Binding patterns and structure-affinity relationships of food azo dyes with lysozyme: a multitechnique approach

Insights into the interaction and inhibitory action of palmatine on lysozyme fibrillogenesis: Spectroscopic and computational studies

Interaction under amyloidogenic condition between naturally occurring protoberberine alkaloid palmatine and hen egg white lysozyme was executed by adopting spectrofluorometric and theoretical molecular docking and dynamic simulation analysis. In spetrofluorometric method, different types of experiments were performed to explore the overall mode and mechanism of interaction. Intrinsic fluorescence quenching of lysozyme (Trp residues) by palmatine showed effective binding interaction and also yielded different binding parameters like binding constant, quenching constant and number of binding sites. Synchronous fluorescence quenching and 3D fluorescence map revealed that palmatine was able to change the microenvironment of the interacting site. Fluorescence life time measurements strongly suggested that this interaction was basically static in nature. Molecular docking result matched with fluorimetric experimental data. Efficient drug like interaction of palmatine with lysozyme at low pH and high salt concentration prompted us to analyze its antifibrillation potential. Different assays and microscopic techniques were employed for detailed analysis of lysozyme amyloidosis.Thioflavin T(ThT) assay, Congo Red (CR) assay, 8-anilino-1-naphthalenesulfonic acid (ANS) assay, Nile Red (NR) assay, anisotropy and intrinsic fluorescence measurements confirmed that palmatine successfully retarded and reduced lysozyme fibrillation. Dynamic light scattering (DLS) and atomic force microscopy (AFM) further reiterated the excellent antiamyloidogenic potency of palmatine.

Unravelling the molecular interactions of phenyl isothiocyanate and benzoyl isothiocyanate with human lysozyme: Biophysical and computational analyses

Phenyl isothiocyanate and benzoyl isothiocyanate are the phytochemicals present in the Brassicaceae family. They have antibacterial, antiapoptotic and antifungal properties. Protein-small molecule interaction studies are done to assess the changes in structure, dynamics, and functions of protein and to decipher the binding mechanism. This study is based on the comparative binding of PT and BT with human lysozyme using in vitro and computational techniques. UV, fluorescence emission, and FRET spectra gave insight into the complex formation, quenching mechanism, and binding parameters. Both PT and BT quenched the intrinsic fluorescence of Lyz by a static quenching mechanism. Synchronous, 3D fluorescence and CD spectroscopy substantiated conformational and microenvironmental alterations in the Lyz. The metal ions and β-cyclodextrin had a pronounced effect on the binding strength of Lyz-PT and Lyz-BT complexes. Accessible surface area analysis was determined to characterise the amino acid residue packing. Molecular docking further validated the wet lab experimental results.

Investigations on the binding properties of hydroxylated polybrominated diphenyl ethers with lysozyme using the multispectral techniques and molecular modeling

As a kind of phenolic chemical with endocrine disrupting potency, hydroxylated polybrominated diphenyl ethers (OH-PBDEs) cause a latent threat to human health from their residue in the environment. Their binding efficiency with lysozyme (LYSO) was studied by molecular simulation combined with fluorescence, UV-vis absorption and circular dichroism (CD), so as to assess their toxicity at the molecular level. Molecular docking data indicate that van der Waals force is the principal interaction force between OH-PBDEs and LYSO. The binding site for 5'-OH-BDE-25 in LYSO is ascertained as the active site, which interaction with the TRP63 and TRP108 residues of LYSO to take shape a strong face-to-face stacked rank (F-shaped). Both 4'-OH-BDE-99 and 3'-OH-BDE-154 display a certain degree of deviation from the active site. Nevertheless, their F-shaped interaction with TRP63 conduce to bind LYSO and stabilize the docking conformation. Combined with dynamics simulation and spectral analysis, the secondary structure of LYSO can be induced by the three kinds of OH-PBDEs. CD spectrum shows that the combination of LYSO and OH-PBDEs will make α- Helix content increased. The combination of OH-PBDEs and LYSO touch upon a static quenching mechanism as a result of steady state fluorescence. The energy decomposition analysis exhibited that LYSO-OH-PBDEs binding site was stable by van der Waals and hydrophobic interaction. As enzyme activity experiments demonstrate that OH-PBDEs can inhibit the activity of LYSO, which is helpful to clarify the molecular toxicity mechanism of OH-PBDEs.

Binding parameters and molecular dynamics of Trypsin-Acid Yellow 17 complexation as a function of concentration

Acid Yellow 17 is a kind of azo dye used in food, textile, and cosmetics. Several studies explain the toxicity of azo dye for our body, but one could not find further information about the effects of these dyes on human macromolecules. In the current study, the interaction of AY17 with trypsin is investigated using several techniques. The UV analysis displayed that the absorption of trypsin could be decreased in the presence of this color. The fluorescence investigation indicated that a static form of quenching happens, and a 50% decrease in the fluorescence intensity, also showed the Vander Waals and hydrogen bond are the main forces in the interaction of this color and trypsin. Furthermore, we can observe that the T_m point of trypsin decreases from 46.5 to 42. On the other hand, the CD results were indicated that the interaction of this color with trypsin could decrease the percent of turn, coil and α-helix in trypsin structure. The computational study was undertaken to obtain more information about the interaction between trypsin and AY17. The results were in agreement with the experimental investigation and indicated that the interaction between this color and trypsin leads to less compactness in the trypsin structure.

Inspirations of Biomimetic Affinity Ligands: A Review

Affinity chromatography is a well-known method dependent on molecular recognition and is used to purify biomolecules by mimicking the specific interactions between the biomolecules and their substrates. Enzyme substrates, cofactors, antigens, and inhibitors are generally utilized as bioligands in affinity chromatography. However, their cost, instability, and leakage problems are the main drawbacks of these bioligands. Biomimetic affinity ligands can recognize their target molecules with high selectivity. Their cost-effectiveness and chemical and biological stabilities make these antibody analogs favorable candidates for affinity chromatography applications. Biomimetics applies to nature and aims to develop nanodevices, processes, and nanomaterials. Today, biomimetics provides a design approach to the biomimetic affinity ligands with the aid of computational methods, rational design, and other approaches to meet the requirements of the bioligands and improve the downstream process. This review highlighted the recent trends in designing biomimetic affinity ligands and summarized their binding interactions with the target molecules with computational approaches.

Role of salts and solvents on the defibrillation of food dye "sunset yellow" induced hen egg white lysozyme amyloid fibrils

Several food dyes are known to induce amyloid fibrillation when interacting with proteins. Here, we studied the role of sunset yellow (SY) in the amyloid fibrillation of hen egg white lysozyme (HEWL) and characterized the changes using spectroscopy techniques. Turbidity results showed that SY dye induces aggregation in HEWL in concentrations dependent manner. The aggregation induced by SY dye is kinetically very fast, no lag phase was detected, and the kinetics process follows an isodesmic kinetics pathway. The SY-dye induce aggregates have cross-β secondary structure confirmed by far-UV CD measurements. The effect of salts and solvents was also seen on SY-induced aggregates. Turbidity, far-UV CD, and kinetics results suggest that certain concentrations of NaCl and (NH₄)₂SO₄ solubilize the SY-induce amyloid fibrils, but (NH₄)₂SO₄ is more effective. Similarly, solvents are also solubilized the SY-induces HEWL amyloid fibrillation but the order of defibrillation is as follows: Isopropanol> ethanol > methanol which signified that isopropanol is more effective than other solvents. The salts and solvents data suggest that the electrostatic, as well as hydrophobic interaction, is responsible for SY-induced amyloid fibrillation. These conformational changes should be examined, more seriously for the purpose of food safety.

A comparative in silico study to detect the effect of food-additives on metabolic protein and its perturbations compensated by osmolytes

Since its inception, food additive has been an integral part of the food processing industry with various commercial roles. Besides its advantages, various studies have already highlighted its long-term adverse effects on human health. However, in terms of protein structures and functions, the innate mechanism that triggers these effects has not been elucidated in previously reported studies. Our work takes an in silico approach to delve into structural implications resulting from these additives with three well studied metabolic proteins-lysozyme, bovine serum albumin (BSA) and ribonuclease A. Three classes of food additives- synthetic color, preservatives, and phosphate-containing, are taken here to understand their effects on the aforementioned metabolic proteins. Conventional molecular docking and dynamics (MD) studies reveal that these additives induce significant structural perturbations. Among them, carmoisine brings about the most secondary structural changes for lysozyme and ribonuclease A, whereas sodium tripolyphosphate affects BSA the most. To restore the secondary structural loss, we further examine the roles of osmolytes through cross-docking and higher timescale MD simulations. These studies unravel that application of osmolytes like raffinose and trehalose triggers structural restoration for BSA, lysozyme and ribonuclease A, and highlight their roles as co-formulants to alleviate the adverse effects of food additives.

Altered Expression of Protamine-like and Their DNA Binding Induced by Cr(VI): A Possible Risk to Spermatogenesis?

Chromium (VI) is the most dangerous oxidation state among the stable forms of chromium. In this work, we evaluated the effect of exposing Mytilus galloprovincialis for 24 h to 1, 10, and 100 nM chromium (VI) on the properties of Protamine-like (PLs) and their gene levels in the gonads. Specifically, we analyzed, by AU-PAGE and SDS-PAGE, PLs extracted from unexposed and exposed mussels. In addition, via EMSA, we evaluated the ability of PLs to bind DNA and also verified their potential to protect DNA from oxidative damage. Finally, we assessed possible alterations in gonadal expression of mt10, hsp70, and genes encoding for PLs-II/PL-IV and PL-III. We found that for all experimental approaches the most relevant alterations occurred after exposure to 1 nM Cr(VI). In particular, a comigration of PL-II with PL-III was observed by SDS-PAGE; and a reduced ability of PLs to bind and protect DNA from oxidative damage was recorded. This dose of chromium (VI) exposure was also the one that produced the greatest alterations in the expression of both mt10 and PL-II/PL-IV encoding genes. All of these changes suggest that this dose of chromium (VI) exposure could affect the reproductive health of Mytilus galloprovincialis.

Investigation of molecular mechanisms of interaction between myofibrillar proteins and 1-heptanol by multiple spectroscopy and molecular docking methods

In this study, we investigated the interaction between myofibrillar proteins (MPs) and selected alcohols (1-pentanol, 1-hexanol, and 1-heptanol). Only 1-heptanol exhibited the binding ability to MPs, and the binding ability significantly increased with increasing protein concentration (p < 0.05). In addition, both static and dynamic quenching occurred during the interaction, with a red shift of the maximum absorption peak in the synchronous fluorescence spectra indicating a change in the microenvironment of the MPs. The results of circular dichroism measurements suggested that the interaction between MPs and 1-heptanol altered the secondary structure of the MPs. Furthermore, thermodynamic analysis showed that hydrogen bonding and van der Waals forces dominated the interaction between MPs and 1-heptanol, which was confirmed by the results of molecular docking/dynamics simulations. This study provides an in-depth understanding of the interaction between MPs and alcohols, which can help to improve the flavor control in meat.

Investigating the interaction of CdTe quantum dots with plasma protein transferrin and their interacting consequences at the molecular and cellular level

This study investigated the interacting mechanism of CdTe quantum dots (QDs) with typical plasma protein transferrin (TF) as well as the impact of the formation of QDs-TF complex on the structure of TF and the cytotoxicity of mouse primary kidney cells. Dialysis experiments and cell viability assays revealed that the formation of QDs-TF complex reduced the contents of Cd released from CdTe QDs and thus counteracted the cytotoxicity of CdTe QDs. The assay of isothermal titration calorimetry found that CdTe QDs complexed with TF majorly through hydrophobic interaction. Multi-spectroscopic measurements showed that CdTe QDs caused the loosening of polypeptide chain, the changes of secondary and tertiary structures as well as the attenuated aggregation of TF molecule. Moreover, these structural and conformational changes were attributed to the nano-effects of CdTe QDs rather than the released Cd. This study is of great significance for fully evaluating the biocompatibility of Cd-QDs and comprehensively understanding the mechanism of Cd-QDs toxicity at the molecular and cellular level.

Aging of microplastics affects their surface properties, thermal decomposition, additives leaching and interactions in simulated fluids

Most microplastics (MPs) have undergone extensive aging in the environment. Aged MPs exhibit different physical and chemical properties from unaged ones. Here, we studied the effects of accelerated aging on the characteristics and pyrolysis of commercial pigmented MPs, as well as pigments leaching and their interactions in simulated gastric and intestinal fluids of mammals. We report that the carbonyl index, surface area, and color change of MPs increased after aging treatment. Cracks and fragmentation of MPs facilitated the accessibility of light and oxygen to internal layer and therefore accelerated the aging process. TGA/GC-MS analysis showed that the high temperature resistance of MPs decreased after aging. Thermal decomposition of pigments and polyethylene occurred in temperature ranges of 340-406 °C and 406-550 °C, respectively. Mono (di)-alkenes and saturated alkanes were the thermal decomposition products of polyethylene. Aging of MPs also caused an increased release of pigments and prolonged aging time led to more release in simulated fluids. Pigments would result in fluorescence quenching of the enzymes through binding interactions once they were released from MPs into simulated fluids. Charge neutralization and polymer bridging accounted for the formation of pigment-enzyme complexes and flocs. These novel findings will allow us to better assess how aging process affects the characteristics, leaching, and toxicity of MPs.

Exploring the conformational changes in fibrinogen by forming protein corona with CdTe quantum dots and the related cytotoxicity

This study describes synthesis of N‑acetyl‑l‑cysteine-capped CdTe quantum dots (QDs) and investigates their interaction with plasma protein fibrinogen (FIB) and the structural changes of FIB. It is shown that the interaction of QDs with FIB is a spontaneous process and the major driving forces are van der Waals forces and hydrogen bonds. Multi-spectroscopic measurements show that the intrinsic fluorescence of FIB was quenched and secondary and tertiary structures were altered due to the interaction with QDs. In addition, the aggregation state of FIB was altered in the presence of QDs. Furthermore, the formed complexes of FIB with QDs reduced the cytotoxicity of QDs. The coating of FIB on QDs could lower intracellular QDs uptake and therefore result in less released cadmium ions and ROS productions. This study, therefore, might be helpful to the comprehensive understanding of QDs toxicity and provide evidence for assessing the safe application of nanoparticles.

What is new in lysozyme research and its application in food industry? A review

Lysozyme, an important bacteriostatic protein, is widely distributed in nature. It is generally believed that the high efficiency of lysozyme in inhibiting gram-positive bacteria is caused by its ability to cleave the β-(1,4)-glycosidic bond between N-acetylmuramic acid and N-acetylglucosamine. In recent years, there has been growing interest in modifying lysozyme via physical or chemical interactions in order to improve its sensitivity against gram-negative bacterial strains. This review addresses some significant techniques, including sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), infrared (IR) spectra, fluorescence spectroscopy, nuclear magnetic resonance (NMR), UV-vis spectroscopy, circular dichroism (CD) spectra and differential scanning calorimetry (DSC), which can be used to characterize lysozymes and methods that modify lysozymes with carbohydrates to enhance their various physicochemical characteristics. The applications of biomaterials based on lysozymes in different food matrices are also discussed.

Biointeractions of Herbicide Atrazine with Human Serum Albumin: UV-Vis, Fluorescence and Circular Dichroism Approaches

The herbicide atrazine is widely used across the globe, which is a great concern. To investigate its potential toxicity in the human body, human serum albumin (HSA) was selected as a model protein. The interaction between atrazine and HSA was investigated using steady-state fluorescence spectroscopy, synchronous fluorescence spectroscopy, UV-Vis spectroscopy, three-dimensional (3D) fluorescence spectroscopy and circular dichroism (CD) spectroscopy. The intrinsic fluorescence of HSA was quenched by the atrazine through a static quenching mechanism. Fluorescence spectra at two excitation wavelengths (280 and 295 nm) showed that the fluorescence quenched in HSA was mainly contributed to by tryptophan residues. In addition, the atrazine bound to HSA, which induced changes in the conformation and secondary structure of HSA and caused an energy transfer. Thermodynamic parameters revealed that this binding is spontaneous. Moreover, electrostatic interactions play a major role in the combination of atrazine and HSA. One atrazine molecule can only bind to one HSA molecule to form a complex, and the atrazine molecule is bound at site II (subdomain IIIA) of HSA. This study furthers the understanding of the potential effects posed by atrazine on humans at the molecular level.

A biomimetic approach to conjugate vitamin B6 cofactor with the lysozyme cocooned fluorescent AuNCs and its application in turn-on sensing of zinc(II) in environmental and biological samples

This communication focusses on the synthesis of red fluorescent lysozyme cocooned gold nanoclusters (Lyso-AuNCs) that have been successfully applied for the selective and specific recognition of the vitamin B₆ cofactor pyridoxal-5'-phosphate (PLP). The red fluorescence of Lyso-AuNCs showed remarkable color change to yellow upon conjugation with PLP due to the formation of a Schiff base between the free -NH₂ present in the lysozyme and the -CHO group of PLP. The developed PLP conjugated Lyso-AuNCs (PLP_Lyso-AuNCs) was applied for the selective turn-on recognition of Zn²⁺ ions in aqueous medium. The yellow fluorescence of PLP_Lyso-AuNCs exhibited significant enhancement at 475 nm in the presence of Zn²⁺ producing bluish-green fluorescence attributed to the complexation-induced aggregation of nanoclusters. The nanoprobe exhibits nanomolar limit of detection for Zn²⁺ ions (39.2 nM) and the practicality of the nanoprobe was validated in various environmental water samples and biological plasma, urine, and beetroot extract, with fairly good recovery percent. Also, the system was successfully implemented for the intracellular detection and monitoring of Zn²⁺ in live HeLa cells. Graphical abstract Applications of red emitting lysozyme cocooned gold nanoclusters (Lyso-AuNCs) for the selective recognition of the vitamin B₆ cofactor pyridoxal-5'-phosphate (PLP) and the conjugated nano-assembly PLP_Lyso-AuNCs for turn-on detection of Zn²⁺ ions in various environmental and biological samples.

Ecofriendly gold nanoparticles - Lysozyme interaction: Thermodynamical perspectives

In the featured work interaction between biosynthesized gold nanoparticles (GNP) and lysozyme (Lys) has been studied using multi-spectroscopic approach. A moderate association constant (K_app) of 2.66×10⁴L/mol has been observed indicative of interactive nature. The binding constant (K_b) was 1.99, 6.30 and 31.6×10⁴L/mol at 291, 298 and 305K respectively and the number of binding sites (n) was found to be approximately one. Estimated values of thermodynamic parameters (Enthalpy change, ΔH=141.99kJ/mol, entropy change, ΔS=570J/mol/K, Gibbs free energy change, ΔG=-27.86kJ/mol at 298K) suggest hydrophobic force as the main responsible factor for the Lys-GNP interaction and also the process of interaction is spontaneous. The average binding distance (r=3.06nm) and the critical energy transfer distance (R_o=1.84nm) between GNP and Lys was also evaluated using Förster's non-radiative energy transfer (FRET) theory and results clearly indicate that non-radiative type energy transfer is possible. Moreover, the addition of GNP does not show any significant change in the secondary structure of Lys as confirmed from circular dichroism (CD) spectra. Furthermore, NMR spectroscopy also indicates interaction between Lys and GNP. The resulting insight is important for the better understanding of structural nature and thermodynamic aspects of binding between the Lys and GNP.

Interaction and inhibitory influence of the azo dye carmoisine on lysozyme amyloid fibrillogenesis

The azo dye carmoisine has a significant inhibitory effect on fibrillogenesis in lysozyme.

Binding properties of drospirenone with human serum albumin and lysozyme in vitro

The interaction of drospirenone (DP) with human serum albumin (HSA)/lysozyme (LYZ) was investigated using different optical techniques and molecular models. Results from the emission and time resolved fluorescence studies revealed that HSA/LYZ emission quenching with DP was initiated by static quenching mechanism. The LYZ-DP system was more easily influenced by temperature than the HSA-DP system. Displacement experiments demonstrated that the DP binding site was mainly located in site 1 of HSA. Based on the docking methods, DP was mainly bound in the active site hinge region where Trp-62 and Trp-63 are located. Conformation study showed that DP had different effects on the local conformation of HSA and LYZ molecules.

Molecular mechanism investigation of the neutralization of cadmium toxicity by transferrin

Molecular docking results of the CdCl₂–transferrin complex: the preferred binding sites in transferrin are labelled as sites H1–H4 and E1–E16.

Binding properties and structure-affinity relationships of food antioxidant butylated hydroxyanisole and its metabolites with lysozyme

Considering the harmful impact of food antioxidants on human bodies, thoroughly exposing their potential effects at the molecular level is important. In this study, the binding interactions of butylated hydroxyanisole (BHA), a phenolic antioxidant, and its different major metabolites tert-butylhydroquinone (TBHQ) and tert-butylbenzoquinone (TBQ) with lysozyme were examined via fluorescence, three-dimensional fluorescence, circular dichroism (CD), and ligand-protein docking studies. The three compounds caused strong quenching of lysozyme fluorescence by a static quenching mechanism but with different quenching efficiencies and different effects on the α-helix content of the lysozyme. The order of binding affinity of lysozyme for all test compounds is as follows: BHA>TBQ>TBHQ. Thermodynamic parameters indicated that hydrogen bonding and van der Waals forces perform dominant functions in the binding between these compounds and lysozyme. Furthermore, structure-affinity relationships between the model compounds and lysozyme were established on the basis of computational analyses.

Chelerythrine–lysozyme interaction: spectroscopic studies, thermodynamics and molecular modeling exploration

The binding of the iminium and alkanolamine forms of chelerythrine to lysozyme (Lyz) was investigated by spectroscopy and molecular modeling studies.