbonic anhydrase, chymotrypsin, horseradish peroxidase, and cellulase enzymes. Compared with similar biophysical analyses by circular dichroism, DSF allows for determination of thermodynamic parameters of unfolding while providing greater than 24-fold reduction in experimental time. This study opens the door to rapid characterization of protein stability on low concentration protein samples.

Investigation of binding properties of umbelliferone (7hydroxycoumarin) to lysozyme

The binding interaction of lysozyme and umbelliferone (7hydroxcoumarin, 7HC) was investigated by UV-vis absorption and fluorescence quenching. It was obtained from fluorescence spectra that the fluorescence quenching of lysozyme by 7HC was probably a result of the formation of lysozyme-7HC complex and binding parameters were determined according to the Stern-Volmer equation. The effects of various common metal ions on the binding were also studied. The thermodynamic parameters were calculated at different temperatures which indicated that hydrophobic interaction. The binding distance (r) between the donor (lysozyme) and the acceptor (7HC) was 3.81 nm based on the Förster theory of non-radioactive resonance energy transfer.

Spectroscopic analyses on interaction of Naphazoline hydrochloride with bovine serum albumin

The fluorescence and ultraviolet spectroscopy were explored to study the interaction between Naphazoline hydrochloride (Naphcon) and bovine serum albumin (BSA) at three different temperatures (292, 301, and 310 K) under imitated physiological conditions. The quenching mechanism of BSA by Naphacon was interpreted using the Stern-Volmer mechanism, and a combined quenching (dynamic and static quenching). The binding constants, binding sites and the corresponding thermodynamic parameters (ΔG, ΔH, and ΔS) of the interaction system were calculated at different temperatures. According to Förster non-radiation energy transfer theory, the binding distance between BSA and Naphcon was found to be 4.71 nm. Synchronous fluorescence spectroscopy showed the conformation of BSA changed in the presence of Naphacon. In addition, the effect of some common metal ions (Mg(2+), Ca(2+), Ni(2+), Cu(2+), and Fe(2+)) on the binding constant between Naphcon and BSA was examined.

Interaction of pyrrolizine derivatives with bovine serum albumin by fluorescence and UV-Vis spectroscopy

The interaction between pyrrolizine derivatives (PD) and bovine serum albumin (BSA) under imitated physiological conditions was analyzed by fluorescence and ultraviolet spectra. The experiments were conducted at three different temperatures (302, 306 and 310 K) and the results showed that PD caused the fluorescence quenching of BSA through a combined quenching procedure. The binding constant (K(a)), binding-site number (n) between PD and BSA at different temperatures were obtained. According to Förster non-radiation energy transfer theory, the binding distance (r) between BSA and PD was calculated. The corresponding thermodynamic parameters (ΔG, ΔH, and ΔS) were also obtained. The comparison of binding potency of PD and BSA suggested that the substituent on the benzene ring could enhance the binding affinity of PD and BSA. Finally, we investigated the possible sub-domain on BSA where bind PD by displacement experiments.

The use of nanoscale visible light-responsive photocatalyst TiO2-Pt for the elimination of soil-borne pathogens

Exposure to the soil-borne pathogens Burkholderia pseudomallei and Burkholderia cenocepacia can lead to severe infections and even mortality. These pathogens exhibit a high resistance to antibiotic treatments. In addition, no licensed vaccine is currently available. A nanoscale platinum-containing titania photocatalyst (TiO₂-Pt) has been shown to have a superior visible light-responsive photocatalytic ability to degrade chemical contaminants like nitrogen oxides. The antibacterial activity of the catalyst and its potential use in soil pathogen control were evaluated. Using the plating method, we found that TiO₂-Pt exerts superior antibacterial performance against Escherichia coli compared to other commercially available and laboratory prepared ultraviolet/visible light-responsive titania photocatalysts. TiO₂-Pt-mediated photocatalysis also affectively eliminates the soil-borne bacteria B. pseudomallei and B. cenocepacia. An air pouch infection mouse model further revealed that TiO₂-Pt-mediated photocatalysis could reduce the pathogenicity of both strains of bacteria. Unexpectedly, water containing up to 10% w/v dissolved soil particles did not reduce the antibacterial potency of TiO₂-Pt, suggesting that the TiO₂-Pt photocatalyst is suitable for use in soil-contaminated environments. The TiO₂-Pt photocatalyst exerted superior antibacterial activity against a broad spectrum of human pathogens, including B. pseudomallei and B. cenocepacia. Soil particles (<10% w/v) did not significantly reduce the antibacterial activity of TiO₂-Pt in water. These findings suggest that the TiO₂-Pt photocatalyst may have potential applications in the development of bactericides for soil-borne pathogens.

Fluorescent labeling of proteins with amine-specific 1,3,2-(2H)-dioxaborine polymethine dye

A novel water-soluble amine-reactive dioxaborine trimethine dye was synthesized in a good yield and characterized. The potential of the dye as a specific reagent for protein labeling was demonstrated with bovine serum albumin and lysozyme. Its interaction with proteins was studied by fluorescence spectroscopy and gel electrophoresis. The covalent binding of this almost nonfluorescent dye to proteins results in a 75- to 78-fold increase of its emission intensity accompanied by a red shift of the fluorescence emission maximum by 27 to 45 nm, with fluorescence wavelengths of labeled biomolecules being more than 600 nm. The dye does not require activation for the labeling reaction and can be used in a variety of bioassay applications.

Synthesis and α-glucosidase inhibitory mechanisms of bis(2,3-dibromo-4,5-dihydroxybenzyl) ether, a potential marine bromophenol α-glucosidase inhibitor

Bis(2,3-dibromo-4,5-dihydroxybenzyl) ether (BDDE), derived from the marine algae, is a potential α-glucosidase inhibitor for type 2 diabetes treatment. In the present study, a synthetic route was established as a valid approach to obtain BDDE. Fluorescence spectra, circular dichroism spectra and molecular docking methods were employed to elucidate the inhibitory mechanisms of BDDE against α-glucosidase. The results showed that BDDE could be prepared effectively and efficiently with the established synthetic methods. Synthetic BDDE bound with α-glucosidase and induced minor conformational changes of the enzyme. The docking results indicated the interaction between BDDE and α-glucosidase was driven by both hydrophobic forces and hydrogen bonds. The docked BDDE molecule was completely buried in the α-glucosidase binding pocket with part of the molecule reaching the catalytic center and overlapping with the position of glucose, and the rest of the molecule extending towards protein surface. This study provides useful information for the understanding of the BDDE-α-glucosidase interaction and for the development of novel α-glucosidase inhibitors.

Methods for imaging and detecting modification of proteins by reactive lipid species

Products of lipid peroxidation are generated in a wide range of pathologies associated with oxidative stress and inflammation. Many oxidized lipids contain reactive functional groups that can modify proteins, change their structure and function, and affect cell signaling. However, intracellular localization and protein adducts of reactive lipids have been difficult to detect, and the methods of detection rely largely on antibodies raised against specific lipid-protein adducts. As an alternative approach to monitoring oxidized lipids in cultured cells, we have tagged the lipid peroxidation substrate arachidonic acid and an electrophilic lipid, 15-deoxy-Delta(12,14)-prostaglandin-J2 (15d-PGJ2), with either biotin or the fluorophore BODIPY. Tagged arachidonic acid can be used in combination with conditions of oxidant stress or inflammation to assess the subcellular localization and protein modification by oxidized lipids generated in situ. Furthermore, we show that reactive lipid oxidation products such as 15d-PGJ2 can also be labeled and used in fluorescence and Western blotting applications. This article describes the synthesis, purification, and selected application of these tagged lipids in vitro.