Conformational dynamics of trypsin in the presence of caffeic acid: a spectroscopic and computational investigation

Theoretical assessment of the adsorption mechanism of carvone enantiomers on cow btOR1A1: New microscopic interpretations

In this study, the olfactory threshold concentration was introduced in the statistical physics approach to provide fruitful and deep discussions. Indeed, a modified mono-layer mono-energy model established using statistical physics theory was successfully used to theoretically study the adsorption involved in the olfactory response of (R)-(-)-carvone and (S)-(+)-carvone key food odorants (KFOs) on cow (Bos taurus) olfactory receptor btOR1A1 through the analysis of the different model physicochemical parameters. Thus, stereographic results indicated that the two carvone enantiomers were non-parallelly docked on btOR1A1 binding sites during the adsorption process since the different values of n were superior to 1. Molecular docking studies suggest that the high olfactory response of (R)-(-)-carvone was attributed to the specific types of interactions observed. The energetic results showed via the fitted values of the molar adsorption energies, which were positive and lower than 5 kJ/mol, that the studied enantiomers were exothermically physisorbed via conventional hydrogen bond, pi-alkyl, alkyl, pi-sigma, and van der Waals interactions for (R)-(-)-carvone-btOR1A1 complex and via carbon hydrogen bond, alkyl, pi-alkyl, pi-sigma, and van der Waals interactions for (S)-(+)-carvone-btOR1A1 complex. Moreover, the cow olfactory responses were detected only when 0.49 % and 8.63 % of btOR1A1 binding sites are fired or occupied by (R)-(-)-carvone and (S)-(+)-carvone, respectively. These parameters may also be employed to quantitatively characterize the two olfactory systems.

The molecular mechanisms of TRβ receptor interaction with polychlorinated biphenyls: A multispectral and computational exploration

The thyroid hormone (TH) system is susceptible to the toxic effects of polychlorinated biphenyls (PCBs). Pollutants may disrupt the TH system by binding to serum TH transport proteins or interacting with thyroid hormone receptors (TRs) in target cells. However, the molecular mechanism of interaction with the Thyroid Hormone Receptor Beta (TRβ) is not fully understood. This study employed fluorescence, UV-visible absorption, three-dimensional fluorescence, and Fourier-transform infrared spectroscopy, along with molecular docking and molecular dynamics simulations, to investigate the interaction between TRβ and PCBs. Moreover, molecular docking and fluorescence resonance energy transfer (FRET) findings suggest that TRβ and PCBs underwent resonance energy transfer consistent with Förster's theory. The root mean square deviation (RMSD) and docking outcomes indicate that the TRβ-PCB29 complex exhibited optimal structural stability. Thus, the study concludes that integrating spectroscopic data with molecular docking is essential for a comprehensive analysis. Further analysis of intermolecular interactions using quantum chemistry and reduced density gradient analysis (RDG) analysis revealed that van der Waals forces are the primary drivers of PCBs to TRβ.

Photophysical Properties, Fluorescence Quenching of Metformin Hydrochloride by Caffeine, and its Docking with the AMP-activated protein kinase receptor

In this research, the photophysical properties of metformin hydrochloride (MF-HCl) were studied using spectroscopic and molecular docking techniques. The interaction between metformin hydrochloride and caffeine is essential for understanding the pharmacokinetics of metformin, particularly in populations with high caffeine consumption. Metformin is a first-line medication for managing type 2 diabetes, while caffeine is a widely consumed dietary stimulant. Knowing how caffeine may affect the action of metformin is crucial for effective diabetes management. The spectroscopic techniques results showed that the photophysical properties (fluorescence quantum yields, lifetime, radiative, and non-radiative decay) of the drug are influenced by solvent polarity and drug concentration. The binding mechanism of metformin hydrochloride-caffeine (MF-HCl-CAF) was identified through the fluorescence quenching method. The quenching of drugs induced by caffeine is due to ground state complex formation. The binding occurs due to hydrogen bonds and Van der Waals forces in the reaction. The förster resonance energy transfer (FRET) between metformin hydrochloride and caffeine was also calculated using flourtools.com software. The threshold distance (R0), for 50% energy transfer from metformin hydrochloride to caffeine is 1.81 nm and the binding distance (r), between caffeine and the amino acid residue in metformin hydrochloride is 1.55 nm. Dynamic light scattering (DLS), Zeta potential, and Fourier transform infrared (FTIR) spectroscopy confirm the conformational change of the drugs, as the caffeine molecule binds to metformin hydrochloride molecules. The molecular docking of metformin hydrochloride with the amp-activated protein kinase receptor (PDB Id: 1z0n) is analyzed. Again the docking of both metformin hydrochloride and caffeine (two ligands) with the protein receptor (PDB Id: 1z0n) was also analyzed and the results agreed with the fluorescence quenching techniques.

Heterologous expression, purification, and biochemical characterization of protease 3075 from Cohnella sp. A01

Proteases as one of the most significant categories of commercial enzymes, serve nowadays as the key ingredients in detergent formulations. Therefore, identifying detergent-compatible proteases with better properties is a continuous exercise. Accordingly, we were interested in the recombinant production and characterization of protease 3075 as a novel enzyme from thermophilic indigenous Cohnella sp. A01. The biochemical and structural features of the protease were probed by employing bioinformatic methods and in vitro studies. The bioinformatics analysis discovered that protease 3075 belongs to the C56-PfpI superfamily. The protease 3075 gene was cloned and heterologous expressed in Escherichia coli (E. coli) BL21. It was found that the enzyme contains 175 amino acids and 525 bp with a molecular weight of 19 kDa. Protease 3075 revealed acceptable activity in the range of 40-80°C and pH 5.5-8. The optimum activity of the enzyme was observed at 70°C and pH 6. The activity of protease 3075 increased about 4-fold in the presence of Tween 80 and acetone, while its activity attenuated in the presence of iodoacetic acid and iodoacetamide. Docking analyses revealed the dominant interaction between Tween 80 and protease 3075, mediated by hydrogen bonds and Van der Waals forces. Furthermore, molecular dynamics simulations (MDS) showed that Tween 80 increased the stability of the protease 3075 structure. Altogether, our data provided a novel enzyme by genetic manipulation process that could have significant industrial applications.

Enzyme engineering of choline oxidase for improving stability

Functioning as a flavoprotein, choline oxidase facilitates the transformation of choline into glycine betaine. Notably, choline oxidase and its resultant product, glycine betaine, find extensive applications across various industries and fields of study. However, its high sensitivity and tendency to lose functional activity at high temperatures reduces its industrial usage. MD simulation and mutation studies have revealed the role of certain residues responsible for the enzyme's thermal instability. This study focuses on inducing thermal stability to choline oxidase of A. globiformis through computational approaches at a maximum temperature of 60 °C. MD simulation analysis showed that Trp 331, Val 464 and Ser 101 contribute to structural instability, leading to the instability at 60 °C. Mutation of these residues with phenylalanine residues and simulation of the mutated enzyme at 60 °C exhibited thermostability and insignificant residual fluctuation. The re-docking and MM/GBSA analyses further validated the mutated enzyme's binding affinity and catalytic activity.