Probing the toxic effect of chlorpyrifos as an environmental pollutant on the structure and biological activity of lysozyme under physiological conditions.

The pervasive use of pesticides like chlorpyrifos (CPY) has been associated with deleterious effects on biomolecules, posing significant risks to environmental integrity, public health, and overall ecosystem equilibrium. Accordingly, in this study, we investigated the potential binding interaction between the well-conserved enzyme, lysozyme (LSZ), and CPY through various spectroscopic techniques and molecular modeling. The UV-vis absorption and fluorescence experiments confirmed the complex formation and static quenching of the intrinsic fluorescence intensity. LSZ revealed a singular binding site for CPY, with binding constants around 105 M-1 across different temperature ranges. Analysis of thermodynamic parameters showed the spontaneous nature of the complexation process, while also revealing the pivotal role of hydrophobic interactions in stabilizing the LSZ-CPY system. According to circular dichroism and Fourier transform infrared studies, CPY binding changed the secondary structure of LSZ by boosting α-helix presence and reducing the levels of ß-sheet and ß-turn content. Further, CPY decreased the stability and activity of LSZ. Computational docking delineated the specific and highly preferred binding site of CPY within the structure of LSZ. Molecular dynamic simulation indicated the enduring stability of the LSZ/CPY complex and revealed structural modifications in the LSZ after binding with CPY. This research provides a detailed understanding of the intermolecular dynamics between CPY and LSZ, concurrently elucidating the molecular-level implications for the potential hazards of pesticides in the natural environment.

Thermodynamic and functional changes of alpha-chymotrypsin after interaction with gallic acid.

In the present study, the interaction mechanism between gallic acid (GA) and α-Chymotrypsin (α-CT) was investigated by employing a series ofspectroscopic methods, computational docking and molecular dynamic (MD) simulation. Fluorescence spectra analysis indicated the formation of a stable complex between GA and α-CT, where the quenching of the fluorescence emission was predominantly characterized by a static mechanism. TheCA obtained binding constants for the α-CT-GA complex were in the order of 103 M-1, indicating the moderate binding affinity of GA for α-CT. The corresponding CD findings showed that the interaction between GA and α-CT resulted in an alteration of the protein's secondary structure. The findings of the enzyme activity investigation clearly showed that the presence of GA led to a notable decline in the enzymatic activity of α-CT, highlighting GA's function as an effective inhibitor for α-CT. The molecular docking simulations revealed the optimal binding site for the GA molecule within the α-CT structure and MD simulations confirmed the stability of the α-CT-GA complex. This research expands our comprehension regarding the behavior of enzymes in the presence of small-molecule ligands and opens avenues for food safety.

Structural alterations and inhibition of lysozyme activity upon binding interaction with rotenone: Insights from spectroscopic investigations and molecular dynamics simulation.

The pervasive employment of pesticides such as rotenone on a global scale represents a substantial hazard to human health through direct exposure. Therefore, exploring the interactions between such compounds and body macromolecules such as proteins is crucial in comprehending the underlying mechanisms of their detrimental effects. The present study aims to delve into the molecular interaction between rotenone and lysozyme by employing spectroscopic techniques along with Molecular dynamics (MD) simulation in mimicked physiological conditions. The binding interaction resulted in a fluorescence quenching characterized by both dynamic and static mechanisms, with static quenching playing a prominent role in governing this phenomenon. The analysis of thermodynamic parameters indicated that hydrophobic interactions primarily governed the spontaneous bonding process. FT-IR and circular dichroism findings revealed structural alternations of lysozyme upon complexation with rotenone. Also, complexation with rotenone declined the biological activity of lysozyme, thus rotenone could be considered an enzyme inhibitor. Further, the binding interaction substantially decreased the thermal stability of lysozyme. Molecular docking studies showed the binding location and the key residues interacting with rotenone. The findings of the spectroscopic investigations were confirmed and accurately supported by MD simulation studies.

Interaction between the antioxidant compound safranal and α-chymotrypsin in spectroscopic fields and molecular modeling approaches.

Among various herbal plants, saffron has been the subject of study in various medical and food fields. Among the compounds of saffron, safranal is one of them. Safranal is a monoterpene aldehyde. The precursor of safranal is called picrocrocin, whose hydrolysis leads to the production of safranal. picrocrocin has two sugar components and aglycone. sugar component was separated during the drying process of saffron and safranal is produced. Saffron is the cause of the saffron aroma. Previous studies have shown that safranal offers many benefits such as antioxidants, blood pressure regulation and anti-tumor qualities. On the other hand, α-Chy is an enzyme secreted by the pancreas into the intestine and then acts as an efficient protease. In this study, various methods, such as molecular dynamics (MD) simulation and molecular binding, and different spectroscopic techniques, as well as protein stability techniques, were used to investigate the possible interactions between safranal and α-Chy. UV spectroscopic studies were showing that the existence of safranal decreased α-Chy absorption intensity. safranal caused the intrinsic fluorescence of α-Chy to be quenched too. According to the Stern-Volmer equation, the interaction between safranal and α-Chy was of the static type. In thermodynamic calculations, the interaction between safranal and α-Chy was stabilized by hydrophobic forces. And it was found that this interaction continued spontaneously. These results were, thus, consistent with the Docking data simulation (with the negative ΔG° number and positive changes in enthalpy and entropy). The thermal stability of α-Chy was also measured, showing that its melting point was shifted to a higher threshold as a result of the interaction. also, MD simulation indicated that α-Chy became more stable in the presence of safranal. In this paper, all the results of the laboratory techniques were confirmed by molecular dynamic simulations, so the correctness of the results was confirmed. From this research, we hope to carefully observe the possible changes in the behavior and structure of the enzyme in the presence of safranal.Communicated by Ramaswamy H. Sarma.

Noncovalent interactions of bovine trypsin with curcumin and effect on stability, structure, and function.

The structural studies of trypsin with curcumin in Tris-hydrochloride (Tris-HCl) buffer solution (pH 8.0) was explored by UV-vis spectroscopic and fluorescence quenching method, kinetic reaction, circular dichroism (CD), Thermal denaturation, molecular docking, and molecular dynamic simulation. The curcumin could decrease trypsin absorbance. It was showed that curcumin could quench the fluorescence of trypsin by static quenching mechanism. This is in agreement with UV-vis results and CD studies in which the α-helix becomes more, and ß-sheet becomes less than trypsin without ligand. The binding constant, the number of binding sites and thermodynamic parameters (ΔH°, ΔS°, and ΔG°) at two temperatures were calculated. The hydrogen bond and Van der Waals interaction were found as the main forces, which is in congruence with docking results. The outcome of the kinetic reaction indicates an uncompetitive inhibition by curcumin on trypsin. Molecular Dynamic simulation and Thermal denaturation results demonstrate that curcumin makes trypsin unstable and more flexible.

Experimental and theoretical investigations on the interaction of l-methionine molecules with α-chymotrypsin in the aqueous solution using various methods.

l-Methionine (l-Met) is one of the necessary amino acids that play unparalleled roles, influencing both the protein structure and metabolism. Understanding the interactions between proteins and small molecules can be realized by various perspectives, and this is significant for the progression of basic sciences and drug development. In this study, the variations in the stability, function, and structure of α-Chymotrypsin (α-Chy) in the presence of l-Met were investigated using spectroscopic and computational approaches. The results of the UV-vis absorption demonstrated that α-Chy had a maximum peak at 280 nm due to the Trp residue. Hyperchromism shift was seen in the presence of l-Met. Ground state system was formed in the presence of l-Met, as confirmed by the fluorescence studies. Fluorescence variations also revealed static quenching. The CD spectra also represented the alteration of the enzyme with an increase in the α-helix and a decrease in the ß-sheet. The activity of α-Chy was incremented in the presence of l-Met. Therefore, l-Met served as an activator. Molecular docking results also indicated a negative amount for the Gibbs free energy of the binding of l-Met to the enzyme. α-Chy became more stable in the presence of l-Met, based on the molecular dynamics simulation.