Evaluation of the binding of UFCB and Pb-UFCB to pepsin: Spectroscopic analysis and enzyme activity assay

Nanoplastics composite norfloxacin induced changes in conformation and function of lysozyme and differential effects of co-exposure contamination

The concurrent environmental contamination by nanoplastics (NPs) and norfloxacin (NOR) is a burgeoning concern, with significant accumulations in various ecosystems and potential ingress into the human body via the food chain, posing threats to both public health and ecological balance. Despite the gravity of the situation, studies on the co-exposure contamination effects of these substances are limited. Moreover, the response mechanisms of key functional proteins to these pollutants are yet to be fully elucidated. In this work, we conducted a comprehensive assessment of the interaction mechanisms of NPs and NOR with lysozyme under both single and co-exposure condition, utilizing dynamic light scattering, ζ-potential measurements, multi-spectroscopy methods, enzyme activity assays and molecular docking, to obtain a relationship between the compound effects of NPs and NOR. Our results indicate that NPs adsorb NOR on their surface, forming more stable aggregates. These aggregates influence the conformation, secondary structure (α-Helix ratio decreased by 3.1 %) and amino acid residue microenvironment of lysozyme. And changes in structure affect the activity of lysozyme (reduced by 39.9 %) with the influence of composited pollutants exerting stronger changes. Molecular simulation indicated the key residues Asp 52 for protein function located near the docking site, suggesting pollutants preferentially binds to the active center of lysozyme. Through this study, we have found the effect of increased toxicity on lysozyme under the compounded conditions of NPs and NOR, confirming that the increased molecular toxicity of NPs and NOR is predominantly realized through the increase in particle size and stability of the aggregates under weak interactions, as well as induction of protein structural looseness. This study proposes a molecular perspective on the differential effects and mechanisms of NPs-NOR composite pollution, providing new insights into the assessment of in vitro responses to composite pollutant exposure.

The size-dependent effects of nanoplastics in mouse primary hepatocytes from cells to molecules

Nanoplastics (NPs) are easily ingested by organisms and their major accumulation organ was determined to be liver. To date, the size-dependent cytotoxicity of NPs on mammalian hepatocytes remains unclear. This study utilized mouse primary hepatocytes and catalase (CAT) as specific receptors to investigate the toxicity of NPs from cells to molecules, focusing on size-dependent effects. Results showed that the larger the particle size of NP at low doses (≤50 mg/L), the most pronounced inhibitory effect on hepatocyte viability. 20 nm NPs significantly inhibit cell viability only at high doses (100 mg/L). Larger NP particles (500 nm and 1000 nm) resulted in a massive release of lactate dehydrogenase (LDH) from the cell (cell membrane damage). Reactive oxygen species (ROS), superoxide dismutase (SOD) and CAT tests suggest that NPs disturbed the cellular antioxidant system. 20 nm NPs show great strength in oxidizing lipids and disrupting mitochondrial function compared to NPs of other particle sizes. The degree of inhibition of CAT activity by different sized NPs was coherent at the cellular and molecular levels, and NP-500 had the most impact. This suggests that the structure and microenvironment of the polypeptide chain in the vicinity of the CAT active site is more susceptible to proximity and alteration by NP-500. In addition, the smaller NPs are capable of inducing relaxation of CAT backbone, disruption of H-bonding and reduction of α-helix content, whereas the larger NPs cause contraction of CAT backbone and increase in α-helix content. All NPs induce CAT fluorescence sensitization and make the chromophore microenvironment hydrophobic. This study provides new insights for NP risk assessment and applications.

Novel evidence on iodoacetic acid-induced immune protein functional and conformational changes: Focusing on cellular and molecular aspects

Elevated levels of iodide occur in raw water in certain regions, where iodination disinfection byproducts are formed during chloramine-assisted disinfection of naturally iodide-containing water. Iodoacetic acid (IAA) is one of the typical harmful products. The mechanisms underlying IAA-induced immunotoxicity and its direct effects on biomolecules remained unclear in the past. Cellular, biochemical, and molecular methods were used to investigate the mechanism of IAA-induced immunotoxicity and its binding to lysozyme. In the presence of IAA, the cell viability of coelomocytes was significantly reduced to 70.8 %, as was the intracellular lysozyme activity. Upon binding to IAA, lysozyme underwent structural and conformational changes, causing elongation and unfolding of the protein due to loosening of the backbone and polypeptide chains. IAA effectively quenched the fluorescence of lysozyme and induced a reduction in particle sizes. Molecular docking revealed that the catalytic residue, Glu 35, which is crucial for lysozyme activity, resided within the docking range, suggesting the preferential binding of IAA to the active site of lysozyme. Moreover, electrostatic interaction emerged as the primary driving force behind the interaction between IAA and lysozyme. In conclusion, the structural and conformational changes induced by IAA in lysozyme resulted in impaired immune protein function in coelomocytes, leading to cellular dysfunction.

Characterizing the binding interactions between virgin/aged microplastics and catalase in vitro

Microplastics (MPs) undergo physical, chemical, and biological aging in the environment, leading to changes in their physicochemical properties, affecting migration characteristics and toxicity. Oxidative stress effects induced by MPs in vivo have been extensively studied, but the toxicity difference between virgin and aged MPs and the interactions between antioxidant enzymes and MPs in vitro have not been reported yet. This study investigated the structural and functional changes of catalase (CAT) induced by virgin and aged PVC-MPs. It was shown that light irradiation aged the PVC-MPs, and the aging mechanism was photooxidation, resulting in a rough surface and appearing holes and pits. Because of the changes in physicochemical properties, aged MPs had more binding sites than virgin MPs. Fluorescence and synchronous fluorescence spectra results suggested that MPs quenched the endogenous fluorescence of CAT and interacted with tryptophane and tyrosine residues. The virgin MPs had no significant effect on the skeleton of CAT, while the skeleton and the polypeptide chains of CAT became loosened and unfolded after binding with the aged MPs. Moreover, the interactions of CAT with virgin/aged MPs increased the α-helix and decreased the β-sheet contents, destroyed the solvent shell, and resulted in a dispersion of CAT. Due to the large size, MPs cannot enter the interior of CAT and have no effects on the heme groups and activity of CAT. The interaction mechanism between MPs and CAT may be that MPs adsorb CAT to form the protein corona, and aged MPs had more binding sites. This study is the first comprehensive investigation of the effect of aging on the interaction between MPs and biomacromolecules and highlights the potential negative effects of MPs on antioxidant enzymes.

A comprehensive insight into the effects of caffeic acid (CA) on pepsin: Multi-spectroscopy and MD simulations methods

The interaction between caffeic acid (CA) and pepsin was investigated using multi-spectroscopy approaches and molecular dynamic simulations (MDS). The effects of CA on the structure, stability, and activity of pepsin were studied. Fluorescence emission spectra and UV-vis absorption peaks all represented the static quenching mechanism of pepsin by CA. Moreover, the fluorescence spectra displayed that the interaction of CA exposed the tryptophan chromophores of pepsin to a more hydrophilic micro-environment. Consistent with the simulation results, thermodynamic parameters revealed that CA was bound to pepsin with a high binding affinity. The Van der Waals force and Hydrogen bond interaction were the dominant driving forces during the binding process. The circular dichroism (CD) spectroscopy analysis showed that the CA binding to pepsin decreased the contents of α-Helix and Random Coil but increased the content of β-sheet in the pepsin structure. Accordingly, MD simulations confirmed all the experimental results. As a result, CA is considered an inhibitor with adverse effects on pepsin activity.

Investigation of the interaction behavior between quercetin and pepsin by spectroscopy and MD simulation methods

The ability of a therapeutic compound to bind to proteins is critical for characterizing its therapeutic impacts. We have selected quercetin (Qu), a most common flavonoid found in plants and vegetables among therapeutic molecules that are known to have anti-inflammatory, antioxidant, anti-genotoxic, and anti-cancer effects. The current study aimed to see how quercetin interacts with pepsin in an aqueous environment under physiological conditions. Absorbance and emission spectroscopy, circular dichroism (CD), and kinetic methods, as well as molecular dynamic (MD) simulation and docking, were applied to study the effects of Qu on the structure, dynamics, and kinetics of pepsin. Stern-Volmer (K_sv) constants were computed for the pepsin-quercetin complex at three temperatures, showing that Qu reduces enzyme emission spectra using a static quenching. With Qu binding, the V_max and the k_cat/K_m values decreased. UV-vis absorption spectra, fluorescence emission spectroscopy, and CD result indicated that Qu binding to pepsin leads to microenvironmental changes around the enzyme, which can alter the enzyme's secondary structure. Therefore, quercetin caused alterations in the function and structure of pepsin. Thermodynamic parameters, MD binding, and docking simulation analysis showed that non-covalent reactions, including the hydrophobic forces, played a key role in the interaction of Qu with pepsin. The findings conclude of spectroscopic experiments were supported by molecular dynamics simulations and molecular docking results.

Molecular interaction of di-ester bonded cationic Gemini surfactants with pepsin: in vitro and in silico perspectives

The implications of surfactant-enzyme/protein interactions in a variety of fields, including biotechnology, cosmetics, paints and pharmaceuticals, have attracted a lot of attention in contemporary studies. Herein, we have employed several in vitro and in silico techniques such as excitation and absorption spectroscopies, circular dichroism and FT-IR spectroscopies, density functional and molecular dynamics simulations to understand the interaction behavior of oxy-diester-based green cationic Gemini surfactants, N1,N1,N14,N14-tetramethyl-2,13-dioxo-N1,N14-dialkyl-3,6,12-tetraoxateradecane-1,14-diaminiumdichloride (abbreviated as Cm-E2O2-Cm, where 'm' stands for alkyl chain length, m = 12 and 14) with one of the main digestive proteins, pepsin. The spectroscopic techniques confirm the static quenching effect of surfactants on pepsin. The calculated physical parameters (Ksv, Kb and ΔG) and their order reveal the distinguished implications for the surfactants' chain lengths. The spontaneity of interaction was also confirmed by negative Gibbs free energy change values. The extrinsic spectroscopic study with pyrene as fluorescence probe, FT-IR and CD techniques indicated a potential conformational change in pepsin induced by the Gemini surfactants. DFT, docking and MD simulations provided the theoretical understanding regarding the quantum mechanical environment, location of binding and stability of the protein-surfactant complexation in energy terms. We believe this study will be a humble addition to our existing knowledge in the field of protein-surfactant interactions.Communicated by Ramaswamy H. Sarma.

Potential toxicity of bisphenol A to α-chymotrypsin and the corresponding mechanisms of their binding

Bisphenol A (BPA) is an endocrine disruptor widely existing in plastics and resins, which can accumulate in animals and human bodies, posing a potential threat to the physiological and biochemical reactions of human beings or other organisms. α-Chymotrypsin is a kind of proteolytic enzyme existing in humans and animals, which can cause diseases when its activity is excessive. However, there is a lack of research on the mechanism of endocrine disruptors affecting α-chymotrypsin activity. In this study, the interaction between BPA and α-chymotrypsin was proved via multiple spectroscopic approaches, enzyme activity change, isothermal titration calorimetry and molecular docking. Results showed that α-chymotrypsin's polypeptide chains were unfolded, and protein skeletons were loosened with the exposure to BPA. α-Helix content increased and β-sheet content was decreased. The particle size of the BPA-α-chymotrypsin complex became smaller. Fluorescence sensitization may also be explained by a perturbation of the chromophore Trp 141. The thermodynamic parameters of the binding reaction were measured by isothermal titration calorimetry (ITC), which showed that there was hydrophobic interaction between BPA and α-chymotrypsin, which was consistent with the results of molecular docking. Moreover, BPA may stop near the active center of α-chymotrypsin and interact with the key residues His 57 and Ser 195. The above phenomenon explained the result that the activity of α-chymotrypsin increased to 139% when exposed to high dose BPA (40 μM). Taken together, the effects of BPA on the structure and function of α-chymotrypsin were clarified at the molecular level, which made up the gap in the mechanism of BPA on the proteolytic enzyme, and provided a reliable basis for disease avoidance and prevention.

Size-dependent effects of nanoplastics on structure and function of superoxide dismutase

The ubiquitous existence of nano-plastics (NPs) has attracted widespread concern. Currently, the uptake of NPs by organisms and cells has been reported. However, knowledge about the interaction between NPs and protein is still limited, and there is a gap in research on the size-dependent toxicity of NPs toward protein. In this study, multi-spectroscopic techniques and enzyme activity determination were used to explore the structure and function changes of the main antioxidant enzyme superoxide dismutase (SOD), caused by the binding of NPs with different particle sizes. Results indicated NPs with different sizes can directly interact with SOD. NPs with smaller sizes result in looser skeletons of SOD, while the larger lead to tighter peptide chains. In addition, NPs can bind with SOD to form complexes, and the smaller the NPs are easier to be induced to coalesce by SOD. The surface curvature of 100 nm NPs was more conducive to varying the secondary structure of SOD. NPs of 100 nm and 500 nm can cause greater sensitization of SOD endogenous fluorescence, and increase the polarity around tyrosine residue. The enzyme activity assay further revealed the functional differences caused by the size-dependent effects of NPs. NPs of 100 nm and 20 nm induced a more significant change in SOD activity (increased by 20% and 8%, respectively), while NPs of 500 nm and 1000 nm had a little impact on it. Together, smaller NPs have a greater impact on the structure and function of SOD. This study revealed the size-dependent toxicity of NPs to protein, which provided a rationale for the necessary avoidance and substitution of NPs in engineering applications.

Study on the interaction between nimodipine and five proteinases and the effects of naringin and vitamin C on these interactions by spectroscopic and molecular docking methods

The interaction mechanisms of nimodipine with pepsin, trypsin, α-chymotrypsin, lysozyme and human serum albumin were investigated by multispectral and molecular docking methods. Vitamin C and naringin were the main active components of grapefruit juice, and nimodipine was the typical drug that interacts with this juice. Fluorescence spectroscopy was used to study the interaction of nimodipine with five proteinases (pepsin, trypsin, α-chymotrypsin, lysozyme and human serum albumin) and the effects of vitamin C and naringin on these interactions. The fluorescence quenching results showed that nimodipine can quench the intrinsic fluorescence of these five proteinases by a static quenching procedure. Nimodipine binds to pepsin and α-chymotrypsin, through hydrogen bonding and van der Waals forces, whereas it binds to trypsin, lysozyme and human serum albumin mainly by hydrophobic interactions. The microenvironment of the five proteinases changed. The probability of nonradiative energy transfer between the five proteinases and nimodipine was high. Both vitamin C and naringin reduced the binding constant of nimodipine to the four proteinases (except α-chymotrypsin) and might increase the concentration of free nimodipine. Thus, vitamin C or naringin in fruits or foods could increase the blood concentration of free nimodipine and perhaps a reduction in nimodipine dose was needed.

The combination of ultrafine carbon black and lead provokes cytotoxicity and apoptosis in mice lung fibroblasts through oxidative stress-activated mitochondrial pathways

Ultrafine particulates (UFPs) are considered one of the most hazardous of all air pollutants, which can be directly inhaled into the human body and cause direct damage to lung tissues. Lung fibroblasts (LF) play an important role in the structure and function of lung and there are few studies on primary cells at present. So, the article focuses on LF as the research objective and ultrafine carbon black (UFCB) and Pb-UFCB (loaded with lead) as a representative of UFPs to study the effect on LF. The results showed that UFCB and Pb-UFCB inhibited LF proliferation due to cell cycle arrested in the S phase, and induced apoptosis. Additionally, UFCB or Pb-UFCB could induce oxidative stress manifested as the increase of intracellular reactive oxygen species. The redox imbalance was further confirmed by measuring the changes of related enzymes, including the activity of superoxide dismutase and catalase and the level of reduced glutathione and malondialdehyde in cells. Moreover, the elevated lactate dehydrogenase in the culture medium indicated that cell membrane had been injured. And mitochondrial function was impaired by the imbalance of ATP synthesis and hydrolysis. In summary, both induced oxidative stress, which is the main driving force of LF early apoptosis, disruption of cell membrane integrity and mitochondrial function. Here, we provide a meaningful and challenging subject to explore the toxic effect and mechanism between UFPs and lung tissue at cellular levels, and theoretical basics for the possible changes of lung tissue function in vivo.