Exploring the differences and similarities between urea and thermally driven denaturation of bovine serum albumin: intermolecular forces and solvation preferences

Insight into the allergenicity and structure changes of parvalbumin from Trachinotus ovatus induced by dense-phase carbon dioxide

Parvalbumin (PV) is a major allergen in fish, and traditional treatments cannot reduce its sensitization. The effects of dense-phase carbon dioxide (DPCD) treatment on the sensitization and spatial structure of PV in Trachinotus ovatus were evaluated in this study. Western blotting and indirect ELISA were used to determine the allergenicity changes and spatial conformations of PV treated by DPCD. Tris-tricine-SDS-PAGE, circular dichroism, surface hydrophobicity, endogenous fluorescence, UV spectrophotometry, free amino group, total sulfhydryl group and SEM analyses were applied to characterize PV structure. The results showed that DPCD treatment (15 MPa, 30 min, 50 °C) could reduce PV-induced allergic reactions by 39-41 %, which destroyed the normal conformational epitopes and reduced the risk of PV-induced allergy. The secondary structure changed from ordered to disordered with a decreased content of α-helical groups, while the internal hydrophobic groups were exposed. The total sulfhydryl group content decreased significantly (P < 0.05). The surface hydrophobicity and ultraviolet absorption spectrum were enhanced, and the endogenous fluorescence peak shifted to a long wavelength. Meanwhile, the content of free amino groups increased significantly (P < 0.05). This study could provide a theoretical basis and a promising technical approach for reduction of PV allergenicities.

Novel computational and drug design strategies for inhibition of human papillomavirus-associated cervical cancer and DNA polymerase theta receptor by Apigenin derivatives

The present study deals with the advanced in-silico analyses of several Apigenin derivatives to explore human papillomavirus-associated cervical cancer and DNA polymerase theta inhibitor properties by molecular docking, molecular dynamics, QSAR, drug-likeness, PCA, a dynamic cross-correlation matrix and quantum calculation properties. The initial literature study revealed the potent antimicrobial and anticancer properties of Apigenin, prompting the selection of its potential derivatives to investigate their abilities as inhibitors of human papillomavirus-associated cervical cancer and DNA polymerase theta. In silico molecular docking was employed to streamline the findings, revealing promising energy-binding interactions between all Apigenin derivatives and the targeted proteins. Notably, Apigenin 4'-O-Rhamnoside and Apigenin-4'-Alpha-L-Rhamnoside demonstrated higher potency against the HPV45 oncoprotein E7 (PDB ID 2EWL), while Apigenin and Apigenin 5-O-Beta-D-Glucopyranoside exhibited significant binding energy against the L1 protein in humans. Similarly, a binding affinity range of - 7.5 kcal/mol to - 8.8 kcal/mol was achieved against DNA polymerase theta, indicating the potential of Apigenin derivatives to inhibit this enzyme (PDB ID 8E23). This finding was further validated through molecular dynamic simulation for 100 ns, analyzing parameters such as RMSD, RMSF, SASA, H-bond, and RoG profiles. The results demonstrated the stability of the selected compounds during the simulation. After passing the stability testing, the compounds underwent screening for ADMET, pharmacokinetics, and drug-likeness properties, fulfilling all the necessary criteria. QSAR, PCA, dynamic cross-correlation matrix, and quantum calculations were conducted, yielding satisfactory outcomes. Since this study utilized in silico computational approaches and obtained outstanding results, further validation is crucial. Therefore, additional wet-lab experiments should be conducted under in vivo and in vitro conditions to confirm the findings.

Charge-induced low-temperature gelation of mixed proteins and the effect of pH on the gelation: A spectroscopic, rheological and coarse-grained molecular dynamics study

We report the gelation of mixed proteins consisting of oppositely charged lysozyme and serum albumins at various pH. The results from rheological tests showed that at a pH of 7, the gelation temperature (Tgel) of the oppositely charged proteins was lower than the melting temperature (Tm) of the individual protein. To ascertain the conformational state of the proteins at the observed Tgel, the attenuated total-reflectance Fourier-transform infrared (ATR-FTIR) spectra of the proteins were acquired. The recorded spectra showed that the proteins were predominantly alpha helical, suggesting that the observed gelation was electrostatically triggered. However, as the solution pH was changed to acid or alkaline regime, all the proteins became similarly charged and showed Tgel < Tm which was attributed to pH-induced denaturation. Surprisingly, however, the serum albumins were remarkably stable at the alkaline pH of 9 and 10 but very labile at the acidic pH. In contrast, the LYZ was more stable at the acidic than alkaline pH. To understand the role of the opposite charges in the gelation, coarse-grained molecular dynamics (CGMD) simulations revealed an increase in the aggregation of the oppositely charged proteins compared with the pure or similarly charged protein mixture.

Evaluation of the structure-activity relationship between allergenicity and spatial conformation of ovalbumin treated by pulsed electric field

The aim of the present study was to investigate the effect of pulsed electric field (PEF) treatment on ovalbumin (OVA) induced allergens and reveal potential allergy regulatory mechanisms. At 10 kV/cm, OVA-induced allergic symptoms were significantly reduced, and the capacity of OVA to bind with specific IgG1 and IgE was reduced by 10.32% and 3.61%, respectively. Furthermore, the degranulation of RBL-2H3 cells and allergen activity were also reduced by 4.63% and 22.15%, respectively. Interestingly, the α-helix content was reduced by 5.81% and the fluorescence intensity was increased by 6.90% with PEF treatment. At 10 kV/cm, water contact angle and surface hydrophobicity increased by 8.40% and 0.18%, respectively, indicating that PEF treatment increased the exposure of hydrophobic amino acid residues. PEF treatment alters the hydrogen bonding and hydrophobic interactions in the protein, which masks the binding sites of sensitized epitopes, and consequently reduces allergies.

Changing mechanical properties of photopolymerized, dityrosine-crosslinked protein-based hydrogels

Hydrogels based on renewable resources are a promising class of materials for future applications in pharmaceutics, drug delivery and personalized medicine. Thus, optional adjustments of mechanical properties such as swelling behavior, elasticity and network strength are desired. In this context, hydrogels based on the biological raw materials bovine serum albumin and casein were prepared by dityrosine-crosslinking of their tyrosine residues through visible light-induced photopolymerization. Changing the tyrosine accessibility by urea addition before photopolymerization increased the storage modulus of the hydrogels by 650% while simultaneously being more elastic. Furthermore, contributions of the buffer system composition, variation of protein concentration and storage medium towards mechanical properties of the hydrogel such as storage moduli, elasticity, fracture strain, compressive strength and relative weight swelling ratio are discussed. It could be shown, that changes in precursor solution and storage medium characteristics are crucial parameters towards tuning the mechanical properties of protein-based hydrogels.

Monitoring Protein Global and Local Parameters in Unfolding and Binding Studies: The Extended Applicability of the Diffusion Coefficient─Molecular Size Empirical Relations

Protein unfolding and denaturation are main issues in biochemical and pharmaceutical research. Using a global parameter, the translational diffusion coefficient D, folded, unfolded, and intrinsically disordered proteins of a given molar mass M can be distinguished based on their distinct hydrodynamic properties. For broader applications, we provide generalized, PFG-NMR-based empirical D-M relations validated at different temperatures and ready to use with the corresponding corrections in different media. We demonstrate that these relations enable a more accurate molecular mass determination and show fewer potential errors than those of the common methods based on small-molecular diffusion standards. We monitor unfolding of three model proteins using 8 M urea and dimethyl sulfoxide (DMSO)-water mixtures as denaturing agents, highlighting the effect of disulfide bonds. Denaturation in 8 M urea is pH-dependent; in addition, for proteins with highly stable disulfide bonds, a reducing agent (TCEP) is required to achieve complete unfolding. Regarding the effect of local parameters, we show that at low DMSO concentrations─common conditions in pharmaceutical binding studies─the PFG-NMR-derived global parameters are not significantly affected. Still, the atomic environments can change, and the bound solvent molecule can inhibit the binding of a partner molecule. Using proteins with natural isotopic abundance, this effect can be proven by fast ¹H-¹⁵N 2D correlation spectra. Our results enable fast and easy estimation of protein molecular mass and the degree of folding in various media; moreover, the effect of the cosolvent on the atomic-level structure can be traced without the need of isotope labeling.

Structural adaptations in the bovine serum albumin protein in archetypal deep eutectic solvent reline and its aqueous mixtures

The global concern over the environmental impact and challenges associated with the use of conventional solvents in biotransformation processes have pushed the search for alternative solvents. Recently, deep eutectic solvents (DESs) have appeared as a promising replacement with better biocompatibility and have been postulated to hold great potential in protein engineering and crystallization processes. In this context, herein, we have investigated the effect of reline (a choline chloride : urea mixture in 1 : 2 proportion) DES in its pure and hydrated forms on the structural stability and conformation of the bovine serum albumin (BSA) protein using all-atom molecular dynamics simulations. We observe a substantial overall expansion of the BSA structure with a simultaneous increment in the solvent accessible surface area, signifying the influence of reline on the BSA tertiary structure. These induced structural perturbations are quite pronounced in reline-water mixtures. Concomitantly, a notable reline concentration-dependent disruption of the BSA secondary structure through the melting of α-helices, mainly driven by H-bonding interactions, is observed. In the presence of pure reline, significant rigidity in the protein backbone is also observed. Thus, despite the expansion, the BSA tertiary structure in pure reline is found to be most close to the native protein structure and remains in a partially folded state at all the studied reline concentrations. In pure reline, BSA-urea hydrogen bonding is more prevalent than BSA-[Ch]⁺. We also observe that in aqueous reline systems, the BSA-water hydrogen bonds are mostly compensated by BSA-urea hydrogen bonds. The aqueous re-equilibration of these partially denatured protein conformations showed a significant recovery of secondary and tertiary structures, where the recovery is most profound for the BSA conformation extracted from pure reline.

The degradation of xanthan gum in ionic and non-ionic denaturants studied by rheology and molecular dynamics simulation

The use of xanthan gum (XG) as a thickener increases solution viscosity, and therefore, the cost of subsequent processes such as fluid transportation and purification. Herein, we investigate the degradation of XG by urea, sodium dodecyl sulfate (SDS) and cetyltrimethylammonium bromide (CTAB). The results showed that CTAB degraded the XG more than SDS or urea. Interestingly, the degree of CTAB-induced degradation varied with the concentration regime. Thus, increasing CTAB concentration from 0.01 to 0.1 M decreased the complex viscosity (|η*|), whereas from 0.2 to 0.5 M the |η*| increased. For XG/SDS, the |η*| was unchanged with increasing SDS concentration from 0.01 to 0.1 M, whereas it decreased from 0.2 to 0.5 M. For XG/urea, the |η*| was stable in all concentrations. At the atomic-scale, computer simulations revealed that the degrading effect of CTAB was due to preferential interaction with the XG sidechain. These findings can enhance industrial applications of XG.

Insight into the mechanism of urea inhibit ovalbumin-glucose glycation by conventional spectrometry and liquid chromatography-high resolution mass spectrometry

The inhibition effect of urea on ovalbumin (OVA) glycation was investigated, and the mechanism was evaluated through the changes in protein structure as well as glycation sites and average degree of substitution per peptide molecule (DSP) by conventional spectrometry and liquid chromatography-high resolution mass spectrometry (LC-HRMS). A urea concentration of 3 M was chosen as the optimum condition. Ultraviolet and fluorescence spectra suggested that both glycation and urea treatment could unfold the OVA, but urea inhibited the glycation-induced protein unfolding. Circular dichroism spectra showed that urea treatment could increase the β-sheet content and reduce the α-helix content of OVA. LC-HRMS indicated that the number of glycation sites was reduced from 15 to 3, and DSP values decreased with urea treatment. In conclusion, urea could significantly inhibit the OVA-glucose glycation, and the sites competition as well as structure unfolding inhibition resulted from urea could be the main factors.

Highly precise characterization of the hydration state upon thermal denaturation of human serum albumin using a 65 GHz dielectric sensor

The biological functions of proteins depend on harmonization with hydration water surrounding them. Indeed, the dynamical transition of proteins, such as thermal denaturation, is dependent on the changes in the mobility of hydration water. However, the role of hydration water during dynamical transition is yet to be fully understood due to technical limitations in precisely characterizing the amount of hydration water. A state-of-the-art CMOS dielectric sensor consisting of 65 GHz LC resonators addressed this issue by utilizing the feature that oscillation frequency sensitively shifts in response to the complex dielectric constant at 65 GHz with extremely high precision. This study aimed to establish an analytical algorithm to derive the hydration number from the measured frequency shift and to demonstrate the transition of hydration number upon the thermal denaturation of human serum albumin. The determined hydration number in the native state drew a "global" hydration picture beyond the first solvation shell, with substantially reduced uncertainty of the hydration number (about ±1%). This allowed the detection of a rapid increase in the hydration number at about 55 °C during the heating process, which was in excellent phase with the irreversible rupture of the α-helical structure into solvent-exposed extended chains, whereas the hydration number did not trace the forward path in the subsequent cooling process. Our result indicates that the weakening of water hydrogen bonds trigger the unfolding of the protein structure first, followed by the changes in the number of hydration water as a consequence of thermal denaturation.

Interaction between tau and water during the induced aggregation revealed by near-infrared spectroscopy

Near-infrared (NIR) spectra are sensitive to the variation of water structure. In this work, NIR spectroscopy was used to investigate the variation of hydration water during the aggregation of R2/wt induced by heparin. The osmolytes, urea and trehalose, were used to slow down and speed up the aggregation. The spectra of R2/wt aqueous solution obtained by NIR spectroscopy at 37 °C were adopted to analyze the structure of water during the aggregation. The spectral features of different water species were observed by principal component analysis (PCA) from the resolution enhanced NIR spectra. The existence of the water molecules with one and two hydrogen bonds around the NH and CH groups of R2/wt, respectively, was suggested, and the variation of the hydrogen-bonded water was found to be an indicator to monitor the process of aggregation. Then, the variation of the water species during the aggregation was analyzed by two-dimensional correlation spectroscopy. The water hydrogen bonded with NH group was found to change earlier than the water around the hydrophobic groups. The results suggest that β-sheet forms though the hydrogen bonds of amide groups in the early stage of the aggregation, and the destruction of the hydrogen bond network of the water around the side chains maybe the main reason for the formation of the ordered amyloid fibers.

Molecular dynamics studies of the protective and destructive effects of sodium dodecyl sulfate in thermal denaturation of hen egg-white lysozyme and bovine serum albumin

To investigate the protective and destructive effects of sodium dodecyl sulfate (SDS) in thermal denaturation of proteins, we carried out twelve independent atomistic molecular dynamics (MD) simulations of bovine serum albumin (BSA) and hen egg-white lysozyme (LYZ) in pure water and SDS solutions at 25 and 80 °C, using SDS concentrations of 0.01, 0.05, 0.1 and 1 M. In the case of the BSA in pure water and SDS solutions, it was found that its helicity decreased from 67.02% in reference structure to 35% in pure water at 80 °C due to thermal denaturation, whereas it increased to 49.34, 52.36 and 54% at 0.01, 0.05 and 0.1 M SDS, respectively, owing to the SDS protective effect. In 1 M SDS, however, the surfactant's protective effect was weak, and consequently the helicity of the BSA decreased to 47.01%. In contrast, no protection by SDS was observed for the LYZ in SDS solutions as the loss of its helices increased with SDS concentration from 0.01 to 1 M. In attempt to interpret the SDS effects molecularly, we calculated the diffusion coefficients of SDS in the protein solutions. The calculated values were found to decrease with increasing SDS concentration in the BSA solutions, but to increase with SDS concentration in the LYZ solutions. The decrease or increase in the diffusion coefficient of SDS was attributed to the net negative or positive charge on the proteins at neutral pH, indicating that electrostatic repulsions or attractions affect diffusivity significantly and can moderate SDS-proteins non-covalent interactions. Communicated by Ramaswamy H. Sarma.

In Silico Characterization of the Binding Modes of Surfactants with Bovine Serum Albumin

The binding interactions of the surfactants: anionic sodium dodecyl sulphate (SDS), cationic cetyltrimethylammonium bromide (CTAB), non-ionic octyl glucoside (OG), and zwitterionic 3-[Hexadecyl(dimethyl)ammonio]-1-propanesulfonate (HPS), with bovine serum albumin (BSA) were investigated by computer simulation. The results disclosed that the surfactants bound stably between hydrophobic subdomain IIA and IIIA where tryptophan-213 residue, an important intrinsic fluorophore in BSA is housed. The interactions of the surfactants with the BSA were electrostatic and hydrophobic interactions. The head-groups of SDS, HPS and OG formed hydrogen bonds with the BSA, while that of CTAB was shielded from intermolecular hydrogen-bonding due to intervening methyl groups. Subsequently, molecular dynamics (MD) simulation of the protein-surfactant complexes revealed that hydrogen bonds formed by OG were stronger than those of SDS and HPS. However, the decomposed force-field energies showed that OG had the least interaction energy with the BSA. In addition to MD simulation, it was found by density functional theory (DFT) that the differences in the coulomb interaction energies can be attributed to charge distribution in the surfactants. Overall, free energies calculated by linear interaction energy (LIE) proved that the binding of each surfactant was dominated by differences between van der Waals interactions in bound and free states.