Molecular interactions accounting for protein denaturation by urea

In Situ Observation of Chemically Induced Protein Denaturation at Solvated Interfaces

Proteins unfold in chaotropic salt solutions, a process that is difficult to observe at the single protein level. The work presented here demonstrates that a liquid-based atomic force microscope and graphene liquid-cell-based scanning transmission electron microscope make it possible to observe chemically induced protein unfolding. To illustrate this capability, ferritin proteins were deposited on a graphene surface, and the concentration-dependent urea- or guanidinium-induced changes of morphology were monitored for holo-ferritin with its ferrihydrite core as well as apo-ferritin without this core. Depending on the chaotropic agent the liquid-based imaging setup captured an unexpected transformation of natively folded holo-ferritin proteins into rings after urea treatment but not after guanidinium treatment. Urea treatment of apo-ferritin did not result in nanorings, confirming that nanorings are a specific signature of denaturation of holo-ferritins after exposture to sufficiently high urea concentrations. Mapping the in situ images with molecular dynamics simulations of ferritin subunits in urea solutions suggests that electrostatic destabilization triggers denaturation of ferritin as urea makes direct contact with the protein and also disrupts the water H-bonding network in the ferritin solvation shell. Our findings deepen the understanding of protein denaturation studied using label-free techniques operating at the solid-liquid interface.

Molecular mechanism of the common and opposing cosolvent effects of fluorinated alcohol and urea on a coiled coil protein

Alcohols and urea are widely used as effective protein denaturants. Among monohydric alcohols, 2,2,2-trifluoroethanol (TFE) has large cosolvent effects as a helix stabilizer in proteins. In contrast, urea efficiently denatures ordered native structures, including helices, into coils. These opposing cosolvent effects of TFE and urea are well known, even though both preferentially bind to proteins; however, the underlying molecular mechanism remains controversial. Cosolvent-dependent relative stability between native and denatured states is rigorously related to the difference in preferential binding parameters (PBPs) between these states. In this study, GCN4-p1 with two-stranded coiled coil helices was employed as a model protein, and molecular dynamics simulations for the helix dimer and isolated coil were conducted in aqueous solutions with 2 M TFE and urea. As 2 M cosolvent aqueous solutions did not exhibit clustering of cosolvent molecules, we were able to directly investigate the molecular origin of the excess PBP without considering the enhancement effect of PBPs arising from the concentration fluctuations. The calculated excess PBPs of TFE for the helices and those of urea for the coils were consistent with experimentally observed stabilization of helix by TFE and that of coil by urea. The former was caused by electrostatic interactions between TFE and side chains of the helices, while the latter was attributed to both electrostatic and dispersion interactions between urea and the main chains. Unexpectedly, reverse-micelle-like orientations of TFE molecules strengthened the electrostatic interactions between TFE and the side chains, resulting in strengthening of TFE solvation.

Urea induced unfolding of rai seed cystatin: Influence of glycerol as a chemical chaperone

Cystatin superfamily members, by virtue of their thiol protease regulatory properties, show involvement in myriad physiological processes important for survival and well-being. The current study involves urea-induced denaturation of a novel variant of the cystatin superfamily, rai seed cystatin (RSC), employing a variety of biophysical assays in order to characterize different folding intermediates generated on unfolding. Urea as a denaturant presented the passage of RSC through a series of events resulting in the loss of RSC functional capability, accompanied by changes in the archetype at secondary and tertiary structural levels, as evident from protease inhibitory, UV absorption, and intrinsic fluorescence assays, respectively. ANS fluorescence also revealed routing of RSC through discrete multiple sub-states thus presenting the generation of intermediate states somewhat close to the pre-molten globule and/or molten globule forms of RSC. Furthermore, far-UV circular dichroism analysis revealed a concentration-dependent gradual loss in typical -helical RSC peaks, indicating a nearly 50 % loss in secondary structural elements around 5 M urea treatment. The study also reports the possible role of glycerol in the refolding and/or reactivation of the urea unfolded RSC form. Glycerol presented itself as a potent structural stabilizer as it assisted in the refolding and reactivation of the unfolded RSC in a dosage-dependent manner, concomitantly paving the way for unravelling the mechanistic approach involved in the phenomenon, which can facilitate future studies.

MAX: a simple, affordable, and rapid tissue clearing reagent for 3D imaging of wide variety of biological specimens

Transparency of biological specimens is crucial to obtaining detailed 3-dimensional images and understanding the structure and function of biological specimens. This transparency or tissue clearing can be achieved by adjusting the refractive index (RI) with embedding media and removing light barriers such as lipids, inorganic deposits, and pigments. Many currently available protocols consist of multiple steps to achieve sufficient transparency, making the process complex and time-consuming. Thus, in this study, we tailored the recipe for RI adjustment media named MAX based on the recently reported MACS protocol to achieve a single-step procedure, especially for ECM-rich tissues. This was achieved by the improvement of the tissue penetrability of the RI-matching reagent by combining MXDA with sucrose or iodixanol. While this was sufficient for the 3D imaging in many applications, MAX can also be combined with modular processes for de-lipidation, de-coloration, and de-calcification to further maximize the transparency depending on the special features of the tissues. Our approach provides an easy alternative for tissue clearing and 3D imaging.

Effect of Latex Purification and Accelerator Types on Rubber Allergens Prevalent in Sulphur Prevulcanized Natural Rubber Latex: Potential Application for Allergy-Free Natural Rubber Gloves

Natural rubber (NR) gloves manufactured from NR latex are widely utilized in various applications as a personal protective device due to their exceptional barrier characteristics in infection control. However, the use of NR gloves was associated with concerns on NR protein allergy. With comprehensive leaching procedures now a common practice in NR latex glove factories to eliminate latent rubber proteins and chemical allergens, occurrences and complaints of protein allergy from medical glove users have decreased drastically over the past two decades. The present work aims to eliminate further the residual rubber allergens in NR latex through effective purification of the NR latex and compounding the thus purified latex with an established formulation for allergy-free NR for glove applications. NR latex was purified by deproteinization and saponification, respectively. Several analytical techniques were used to verify rubber allergens eliminated in the purified latexes. Saponified NR (SPNR) latex was the purified NR latex of choice since it is devoid of allergenic proteins and poses the lowest risk of Type I allergy. The purified NR latex was compounded with zinc diethyldithiocarbamate (ZDEC), zinc dibutyldithiocarbamate (ZDBC), and zinc 2-mercaptobenzothiazole (ZMBT), respectively, for glove dipping. Among the investigated accelerators, only ZDBC was not detected in the artificial sweat that came into contact with the dipped articles. Thus, it is deduced that ZDBC poses the lowest risk of Type IV allergy to consumers. Additionally, the morphological and physical properties of dipped articles were assessed. It was revealed that the dipped film from the SPNR latex compounded with ZDBC provided thinner and less yellow products with a more uniform internal structure and a tensile strength comparable to those of commercial NR gloves.

Significantly improved detection performances of immunoassay for ractopamine in urine based on highly urea-tolerant rabbit monoclonal antibody

Highly sensitive and accurate screening of ractopamine (RAC) residue in animal urine is greatly needed to ensure food security. The detection performance of immunoassay for RAC was always seriously harmed by the antibody inactivation derived from urea. Here, we first discovered one rabbit monoclonal antibody (RmAb) to RAC with a high affinity of 0.007 ng mL^-1 and a surprising urea tolerance of 3 M urea, which is beneficial for developing robustly developed immunoassay in urine without sample pretreatment. The limits of detection of developed indirect competitive enzyme-linked immunosorbent assay based on RmAb1 for RAC were 0.0042-0.014 μg L^-1 with the coefficient of variation below 11.7% in swine, sheep, and cow urine, significantly improved 10-100-fold in sensitivity. Moreover, the urea-tolerant mechanism of RmAb1 showed that more non-polar amino acids, more hydrogen bond donors on the surface, and preponderant Pi interaction of antibody-RAC all contributed to the stability of the RmAb1 in a high concentration of urea.

Analysis of the gel properties, microstructural characteristics, and intermolecular forces of soybean protein isolate gel induced by transglutaminase

Soybean protein isolate (SPI) is a high-quality plant protein that is primarily used to process various soybean products coagulated by transglutaminase (TGase). In this study, the degree of hydrolysis (DH), sulfhydryl content (SH), surface hydrophobicity (H0 ), secondary structural constitution, and microstructure of TGase-treated soybean protein (SPI, 7S, and 11S) were determined, as well as the effects of NaCl, urea, and SDS on the properties and intermolecular forces of SPI gel were analyzed. The results show that the H0 and SH content of SPI, 7S, and 11S decreased significantly with TGase treatment time (p < .05), while the DH gradually increased and reached its highest value (3.72%, 7.41%, and 1.27%, respectively) at 30 min. As the concentration of these two secondary structures exhibited an inverse relationship, the degradation of β-turns resulted in the increase in β-sheets. The microstructures of SPI and 11S gels were similar, being denser and more ordered than 7S gel. The low concentration of NaCl solution (0.2 mol/L) enhanced gel properties and intermolecular forces, promoting the formation of SPI gel, whereas a high concentration (0.4-0.8 mol/L) had a significant inhibitory effect. Urea and SDS solutions substantially inhibited the formation of SPI gel, leading to significant decreases in the water holding capacity and hardness as well as a considerable increase in the coagulation time (p < .05). The results revealed that hydrogen bonds and hydrophobic interactions were the main intermolecular forces responsible for the gel formation. This study provides adequate technical support and a theoretical basis for soybean protein gel products.

Phase equilibria, physical and rheological properties of extracellular polymeric substances in the aqueous urea solutions at different temperatures and concentrations

Extracellular polymeric substances (EPS) were extracted from aerobic granule sludge (AGS) using 8 M aqueous urea solution. It seems that the knowledge of these multi-component systems properties and the ability to predict their phase behavior is necessary for the extraction units design as well as process optimization. In this regard, water activity using the Dynamic Vapor Sorption (DVS) method, viscosity and shear stress, pH, and conductivity were measured at 283.15-343.15 K and 0.0108 to 0.0375 wt fraction of EPS. The salting effects in ternary systems assessed and the results were interpreted in terms of solute-water and solute-solute interactions. It was found these systems were not semi-ideal and except at 283.15 K, had a positive deviation from ideal solution behavior and only at this temperature as the optimum extraction temperature, the salting-in effect was observed for each concentration of EPS. The ternary solutions behave like pseudo-plastic fluids while aqueous urea solution is a Newtonian fluid. Increasing the temperature causes a decrease and increase in pH and conductivity of ternary solutions, respectively and the presence of EPS increases those of 8 M urea solution significantly.

Urea-aromatic interactions in biology

Noncovalent interactions are key determinants in both chemical and biological processes. Among such processes, the hydrophobic interactions play an eminent role in folding of proteins, nucleic acids, formation of membranes, protein-ligand recognition, etc.. Though this interaction is mediated through the aqueous solvent, the stability of the above biomolecules can be highly sensitive to any small external perturbations, such as temperature, pressure, pH, or even cosolvent additives, like, urea-a highly soluble small organic molecule utilized by various living organisms to regulate osmotic pressure. A plethora of detailed studies exist covering both experimental and theoretical regimes, to understand how urea modulates the stability of biological macromolecules. While experimentalists have been primarily focusing on the thermodynamic and kinetic aspects, theoretical modeling predominantly involves mechanistic information at the molecular level, calculating atomistic details applying the force field approach to the high level electronic details using the quantum mechanical methods. The review focuses mainly on examples with biological relevance, such as (1) urea-assisted protein unfolding, (2) urea-assisted RNA unfolding, (3) urea lesion interaction within damaged DNA, (4) urea conduction through membrane proteins, and (5) protein-ligand interactions those explicitly address the vitality of hydrophobic interactions involving exclusively the urea-aromatic moiety.

Cloning, expression and nanodiscs assemble of recombinant HIV-1 gp41

Structural studies of membrane proteins have been hurdled by their difficulty for expression in heterogeneous expression systems due to their intrinsically strong hydrophobicity and requirements for association with other cellular membranes. This study aims to design a construct for expression of membrane proteins. Because of its outstanding interest in HIV-1 vaccine design, transmembrane gp41 amino acid residue 662-723 was chosen as a representative membrane protein. Therefore, we constructed expression vectors for expression of gp41_(662-723) alone (pET28a-gp41_(662-723)) or coupled with a fusion partner: GB1 (pET30a-GB1-gp41_(662-723)) and Trx (pET32a-Trx-gp41_(662-723)). For enhancing protein expression, the expression plasmids were transformed into E. coli BL-21 (DE3), E. coli T7 Express lysY/I^q and E. coli Lemo21 (DE3). Interestingly, HIV-1 gp41_(662-723) was expressed as a C-terminus fusion to the fusion partner Trx (Trx-gp41_(662-723)) with an apparent molecular mass of 21.8 kDa. Trx-gp41_(662-723) was overexpressed into E. coli T7 Express lysY/I^q by early induction as OD₆₀₀ ~0.5 followed by incubation at 20 °C/overnight. Our data demonstrated that almost all recombinant Trx-gp41_(662-723) was incorporated into lipid nanodiscs by slowing down the nanodiscs assembly process. Negative-stained electron micrographs revealed homogenous 10 nm Trx-gp41_(662-723)-nanodiscs. While the neutralizing epitopes in the purified Trx-gp41_(662-723) were accessible and recognizable by anti-MPER bNAbs, these epitopes became less accessibly exposed, particularly in the C-terminal region of MPER, after incorporation of Trx-gp41_(662-723) into nanodiscs.

Is Gum Arabic a Good Emulsifier Due to CH...π Interactions? How Urea Effectively Destabilizes the Hydrophobic CH...π Interactions in the Proteins of Gum Arabic than Amides and GuHCl?

The photophysical studies of gum arabic (GA) in the presence of urea, 1,3-dimethylurea (DMU), tetramethylurea (TMU), guanidine hydrochloride (GuHCl), formamide (FA), acetamide (AA), and dimethyl formamide (DMF) were carried out by monitoring the emission, three-dimensional emission contour, and time-correlated fluorescence lifetime techniques. On addition of only 1 × 10-3 M urea, 75.0% of the fluorescence of GA is quenched, while the same occurs in GuHCl at 3.0 M. FA quenched 50% of the fluorescence of GA at 5.0 M. However, DMU, TMU, AA, and DMF resulted in a fluorescence enhancement. The unusual fluorescence trends reveal the existence of CH...π interactions in the proteins of GA. The experimental results and the structural aspects of proteins in GA led us to propose that the aggregation of polyproline helices in GA, through several CH...π interactions, would have a major role to play in the emulsification mechanism of GA.

Enhanced biofilm solubilization by urea in reverse osmosis membrane systems

Chemical cleaning is routinely performed in reverse osmosis (RO) plants for the regeneration of RO membranes that suffer from biofouling problems. The potential of urea as a chaotropic agent to enhance the solubilization of biofilm proteins has been reported briefly in the literature. In this paper the efficiency of urea cleaning for RO membrane systems has been compared to conventionally applied acid/alkali treatment. Preliminary assessment confirmed that urea did not damage the RO polyamide membranes and that the membrane cleaning efficiency increased with increasing concentrations of urea and temperature. Accelerated biofilm formation was carried out in membrane fouling simulators which were subsequently cleaned with (i) 0.01M sodium hydroxide (NaOH) and 0.1M hydrochloric acid (HCl) (typically applied in industry), (ii) urea (CO(NH2)2) and hydrochloric acid, or (iii) urea only (1340 g/Lwater). The pressure drop over the flow channel was used to evaluate the efficiency of the applied chemical cleanings. Biomass removal was evaluated by measuring chemical oxygen demand (COD), adenosine triphosphate (ATP), protein, and carbohydrate content from the membrane and spacer surfaces after cleaning. In addition to protein and carbohydrate quantification of the extracellular polymeric substances (EPS), fluorescence excitation-emission matrix (FEEM) spectroscopy was used to distinguish the difference in organic matter of the remaining biomass to assess biofilm solubilization efficacy of the different cleaning agents. Results indicated that two-stage CO(NH2)2/HCl cleaning was as effective as cleaning with NaOH/HCl in terms of restoring the feed channel pressure drop (>70% pressure drop decrease). One-stage cleaning with urea only was not as effective indicating the importance of the second-stage low pH acid cleaning in weakening the biofilm matrix. All three chemical cleaning protocols were equally effective in reducing the concentration of predominant EPS components protein and carbohydrate (>50% reduction in concentrations). However, urea-based cleaning strategies were more effective in solubilizing protein-like matter and tyrosine-containing proteins. Furthermore, ATP measurements showed that biomass inactivation was up to two-fold greater after treatment with urea-based chemical cleanings compared to the conventional acid/alkali treatment. The applicability of urea as an alternative, economical, eco-friendly and effective chemical cleaning agent for the control of biological fouling was successfully demonstrated.

Hydrogen Bond Interaction of Ascorbic Acid with Urea: Experimental and Theoretical Study

The interactions of ascorbic acid (AA) with urea were investigated by using the cyclic voltammetry, density functional theory, atoms in molecules and natural bond orbital analyses. The experimental and theoretical results show that the hydrogen bonds are formed between AA and urea, wherein the mainly interaction sites are the hydrogen atoms on enediol of AA and the oxygen atom on carbonyl of urea. The electrochemical behavior of AA was significantly affected by above interactions.

Unravelling the hydrophobicity of urea in water using thermodiffusion: implications for protein denaturation

Sensitivity of thermodiffusion to urea–water interactions was studied experimentally and by NEMD simulations, identifying the hydrophobic behaviour of urea.

Insight into the effect mechanism of urea-induced protein denaturation by dielectric spectroscopy

Dielectric relaxation spectroscopy was applied to study how urea affects the phase transition of a thermosensitive polymer, poly(N-isopropylacrylamide) (PNIPAM), which has been widely used as a protein model. It was found that there is a pronounced relaxation near 10 GHz for the ternary system of PNIPAM in urea aqueous solution. The temperature dependence of dielectric parameters indicates that urea can reduce the lower critical solution temperature (LCST) of PNIPAM, i.e., stabilize the globule state of PNIPAM and collapse the PNIPAM chains. Based on our results, the interaction mechanism of urea on the conformational transition of PNIPAM was presented: urea replaces water molecules directly bonding with PNIPAM and acts as the bridging agent for the adjacent side chains of PNIPAM. Accordingly, the mechanism with which urea denatures protein was deduced. In addition, it is worth mentioning that, from the temperature dependence of the dielectric parameters obtained in the presence of urea, an interesting phenomenon was found in which the effect of urea on PNIPAM seems to take 2 M as a unit. This result may be the reason why urea and TMAO exit marine fishes at a specific ratio of 2 : 1.

Effects of Trimethylamine-N-oxide on the Conformation of Peptides and its Implications for Proteins

To provide insights into the stabilizing mechanisms of trimethylamine-N-oxide (TMAO) on protein structures, we perform all-atom molecular dynamics simulations of peptides and the Trp-cage miniprotein. The effects of TMAO on the backbone and charged residues of peptides are found to stabilize compact conformations, whereas effects of TMAO on nonpolar residues lead to peptide swelling. This suggests competing mechanisms of TMAO on proteins, which accounts for hydrophobic swelling, backbone collapse, and stabilization of charge-charge interactions. These mechanisms are observed in Trp cage.

Comparison between chaotropic and detergent-based sample preparation workflow in tendon for mass spectrometry analysis

Exploring the tendon proteome is a challenging but important task for understanding the mechanisms of physiological/pathological processes during ageing and disease and for the development of new treatments. Several extraction methods have been utilised for tendon mass spectrometry, however different extraction methods have not been simultaneously compared. In the present study we compared protein extraction in tendon with two chaotropic agents, guanidine hydrochloride (GnHCl) and urea, a detergent, RapiGest™, and their combinations for shotgun mass spectrometry. An initial proteomic analysis was performed following urea, GnHCl, and RapiGest™ extraction of equine superficial digital flexor tendon (SDFT) tissue. Subsequently, another proteomic analysis was performed following extraction with GnHCl, Rapigest™, and their combinations. Between the two chaotropic agents, GnHCl extracted more proteins, whilst a greater number of proteins were solely identified after Rapigest™ extraction. Protein extraction with a combination of GnHCl followed by RapiGest™ on the insoluble pellet demonstrated, after label-free quantification, increased abundance of identified collagen proteins and low sample to sample variability. In contrast, GnHCl extraction on its own showed increased abundance of identified proteoglycans and cellular proteins. Therefore, the selection of protein extraction method for tendon tissue for mass spectrometry analysis should reflect the focus of the study.