The effects of denaturants on protein conformation and behavior at air/solution interface

In this study, we discuss the interfacial behavior of five proteins with different conformational character, and each is investigated in native and denatured states. The protein molecules are layered and spread onto the air/solution interfaces to form protein monolayer. The surface pressure-time (Pi(t)) and surface pressure-area per molecule (Pi-A) isotherms were measured by using the Langmuir-Blodgett (LB) balance consisted of a Nima trough system. The differences between monolayered protein's behaviors at air/solution interface indicate that denaturants, such as urea, guanidinium chloride and dithiothreitol, have different effects on conformational changes of proteins. Additionally, the interfacial behavior of the proteins in our study provides a fundamental profile about the protein structural stability and implies industrial applications in protein refolding process.     

Impact of the nanoparticle-protein corona on colloidal stability and protein structure

In biological fluids, proteins may associate with nanoparticles (NPs), leading to the formation of a so-called "protein corona" largely defining the biological identity of the particle. Here, we present a novel approach to assess apparent binding affinities for the adsorption/desorption of proteins to silver NPs based on the impact of the corona formation on the agglomeration kinetics of the colloid. Affinities derived from circular dichroism measurements complement these results, simultaneously elucidating structural changes in the adsorbed protein. Employing human serum albumin as a model, apparent affinities in the nanomolar regime resulted from both approaches. Collectively, our findings now allow discrimination between the formation of protein mono- and multilayers on NP surfaces.     

Interfacial water structure controls protein conformation

A phenomenological theory of salt-induced Hofmeister phenomena is presented, based on a relation between protein solubility in salt solutions and protein-water interfacial tension. As a generalization of previous treatments, it implies that both kosmotropic salting out and chaotropic salting in are manifested via salt-induced changes of the hydrophobic/hydrophilic properties of protein-water interfaces. The theory is applied to describe the salt-dependent free energy profiles of proteins as a function of their water-exposed surface area. On this basis, three classes of protein conformations have been distinguished, and their existence experimentally demonstrated using the examples of bacteriorhodopsin and myoglobin. The experimental results support the ability of the new formalism to account for the diverse manifestations of salt effects on protein conformation, dynamics, and stability, and to resolve the puzzle of chaotropes stabilizing certain proteins (and other anomalies). It is also shown that the relation between interfacial tension and protein structural stability is straightforwardly linked to protein conformational fluctuations, providing a keystone for the microscopic interpretation of Hofmeister effects. Implications of the results concerning the use of Hofmeister effects in the experimental study of protein function are discussed.     

Formation of ice-like water structure on the surface of an antifreeze protein

Antifreeze proteins (AFPs) are found in different species from polar, alpine, and subarctic regions where they serve to inhibit ice crystal growth by adsorption to ice surfaces. Computational methods have the power to investigate the antifreeze mechanism in atomic detail. Molecular dynamics simulations of water under different conditions have been carried out to test our water model for simulations of biological macromolecules in extreme conditions: very low temperatures (200 K) and at the ice/liquid water interface. We show that the flexible F3C water model reproduces properties of water in the solid phase (ice I(h)), the supercooled liquid phase, and at the ice/liquid water interface. Additionally, the hydration of the type III AFP from ocean pout was studied as a function of temperature. Hydration waters on the ice-binding surface of the AFP were less distorted and more tetrahedral than elsewhere on the surface. More ice-like hydrating water structures formed on the ice-binding surface of the protein such that it created an ice-like structure in water within its first hydration layer but not beyond, suggesting that this portion of the protein has high affinity for ice surfaces.     

Effect of denaturants on the stability of light-harvesting complex

 The effect of denaturants such as urea and normal alcohols on the formation of light-harvesting (LH) polypeptides/bacteriochlorophyll a (BChla) complex (LH1 complex) in n-octyl-β-D-glucopyranoside (OG) micelle was examined to provide an insight into stability of the complex. The stabilities of the LH1 complex in OG micelle and of the complex in the chromatophore of photosynthetic bacteria were compared by addition of denaturants. The extent of stability of these complexes was monitored by the change in absorbance of Qy band of BChla in these complexes, resulting generally in the blue-shifting of the Qy band from near 870 nm to about 777 nm upon addition of these denaturants. Urea and guanidium hydrochloride (Gnd) showed a relatively weak denaturing effect. Normal alcohols showed stronger denaturing effect, depending on the hydrophobicity of the alcohols. These results imply that the stability of LH1 complex in OG micelle can be largely attributed to the hydrophobic interactions in the complex as well as that of the complex in the chromatophore of photosynthetic bacteria. Received: 23 May 1997 Accepted: 13 September 1997     

Chemical denaturants inhibit the onset of dewetting

The mechanism by which the aqueous cosolvents guanidinium chloride and urea denature proteins is a matter of controversy. Here, we use all-atom molecular dynamics simulations to study the effect of both denaturants on the dewetting of water confined between nanoseparated hydrophobic plates. It is found that the denaturants inhibit the onset of dewetting, so that it occurs at shorter interplate distances than in pure water. Our results support a role for urea and guanidinium in assisting in the solvation of nonpolar surfaces, thereby weakening hydrophobic effects known to be important for protein stability.     

Design of polymeric stabilizers for size-controlled synthesis of monodisperse gold nanoparticles in water

A new methodology is described for the one-step aqueous preparation of highly monodisperse gold nanoparticles with diameters below 5 nm using thioether- and thiol-functionalized polymer ligands. The particle size and size distribution was controlled by subtle variation of the polymer structure. It was shown that poly(acrylic acid) (PAA) and poly(methacrylic acid) (PMAA) were the most effective stabilizing polymers in the group studied and that relatively low molar mass ligands (approximately 2500 g/mol) gave rise to the narrowest particle size distributions. Particle uniformity and colloidal stability to changes in ionic strength and pH were strongly affected by the hydrophobicity of the ligand end group. "Multidentate" thiol-terminated ligands were produced by employing dithiols and tetrathiols as chain-transfer agents, and these ligands gave rise to particles with unprecedented control over particle size and enhanced colloidal stability. It was found throughout that dynamic light scattering (DLS) is a very useful corroboratory technique for characterization of these gold nanoparticles in addition to optical spectroscopy and TEM.     

Impact of anionic substitutions on apatite structure and properties

A review of the results of the authors on single and coupled substitutions of F for OH, and of CO₃ and SO₄ for PO₄ in synthetic and natural apatites, their influence on apatite structure and properties, studied by peak fitting FTIR, XRD, TG/DTA and TG/EGA methods, is presented. Calcination of carbonate and sulphate substituted apatites leads to the formation of stable stoichiometric apatite.     

Impact of limited oxidation on protein ion mobility and structure of importance to footprinting by radical probe mass spectrometry

The effect of hydroxyl radical induced oxidation on the collision cross-sections of hen egg lysozyme and bovine ubiquitin was investigated by travelling wave ion mobility mass spectrometry for the first time. The oxidized ions of lysozyme and ubiquitin share common collision cross-sections with their unoxidized counterparts suggesting that they share common structures that were unaffected by limited oxidation. In the case of bovine ubiquitin, two distinct conformers were detected for the protein in its unoxidized and oxidized states though no change in the levels of each was observed upon oxidation. This supports the validity of Radical Probe Mass Spectrometry (RP-MS) using an electrical discharge source for protein footprinting experiments. Travelling wave ion mobility mass spectrometry has been used for the first time to confirm that limited oxidation does not have an impact on the global structure of proteins.     

Changes in water structure induced by the guanidinium cation and implications for protein denaturation

The effect of the guanidinium cation on the hydrogen bonding strength of water was analyzed using temperature-excursion Fourier transform infrared spectra of the OH stretching vibration in 5% H 2O/95% D 2O solutions containing a range of different guanidine-HCl and guanidine-HBr concentrations. Our findings indicate that the guanidinium cation causes the water H-bonds in solution to become more linear than those found in bulk water, and that it also inhibits the response of the H-bond network to increased temperature. Quantum chemical calculations also reveal that guanidinium affects both the charge distribution on water molecules directly H-bonded to it as well as the OH stretch frequency of H-bonds in which that water molecule is the donor. The implications of our findings to hydrophobic solvation and protein denaturation are discussed.     

Studies on water retention and water release from some protein systems

The hydrogen-bond properties (WBI index), water retention and water release from the protein-water systems gluten-water, soya protein- water and casein-water, have been investigated using differential scanning calorimetry in the temperature range 223–423 K. The proteins were characterized by their isoelectric point, contents of carboxyl groups and sulfur-containing groups, and readiness of undergo chloromethylation. It was concluded that the marked difference in water-release behaviour is chiefly explained by conformational differences and charge effects.

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Zusammenfassung Wasserstoffbrückenbindugseigenschaften (WBI-Index), Wasserretention und Wasserabgabe von Protein-Masser-Systemen — Gluten-Wasser, Sojaprotein-Wasser und Casein-Wasser — wurden im Temperaturbereich von 233–423 K mit einem Scanning-Kalorimeter untersucht. Die Proteine wurden durch ihren isoelektrischen Punkt, den Gehalt an Carbonylgruppen und Schwefel enthaltenden Gruppen und durch ihre Reaktivität in der Chlormethylierung charakterisiert. Es wurde gefolgert, dass der ausgesprochene Unterschied im Wasserabgabeverhalten in erster Linie auf strukturelle Unterschiede und Ladungseffekte zurückzuführen ist.

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223–423 K , , — , — — . , , . , .

     

Impact of pyrophosphate and O-ethyl-substituted pyrophosphate groups on DNA structure

Design of novel DNA probes to inhibit specific repair pathways is important for basic science applications and for use as therapeutic agents. As shown previously, single pyrophosphate (PP) and O-ethyl-substituted pyrophosphate (SPP) modifications can inhibit the DNA glycosylase activities on damaged DNA. To understand the structural basis of this inhibition, the influence of the PP and SPP internucleotide groups on the helical parameters and geometry of a double-stranded DNA was studied by using molecular modeling tools including molecular dynamics and quantum mechanical-molecular mechanical (QM/MM) approaches. Native and locally modified PP- and SPP-containing DNA duplexes of dodecanucleotide d(C1G2C3G4A5A6T7T8C9G10C11G12) were simulated in aqueous solution. The energies and forces were computed by using the PBE0/6-31+G** approach in the QM part and the AMBER force-field parameters in the MM part. Analysis of the local base-pair helical parameters, internucleotide distances, and overall global structure at the located stationary points revealed a close similarity of the initial and modified duplexes, with only torsion angles of the main chain being altered in the vicinity of introduced chemical modification. Results show that the PP and SPP groups are built into a helix structure without elongation of the internucleotide distance due to flipping-out of phosphate group from the sugar-phosphate backbone. The mechanism of such embedding has only a minor impact on the base pairs stacking and Watson-Crick interactions. Biochemical studies revealed that the PP and SPP groups immediately 5', but not 3', to the 8-oxoguanosine (8oxodG) inhibit translesion synthesis by a DNA polymerase in vitro. These results suggest that subtle perturbations of the DNA backbone conformation influence processing of base lesions.     

Comprehensive headspace gas chromatographic analysis of denaturants in denatured ethanol

To discourage consumption, ethanol is often denatured using both volatile (e.g., methyl ethyl ketone and isopropanol) and nonvolatile (e.g., denatonium benzoate) chemical substances. As a result, the analysis of denatured ethanol samples is usually performed by multiple techniques such as gas chromatography for the volatile denaturants and liquid chromatography for the nonvolatile ones. However, the need for multiple techniques increases the cost of analysis and forms a severe obstruction for on‐site product control. Using the full evaporation technique combined with gas chromatography and flame ionization detection, only one analytical methodology has to be used here to determine both volatile and nonvolatile denaturants in denatured ethanol. Denatonium benzoate is determined as benzyl chloride following an in‐vial reaction. Compared to conventional techniques, the novel method performs equally well, but it is simpler to apply. At the same time, drawbacks of alternative methods are circumvented such as equilibration issues and alterations to the stationary phase when using liquid chromatography with ion pairing agents or matrix effects when applying static headspace gas chromatography. The developed method showed good linearity, repeatability, and recovery toward all analytes and was applied to the analysis of commercial denatured ethanol for disinfection and ethanol‐based windscreen washer fluids.     

Impact of water on the OH + HOCl reaction

The effect of a single water molecule on the OH + HOCl reaction has been investigated. The naked reaction, the reaction without water, has two elementary reaction paths, depending on how the hydroxyl radical approaches the HOCl molecule. In both cases, the reaction begins with the formation of prereactive hydrogen bond complexes before the abstraction of the hydrogen by the hydroxyl radical. When water is added, the products of the reaction do not change, and the reaction becomes quite complex yielding six different reaction paths. Interestingly, a geometrical rearrangement occurs in the prereactive hydrogen bonded region, which prepares the HOCl moiety to react with the hydroxyl radical. The rate constant for the reaction without water is computed to be 2.2 × 10(-13) cm(3) molecule(-1) s(-1) at room temperature, which is in good agreement with experimental values. The reaction between ClOH···H(2)O and OH is estimated to be slower than the naked reaction by 4-5 orders of magnitude. Although, the reaction between ClOH and the H(2)O···HO complex is also predicted to be slower, it is up to 2.2 times faster than the naked reaction at altitudes below 6 km. Another intriguing finding of this work is an interesting three-body interchange reaction that can occur, that is HOCl + HO···H(2)O → HOCl···H(2)O + OH.     

Effect of polysaccharide structure on protein adsorption

Using X-ray photoelectron spectroscopy for quantification, the adsorption has been studied of chicken egg lysozyme, human serum albumin (HSA), bovine colostrum lactoferrin, and γ-globulin (IgG) from single solutions onto surface-immobilised polysaccharide coatings, which were produced by the covalent attachment of a series of carboxymethyldextrans (CMDs) onto aminated fluoropolymer surfaces. CMDs with differing degrees of carboxymethyl substitution were synthesized by the reaction of dextran with bromoacetic acid under different reactant ratios. Substantial amounts of protein adsorption onto these coatings were observed with the majority of the coating/protein combinations. On the most extensively substituted CMD (1 carboxyl group per 2 dextran units), lysozyme and lactoferrin adsorbed to approximately monolayer amounts whereas there was minimal adsorption of HSA, indicating the importance of electrostatic interfacial interactions. CMD 1:14 was similar whereas the least substituted, least dense coating, from CMD 1:30, adsorbed less lysozyme and lactoferrin but more HSA. Adsorption of the large multidomain protein IgG varied little with the coating. Grazing angle XPS data indicated that for the CMD 1:30 coating there occurred significant in-diffusion of the lower molecular weight proteins. The data suggest that elimination of adsorption of a broad spectrum of proteins is not straightforward with negatively charged polysaccharide coatings; elimination of protein accumulation onto/into such coatings may not be achievable solely with a balance of electrostatic and steric–entropic interfacial forces.     

A new method for assessing the efficiency of stabilizers in polyolefins exposed to chlorinated water media

The chlorine used as disinfectant in tap water degrades most materials, including polyethylene. The most adequate (functional) test method, the pressure test, is complicated and expensive because the chlorinated aqueous media (Cl₂ or ClO₂ in water) are unstable and they undergo reactions that are dependent on the pH. A new method which assesses the protection efficiency of phenolic antioxidants in polyolefins was developed. The method uses a liquid hydrocarbon analogue, squalane, in which antioxidants are dissolved. The organic phase was dispersed in the aqueous chlorinated phase (containing 10 ppm of either Cl₂ or ClO₂; pH = 6.8) at 70 °C by intense stirring. The depletion of antioxidant (Irganox 1010) was monitored by standard DSC determination of the oxidation induction time. It was shown that 300 min of exposure was sufficient to obtain useful data.