New insights on the binding of butyl-paraben to trypsin: experimental and computational approaches

Butyl-paraben (BP) is one of the most widely used preservatives in numerous foodstuffs, skin care products, and a variety of drugs, and trypsin is the main digestive enzyme, the research on the binding between the two is essential for human health. In the present paper, the effect of BP on trypsin has been explored using experimental and computational techniques to evaluate BP toxicity at the protein level. The obtained results from molecular docking and kinetic assay revealed BP was embedded in the hydrophobic cavity-S1 binding pocket of the enzyme to inhibit its activity by a competitive model. Intrinsic fluorescence of trypsin after interaction with BP revealed the static mode of quenching. FRET indicated that the distance of the enzyme to BP is 1.89 nm with high energy efficiency. Thermodynamic results proved that BP spontaneously bound to trypsin in an enthalpy-driven manner, the van der Waals interactions and H-bonds serving as the predominant forces in binding processes. CD spectroscopy and molecular dynamics (MD) simulation revealed that the trypsin structure transformed from the β-Sheet structure to the unordered Coil structure upon interacting with BP. Resonance light scattering (RLS), synchronous fluorescence, and three-dimensional (3 D) spectroscopies further supported the alteration in the conformation of trypsin. Differential scanning calorimetry (DSC) showed that trypsin was somewhat destabilized in the presence of BP. Accordingly, all of the experimental data were confirmed by MD simulation.Communicated by Ramaswamy H. Sarma.

Structural change study of pepsin in the presence of spermidine trihydrochloride: Insights from spectroscopic to molecular dynamics methods

Spermidine is an aliphatic polyamine that directs a set of biological processes. This work aimed to use UV-Vis spectroscopy, fluorescence spectroscopy, thermal stability, kinetic methods, docking, and molecular dynamic simulations to examine the influence of spermidine trihydrochloride (SP) on the structure and function of pepsin. The results of the fluorescence emission spectra indicated that spermidine could quench pepsin's intrinsic emission in a static quenching process, resulting in the formation of the pepsin-spermidine complex. The results discovered that spermidine had a strong affinity to the pepsin structure because of its high binding constant. The obtained results from spectroscopy and molecular dynamic approaches showed the binding interaction between spermidine and pepsin, induced micro-environmental modifications around tryptophan residues that caused a change in the tertiary and secondary structure of the enzyme. FTIR analysis showed hypochromic effects in the spectra of amide I and II and redistribution of the helical structure. Moreover, the molecular dynamic (MD) and docking studies confirmed the experimental data. Both experimental and molecular dynamics simulation results clarified that electrostatic bond interactions were dominant forces.

Exploring the structural basis of conformational alterations of myoglobin in the presence of spermine through computational modeling, molecular dynamics simulations, and spectroscopy methods

Spermine as polyamines can have interaction with the myoglobin (Mb). The intent of this pondering to evaluate the impact of spermine on Mb properties, for example, the structure and thermal stability. For this analysis, the following approaches are employed. Thermodynamics, molecular dynamics (MD), and docking and the use of other spectroscopic procedures. The results of fluorescence spectroscopy and docking showed that binding spermine to Mb was spontaneous. Spermine quenched the fluorescence of Mb through the static quenching process. The thermal stability of Mb was incremented when the concentration of spermine increased. The CD spectra showed Mb's secondary structure shift with a rise in β-sheet and a decrease in α-helicity Mb's in spermine presence. Molecular docking and MD simulation outcomes demonstrate that electrostatic forces show a critical function in stabilizing of this complex, which is in conforming to spectroscopic results.Communicated by Ramaswamy H. Sarma.

The effect of putrescine on stability and structural properties of bovine serum albumin

Serum albumins are the abounding proteins in plasma. Their most important characteristic is that they act as carriers for a type of compound, for example, different drugs. Bovine Serum Albumin (BSA) is a single-chain polypeptide with 583 amino acids. Polyamines such as putrescine can interact with negatively charged molecules. The effect of putrescine on the structure of bovine serum albumin has been surveyed utilizing the method of UV-Vis spectroscopy, Thermal stability, fluorescence spectroscopy, and molecular docking at temperature 298 K and 308 K at pH 7.4 using Tris-HCl as a buffer. The complex formation between putrescine and bovine serum albumin was discovered as alter in the absorbance at 280 nm. The amount of absorption increases with the addition of putrescine. The adding of putrescine alters the bovine serum albumin and decrements the hydrophobicity of the micro-environment of the Trp residues in the inner hydrophobic zone. The static kind of quenching process was chiefly contained within the quenching of intrinsic emission of the protein. The fluorescence quenching details (K_sv) for complex bovine serum albumin-putrescine revealed one binding site for putrescine. The negative amount of Gibbs free energy change (ΔG°) suggested the binding operation was spontaneous.Communicated by Ramaswamy H. Sarma.

Different electrically charged proteins result in diverse bacterial transport behaviors in porous media

The influence of proteins on bacterial transport and deposition behaviors in quartz sand was examined in both NaCl (10 and 25 mM) and CaCl₂ solutions (1.2 and 5 mM). Bovine Serum Albumin (BSA) and bovine trypsin were used to represent negatively and positively charged proteins in natural aquatic systems, respectively. The presence of negatively charged BSA in suspensions increased the transport and decreased bacterial deposition in quartz sand, regardless of the ionic strength and ion types. Whereas, positively charged trypsin inhibited the transport and enhanced bacterial deposition under all experimental conditions. The potential mechanisms controlling the changes of bacterial transport behaviors varied for different charged proteins. The steric repulsion resulting from BSA adsorption onto both bacteria and quartz sand was found to play a dominant role in the transport and deposition of bacteria in porous media with BSA copresent in suspension. BSA adsorption onto bacterial surfaces and competition for deposition sites onto sand surfaces (adsorption of quartz sand surfaces) contributed to the increased cell transport with BSA in suspension. In contrast, the attractive patch-charged interaction induced by the adsorption of trypsin onto both bacteria and quartz sand had great contribution to the decreased bacterial transport in porous media with trypsin copresent in suspension. The increase in bacteria size, and the adsorption of trypsin onto cell surfaces (resulting in less negative cell surface charge) and quartz sand surfaces (providing extra deposition sites) were found to be the main contributors to the decreased transport and increased deposition of bacteria in quartz sand with trypsin in suspension.