On the molecular mechanism of stabilization of proteins by cosolvents: role of Lifshitz electrodynamic forces

Several ionic and nonionic additives are known to affect structural stability of proteins in aqueous solutions. At a fundamental level, the mechanism of stabilization or destabilization of proteins by cosolvents must be related to three-body interactions between the protein, additive, and the water medium. In this study, the role of the Lifshitz-van der Waals electrodynamic interaction between various additives (sucrose, glycerol, urea, poly(ethylene glycol)-200, betaine, taurine, proline, and valine) and bovine serum albumin (BSA) in water medium was examined. The electrodynamic interaction energy was attractive for all of the additives studied here when both far ultraviolet and infrared relaxations of the additives were included in their dielectric susceptibility representations. However, when only the infrared contribution was included for structure stabilizers and both far ultraviolet and infrared contributions for the structure destabilizers, the resulting electrodynamic interaction energy (E/kT) followed the structure stabilizing and/or destabilizing behavior of the additives; that is, the interaction was attractive for urea and PEG200 (structure destabilizers), whereas it was repulsive for sucrose, glycerol, betaine, taurine, alanine, valine, and proline (structure stabilizers). The electrodynamic interaction energy E/kT at any given surface-to-surface separation distance between the additives and BSA was positively correlated (r(2) = 0.92) with the experimental thermal denaturation temperature (T(d)) of BSA in 1 M solutions of the additives. These analyses provided a mechanistic basis for the experimental observations of exclusion of the structure-stabilizing additives from the protein-water interface and binding of the structure-destabilizing additives to the protein surface. The role of water structure in the three-body electrodynamic interaction is discussed. It is hypothesized that in the case of additives that enhance water structure the hydration shells formed around the additives effectively dampen the contribution of ultraviolet frequencies to the dielectric susceptibility of the additives and thus impart repulsive electrodyanamic interaction between the additive and the protein, whereas the opposite occurs in the case of additives that breakdown the hydrogen-bonded structure of water.     

Atomistic mechanism of protein denaturation by urea

Effects of urea on protein stability have been studied from all-atom molecular dynamics simulations of ubiquitin, G311 protein, and immunoglobulin binding domain (B1) of streptococcal protein G (GB1) in water and 8 M aqueous urea solution. The mechanism of the change in the solvent environment and the early events in protein unfolding by urea have been identified with emphasis on the change in the interactions of hydrophilic and hydrophobic parts of the protein by calculating the potential of mean force (PMF). Urea replaces the protein-protein and protein-water contacts by forming stronger contacts with the protein, which is indicated by the longer survival times of the protein-urea hydrogen bonds.     

On the relation between the molecular mass distribution of gelatin and its ability to stabilize emulsions

The relation between the molecular mass distribution of gelatin and its effectiveness in stabilizing emulsions of dibutyl phthalate and dodecane in water have been investigated. The molecular mass distribution was determined using gel permeation chromatography. The ability of gelatin samples to stabilize emulsions was investigated by observing the coalescence of macroscopic oil droplets in a special device. The results show that all samples with a content of more than 30 wt.-% in the low-molecular mass range are good stabilizers, whereas the stabilizing ability is diminished drastically by decreasing the low molecular mass content below 30 wt.-%. Mechanisms for the stabilization and rupture of the thin water film between the oil droplets are discussed, especially in the case of gelatin adsorption layers at the film interfaces. A model is given for the qualitative explanation of the dependence of the stabilizing ability of gelatins on the molecular mass distribution.     

Fluoride-responsive hydrogel of cholesterol appended pyridinium urea and its metal detecting ability and semi-conducting behaviour

Cholesterol appended pyridinium urea 1 acts as low molecular weight gelator in DMSO:H₂O (1:1, v/v) showing distinct colour change in the presence of aqueous solution of KF as well as tetrabutylammonium fluoride and recognises F^?  specifically. In addition, this hydrogel is noted to detect aqueous solution of Cu²⁺ and Pb²⁺ ions over a series of other metal ions and exhibits good semi-conducting property.     

The Hund paradox and stabilization of molecular chiral states

The “paradox of optical isomers” revealed by Hund in 1927 is re-examined taking into account the interaction of a chiral molecule with phonons of optically inactive solids below the Debye temperature θ_D. It has been shown, that in the strong coupling limit, where the dephasing rate is much higher than the energy splitting frequency, the interaction can lead to a complete loss of coherence between mirror-antipodal states of the molecule due to the phonon-induced dephasing. This, in turn, suppresses tunnelling oscillations between them, so that transitions, which are reversible in time for an isolated chiral molecule become irreversible for the same molecule placed in a low-temperature matrix. In order to propose a particular mechanism of such stabilization, contributions of a single- and multi-phonon processes in the dephasing rate have been evaluated. It has been established that only the two-phonon scattering provides the sufficiently strong dephasing in low-temperature solids. Such a two-phonon mechanism is responsible for the stabilization of molecular chiral states as long as the temperature of the medium is lower θ_D, but exceeds a few Kelvin degrees. These findings are discussed in the context of the evolutionary concept known as “the cold prehistory of life”.     

About mechanism of foam stabilization by solid particles

The main objective of the research was to study the properties of the foam and foam films stabilized by solid particles. The properties of the foam films were compared with the analogous ones of the emulsion films. The experiment provided the rheological characteristics of the dispersion medium. The research provided the study of the correlation of the contact angle, the shear stress, the surface tension and the radii of aggregates by the solid particles and the modifier concentration. The effect of the foam film stabilization by the solid particles is significant.     

Calix[4]arenes containing urea and crown/urea moieties: effects of the crown ether unit and Na towards anion binding ability

Calix[4]arenes containing urea and crown/urea moieties, 7 and 10, respectively have been synthesized. ¹H NMR titrations of 7 and 10 with anions in DMSO-d₆ showed that 7 and 10 formed complexes with Cl⁻, Br⁻, NO₃⁻ and H₂PO₄⁻ to a different extent. The association constants of 7 and 10 towards anions were calculated and found to vary as H₂PO₄⁻>Cl⁻>Br⁻>NO₃⁻. However, compared to 7 the presence of the crown unit in 10 resulted in a slightly higher affinity to Cl⁻ and Br⁻, but a lower affinity to H₂PO₄⁻. Upon addition of Na⁺, the binding ability of 10 towards H₂PO₄⁻ is increased due to ion-pair enhancement.     

Anti-proliferative and pro-apoptotic effects of cinobufagin on human breast cancer MCF-7 cells and its molecular mechanism

Cinobufagin (CBF) is an active ingredient isolated from Venenum Bufonis extracted and dried from the secretory glands of Bufo gargarizans Cantor. The purpose of the study was to investigate the effects and underlying mechanisms of CBF on human breast cancer MCF-7 cells in vitro. Our results showed that CBF exhibited obvious cytotoxicity on MCF-7 cells in a dose- and time-dependent manner, as indicated by CCK-8 assays. Also, Hoechst 33258 staining and flow cytometry assays showed that CBF strongly induced MCF-7 cell apoptosis and G1 phase arrest. In addition, further molecular mechanistic investigation demonstrated that cinobufagin significantly increased Bax expression, decreased Bcl-2 expression level and up-regulated the ratio of the pro-apoptosis/anti-apoptosis protein Bax/Bcl-2, which were demonstrated by RT-qPCR and western blot assays. Taken together, our data confirm that CBF inhibits growth and triggers apoptosis of MCF-7 cells by affecting the expression of Bax and Bcl-2 in vitro.     

Modeling solvent effects in molecular dynamics simulations of proteins

A series of computer simulations has been carried out on bovine pancreatic trypsin inhibitor using various models to mimic the effects of explicit bulk solvent on the structure of the protein. The solvent properties included are the polarization of the solute by the polar bulk solvent and the restraining effect on the motional freedom of the solute due to frictional drag at the solvent–protein surface interface. The former has been included by using a distance–dependent dielectric permittivity to screen the electrostatic interactions, whereas the latter is simulated by adding a limited number of solvent molecules near the protein surface. To achieve the proper mobility of the water molecules, their motion was restrained by adding a harmonic restraining force. It was found that a very small force constant was sufficient to model the static and dynamical behavior of the fully solvated solute, but that it was necessary to include enough explicit waters to occupy the first solvation shell. © 1992 John Wiley & Sons, Inc.     

Electrostatic features of molecular recognition by cyclic urea mimics of chymotrypsin

The molecular electrostatic-potential pattern was used to investigate the electrostatic features of molecular recognition by two cyclic urea mimics of the active site of α-chymotrypsin. The structures of the mimics were obtained by molecular-mechanics evaluation of the conformational potential-energy surface of the molecules. Calculations were done by using two different atomic point-charge sets in order to assess the effect of charge on the electrostatic potential pattern. The molecules studies were: (1) a “full” mimic of chymotrypsin containing the hydroxyl, imidazole, and carboxylate anion functionalities typical of the active site of the enzyme, and (2) a “partial” mimic with only the hydroxyl and imidazole functional groups. Comparison of the molecular electrostatic-potential patterns of the two mimics in both charge sets showed that the largest differences were due to the structural addition of the carboxylate anion, rather than any particular differences in the choice of atomic point charge. For the full mimic, the pattern was essentially dominated by the negative charge on the carboxylate. Small structural changes which optimized the orientation of the catalytic components had little effect on the electrostatic potential pattern of the molecule. In the absence of the anionic functionality, greater differences were noted in the electrostatic potential pattern of the partial mimic in the two charge sets. The choice of atomic point charge was seen to influence the hydrogen-bonding pattern of the hydroxyl and imidazole moieties, resulting in differences in the spatial orientation of the electrostatic potential minima. In general, both charge sets produced molecular electrostatic-potential patterns which indicated that long-range electrostatic interactions would direct the cationic end of the substrate into the electron-rich binding site. However, specific local features of the electrostatic potential pattern were found to depend on point-charge set through the influence of charge on the hydrogen-bonding pattern.     

脲对丙烯酰胺聚合及产物结构的影响

本文研究了添加脲（添加量为丙烯酞胺的０．０６３到０．２００质量比）对丙烯酰胺聚合的影响。脲的加入能取代丙烯酞胺的双分于氢键缔合，使聚丙烯酰胺的水溶性速度提高，玻璃化温度下降。用红外光谱分析和差热分析的结构分析证实了上述机理。     

A study on the mechanism of polyvinyl chloride stabilization by lead salts

Infrared spectroscopic and DTA measurements and chemical analysis have shown that during stabilization of PVC with organic and inorganic basic lead salts various reactions occur: (a) binding of the evolved HCl, by these salts with the formation of lead chloride and complexes, including HCl, which catalyze the PVC degradation; (b) complex-forming reaction with the reactive PVC groups, which decreases the intensity of color of the polymer. In addition, with weak-organic-acid basic lead salts, exchange of labile Cl atoms for acid residues in PVC occurs, which results in an increase in inherent polymer stability.     

Natural bond orbital analyses of persulfoxide stabilization by remote functional groups. The conformationally induced electrostatic stabilization sulfide photooxygenation mechanism

The conformationally induced electrostatic stabilization (CIES) sulfide photooxygenation mechanism was computationally examined using an ab initio model and extended to the study of new donor atoms. The MP2/6-31G(d) geometries and a natural population analysis of natural lone-pair orbitals on the donor atoms support the mechanism and reveal that oxygen and nitrogen donor groups are more stabilizing than sulfur.     

The molecular mechanism of novolak-diazonaphthoquinone resists

Novolak-diazonaphthoquinone (DNQ) resists are photosensitive varnishes that are used in the fabrication of more than 80% of today's integrated circuits. They have played a crucial role in an unprecedented technical revolution, yet until quite recently nobody really knew how they work. We have been concerned with this problem for some time and we realize now that the principal functions of novolak resists, namely the inhibition by DNQ derivatives of the dissolution of novolak films, and the cessation of inhibition on exposure to radiation, are essentially physical phenomena. Dissolution inhibition is caused by an electric stress imposed on the phenol groups of the resin by the inhibitor. This effect penetrates deep into the material through the formation of hydrogen-bonded phenolic strings. Exposure relieves the stress by uncoupling the strings from the source of induction. The concept of phenolic strings is new and unusual, but it is essential for the understanding of dissolution inhibition. With it, all the many aspects of novolak resists can be interpreted in a unified manner.     

硼砂与尿素合成六方氮化硼的机理

研究了N_2气氛下硼砂与尿素反应生成六方氮化硼以及主要副产物产生和变化的过程,采用热重-差示扫描量热法(TG-DSC)、X射线衍射(XRD)、扫描电子显微镜(SEM)等检测手段对反应产物和氮化硼样品进行了分析.研究结果表明,氮化硼在700℃左右完全生成,随焙烧温度的提高其结晶度不断提高.反应副产物偏硼酸钠的生成是导致氮化硼产率较低的主要原因,在高温焙烧过程中偏硼酸钠的存在有利于六方氮化硼的结晶过程.研究结果可为硼砂-尿素法六方氮化硼制备工艺的优化和改进提供理论基础.     

The first urea azine molecule and its coordination to uranium in the first actinide guanidinate complexes

The urea azine molecule (CyNH)(2)C=N-N=C(HNCy)(2) (1) was easily prepared by reaction of the carbodiimide CyN=C=NCy and H(2)NNH(2) and this novel type of bis-guanidine proved useful in affording chelating and bridging ligands for the building of polynuclear compounds, as illustrated by the synthesis of the first uranium guanidinate complexes [(THF)(2)Li(mu-Cl)(2)UCl(mu-L)](2) (2) and [UCl(mu-L)(2)UCl(2)(micro-Cl)(2)UCl(mu-L)](2) (3) (L = - 2H); the X-ray crystal structures of compounds - were determined.     

The mechanism of vesicle fusion as revealed by molecular dynamics simulations

We describe molecular dynamics simulations elucidating the molecular details of the process of fusion for small lipid vesicles. The simulations are based on a coarse grained (CG) lipid model that accurately represents the lamellar state of a variety of phospholipids and enables us to observe intermediate stages during fusion at near atomic detail. Simulations were conducted on a variety of systems containing common phospholipids such as phosphatidylcholine (PC), phosphatidylethanolamine (PE), lysoPC, and mixtures of the above. The fusion intermediates found are in general agreement with the stalk-pore mechanism. Transient pores sometimes form adjacent to the stalk, however, resulting in the mixing of lipids from the outer and inner monolayers. The speed of stalk formation and the opening of the fusion pore can be modulated by altering the lipid composition in qualitative agreement with experimental observations.     

Contribution of charged groups to the enthalpic stabilization of the folded states of globular proteins

In this paper we use the results from all-atom molecular dynamics (MD) simulations of proteins and peptides to assess the individual contribution of charged atomic groups to the enthalpic stability of the native state of globular proteins and investigate how the distribution of charged atomic groups in terms of solvent accessibility relates to protein enthalpic stability. The contributions of charged groups is calculated using a comparison of nonbonded interaction energy terms from equilibrium simulations of charged amino acid dipeptides in water (the "unfolded state") and charged amino acids in globular proteins (the "folded state"). Contrary to expectation, the analysis shows that many buried, charged atomic groups contribute favorably to protein enthalpic stability. The strongest enthalpic contributions favoring the folded state come from the carboxylate (COO(-)) groups of either Glu or Asp. The contributions from Arg guanidinium groups are generally somewhat stabilizing, while N(+)(3) groups from Lys contribute little toward stabilizing the folded state. The average enthalpic gain due to the transfer of a methyl group in an apolar amino acid from solution to the protein interior is described for comparison. Notably, charged groups that are less exposed to solvent contribute more favorably to protein native-state enthalpic stability than charged groups that are solvent exposed. While solvent reorganization/release has favorable contributions to folding for all charged atomic groups, the variation in folded state stability among proteins comes mainly from the change in the nonbonded interaction energy of charged groups between the unfolded and folded states. A key outcome is that the calculated enthalpic stabilization is found to be inversely proportional to the excess charge density on the surface, in support of an hypothesis proposed previously.