Solvation structure of sodium chloride (Na+–Cl-) ion pair in acetonitrile (AN)–dimethyl formamide (DMF) mixtures

Solvation structures of Na⁺–Cl^? ion pair are investigated in acetonitrile (AN)–dimethylformamide (DMF) isodielectric mixtures. The potentials of mean force of Na⁺–Cl^? in the five compositions of mixtures show minima corresponding to a contact ion pair (CIP) and a solvent-shared ion pair (SShIP). The solvent-separated ion pair minima are present in lower mole fractions of AN (x_AN ≤ 0.50). CIPs are found to be more stable than the SShIPs. From a thermodynamic decomposition of the potentials of mean force, we find that the formation of the ion pair is entropically driven in these compositions. The most stable CIP is in pure AN. The local solvation structures around the ion pair are analysed through the running coordination numbers, excess coordination numbers, solvent orientational distributions and density profiles. We find that both Na⁺ and Cl^? are preferentially solvated by DMF.     

Delineating the conformational dynamics of intermediate structures on the unfolding pathway of β-lactoglobulin in aqueous urea and dimethyl sulfoxide

Abstract

The funnel shaped energy landscape model of the protein folding suggests that progression of folding proceeds through multiple pathways, having the multiple intermediates which leads to multidimensional free-energy surface. Herein, we applied all-atom MD simulation to conduct a comparative study on the structure of β-lactoglobulin (β-LgA) in aqueous mixture of 8?M urea and 8?M dimethyl sulfoxide (DMSO), at different temperatures. The cumulative results of multiple simulations suggest a common unfolding pathway of β-LgA, occurred through the stable and meta-stable intermediates (I), in both urea and DMSO. However, the free-energy landscape (FEL) analyses show that the structural transitions of I-states are energetically different. In urea, FEL shows distinct ensemble of intermediates, I1 and I2, separated by the energy barrier of ～3.0?kcal mol^?1. Similarly, we find the population of two distinct I1 and I2 states in DMSO, however, the I1 appeared transiently around ～30–35?ns and is short-lived. But, the I2 ensemble is observed structurally compact and long-lived (～50–150?ns) as compared to unfolding in urea. Furthermore, the I1 and I2 are separated through a high energy barrier of ～6.0?kcal mol^?1. Thus, our results provide the structural insights of intermediates which essentially bear the signature of a different unfolding pathway of β-LgA in urea and DMSO.

Abbreviations β-LgA β-lactoglobulin

DMSO dimethyl sulfoxide

FEL free-energy landscape

GdmCl guanidinium chloride

I intermediate state

MG molten globule state

PME particle mesh Ewald

Q fraction of native contacts

RMSD root mean square deviation

RMSF root mean square fluctuation

R_g radius of gyration

SASA solvent Accessible Surface Area

scSASA the side chain SASA

Trp tryptophan

Communicated by Ramaswamy H. Sarma     

Prediction of adsorption equilibria of water–methanol mixtures in zeolite NaA by molecular simulation

Predictions for the adsorption of mixtures of water and methanol in zeolite NaA are reported. The pressure dependence of the adsorption properties such as equilibrium amounts of adsorption and isosteric heats of adsorption are calculated at 378 K by molecular simulations using effective pair potential models. These data are also determined for the adsorption from liquid mixtures. The models predict selectivity inversion in the investigated range of pressure. The change in adsorption ratios can partly be explained by the structural characteristics of the system.     

Differential effects of dimethyl sulfoxide and sodium butyrate on α-fetoprotein,albumin, and transferrin production by rat hepatomas in culture

Summary Radioimmunoassay was used to determine α-fetoprotein (AFP), albumin, and transferrin production (ng/10⁵ cells/24 h) by two cell lines (7777 and 8994) derived from chemically induced rat hepatomas. α-Fetoprotein production was high (2000 to 4400) in 7777, but was very low (0.2 to 0.4) in 8994. Albumin production varied from 0.4–0.8 (7777) to 14–26 (8994). Both lines produced substantial amounts of transferrin (180 to 240 by 7777 and 29 to 42 by 8994). Addition of dimethyl sulfoxide (DMSO, 1 to 4%) or sodium butyrate (BA, 0.5 to 2.0 mM) to the medium inhibited growth in both lines, but 8994 was more sensitive to these agents than 7777. Dimethyl sulfoxide treatment (2 to 4%) resulted in a dose-related decrease (<10% of control at 4% DMSO) in AFP, albumin, and transferrin production by 7777, but in 8994, DMSO (1 to 2%) resulted in an increase, (up to sixfold) in albumin and transferrin production, without affecting AFP production. By contrast, BA (2 to 4 mM) stimulated the production of all three proteins in both lines, most notably that of albumin (up to sixfold) by 7777 and that of AFP (up to 20-fold) by 8994. It is concluded that both DMSO and BA can enhance the expression of differentiated functions of the hepatoma cell, and that DMSO at the same time can suppress the expression of an oncofetal function. However, neither DMSO nor BA is selective in its effects on specific genes (i.e., normal, adult vs. oncofetal genes), and it appears that their effects may be the result of a more general phenomenon, the expression of which may be related to the stage of differentiation of the cell.     

Functional asymmetry of bidirectional Ca-movements in an archaeal sodium–calcium exchanger (NCX_Mj)

Dynamic features of Ca²⁺ interactions with transport and regulatory sites control the Ca²⁺-fluxes in mammalian Na⁺/Ca²⁺(NCX) exchangers bearing the Ca²⁺-binding regulatory domains on the cytosolic 5L6 loop. The crystal structure of Methanococcus jannaschii NCX (NCX_Mj) may serve as a template for studying ion-transport mechanisms since NCX_Mj does not contain the regulatory domains. The turnover rate of Na⁺/Ca²⁺ exchange (k_cat = 0.5 ± 0.2s⁻¹) in WT–NCX_Mj is 10³–10⁴ times slower than in mammalian NCX. In NCX_Mj, the intrinsic equilibrium (K_int) for bidirectional Ca²⁺ movements (defined as the ratio between the cytosolic and extracellular K_m of Ca²⁺/Ca²⁺ exchange) is asymmetric, K_int = 0.15 ± 0.5. Therefore, the Ca²⁺ movement from the cytosol to the extracellular side is ∼7-times faster than in the opposite direction, thereby representing a stabilization of outward-facing (extracellular) access. This intrinsic asymmetry accounts for observed differences in the cytosolic and extracellulr K_m values having a physiological relevance. Bidirectional Ca²⁺ movements are also asymmetric in mammalian NCX. Thus, the stabilization of the outward-facing access along the transport cycle is a common feature among NCX orthologs despite huge differences in the ion-transport kinetics. Elongation of the cytosolic 5L6 loop in NCX_Mj by 8 or 14 residues accelerates the ion transport rates (k_cat) ∼10 fold, while increasing the K_int values 100–250-fold (K_int = 15–35). Therefore, 5L6 controls both the intrinsic equilibrium and rates of bidirectional Ca²⁺ movements in NCX proteins. Some additional structural elements may shape the kinetic variances among phylogenetically distant NCX variants, although the intrinsic asymmetry (K_int) of bidirectional Ca²⁺ movements seems to be comparable among evolutionary diverged NCX variants.     

Simulation of Solvation Dynamics in H-Bonding Solvents: Dynamics of Solute–Solvent H-Bonds in Methanol–Water Mixtures

Molecular dynamics (MD) simulations have been undertaken in order to investigate the collective solvent reorganization following an instantaneous electronic charge transfer between distinct atomic sites of diatomic probe molecules immersed in methanol–water mixtures. Our previous studies of solvation dynamics in these mixtures [28,29] are extended here to the analysis of nonequilibrium time-dependent solute–solvent site–site pair distribution functions for the equimolar mixture using two different solute sizes. This has allowed us to obtain a more detailed picture of the solvent reorganization in response to the solute's excitation. Special attention is devoted to the dynamics of rupture and formation of hydrogen bonds between the smaller probe solute and solvent molecules, and its relationship to the molecular mechanisms of solvation dynamics in these systems on distinct time scales. This revised version was published online in June 2006 with corrections to the Cover Date.     

Dielectric behavior of DNA in water–organic co-solvent mixtures

The radiowave dielectric dispersions of DNA in different water–organic co-solvent mixtures have been measured in the frequency range from 100 kHz to 100 MHz, where the polarization mechanism is generally attributed to the confinement of counterions within some specific lengths, either along tangential or perpendicular to the polyion chain. The dielectric dispersions have been analyzed on the basis of two partially different dielectric models, a continuum counterion fluctuation model proposed by Mandel and a discrete charged site model, proposed by Minakata. The influence of the quality of the solvent on the dielectric parameters has been investigated in water–methanol and water–glycerol mixtures at different composition, by varying the permittivity ?_m and the viscosity η of the solvent phase. The analysis of the dielectric spectra in solvents where electrostatic and hydrodynamic interactions vary with the solvent composition suggests that both the two models are able, in principle, to account for the observed high-frequency dielectric behavior. However, while some certain assumptions are necessary about the polyion structure within the Mandel model, no structural prerequisite is needed within the Minakata model, where the polarization mechanism invoked considers a radial counterion exchange with the outer medium, which is largely independent of the local polyion conformation.     

Speciation of binary complexes of Co(II), Ni(II) and Cu(II) with L-aspartic acid in propylene glycol–water mixtures

Abstract

Speciation of binary complexes of Co(II), Ni(II) and Cu(II) with L-aspartic acid in (0-60% v/v) propylene glycol-water mixtures was studied pH metrically at 303.0±0.1 K and at an ionic strength of 0.16 mol L^-1. The binary species refined were ML, ML₂, ML₂H₂, ML₂H₃ and ML₂H₄. The stabilities of the complexes followed the Irving-Williams order i.e.Co(II) <Ni(II) < Cu(II). The linear variation of stability constants as a function of dielectric constant of the medium indicated the dominance of electrostatic forces over non-electrostatic forces. Some species were stabilised due to electrostatic interactions and some were destabilised due to the decreased dielectric constant. The order of ingredients influencing the magnitudes of stability constants due to incorporation of errors in their concentrations was alkali > acid > ligand > metal. Equilibria for the formation of binary complexes were proposed based on the forms of the ligand and their existence at different pH values.     

Heterogeneous seeding of HET-s(218–289) and the mutability of prion structures

One fundamental property of prions is the formation of strains—prions that have distinct biological effects, despite a common amino acid sequence. The strain phenomenon is thought to be caused by the formation of different molecular structures, each encoding for a particular biological activity. While the precise mechanism of the formation of strains is unknown, they tend to arise following environmental changes, such as passage between different species. One possible mechanism discussed here is heterogeneous seeding; the formation of a prion nucleated by a different molecular structure. While heterogeneous seeding is not the only mechanism of prion mutation, it is consistent with some observations on species adaptation and drug resistance. Heterogeneous seeding provides a useful framework to understand how prions can adapt to new environmental conditions and change biological phenotypes.     

Pairwise interaction enthalpies of enantiomers of β-amino alcohols in DMSO + H2O mixtures at 298.15 K

The dilution enthalpies of enantiomers of six β-amino alcohols, namely (R)-(-)-2-amino-1-propanol versus (S)-(+)-2-amino-1-propanol, (R)-(-)-2-amino-1-butanol versus (S)-(+)-2-amino-1-butanol, and (R)-(-)-2-amino-1-pentanol versus (S)-(+)-2-amino-1-pentanol in dimethylsulfoxide (DMSO) + H(2)O mixtures (mass fractions of DMSO w = 0 to 0.3) have been determined respectively using an isothermal titration calorimeter (MicroCal ITC200, Northampton, MA, USA) at 298.15 K. According to the McMillan-Mayer theory, the corresponding homochiral enthalpic pairwise interaction coefficients (h(XX)) of the six amino alcohols have been calculated. It is found that across the whole studied composition range of mixed solvent, values of h(XX) for S-enantiomer are almost universally higher than those of R-enantiomer for each amino alcohol and that the variations of h(XX) depend largely on the composition of mixed solvent. The results were interpreted from the point of view of solute-solute interaction mediated by cosolvent DMSO, as well as competition equilibrium between hydrophobic-hydrophobic, hydrophilic-hydrophilic, and hydrophobic-hydrophilic interactions.     

Probing the role of aromatic residues in the self-assembly of Aβ(16–22) in fluorinated alcohols and their aqueous mixtures

The Aβ(16–22) sequence KLVFFAE spans the hydrophobic core of the Aβ peptide and plays an important role in its self-assembly. Apart from forming amyloid fibrils, Aβ(16–22) can self-associate into highly ordered nanotubes and ribbon-like structures depending on the composition of solvent used for dissolution. The Aβ(16–22) sequence which has FF at the 19th and 20th positions would be a good model to investigate peptide self-assembly in the context of aromatic interactions. In this study, self-assembly of Aβ(16–22) and its aromatic analogs obtained by replacement of F19, F20 or both by Y or W was examined after dissolution in fluorinated alcohols and their aqueous mixtures in solvent cluster forming conditions. The results indicate that the presence of aromatic residues Y and W and their position in the sequence plays an important role in self-assembly. We observe the formation of amyloid fibrils and other self-assembled structures such as spheres, rings and beads. Our results indicate that 20% HFIP is more favourable for amyloid fibril formation as compared to 20% TFE, when F is replaced with Y or W. The dissolution of peptides in DMSO followed by evaporation of solvent and dissolution in water appears to greatly influence peptide conformation, morphology and cross-β content of self-assembled structures. Our study shows that positioning of aromatic residues F, Y and W have an important role in directing self-assembly of the peptides.     

Enhancement of permethrin efficacy in acaricide–attractant mixtures for control of the fowl tick Argas persicus (Acari: Argasidae)

Three acaricides, permethrin, propoxur and diazinon, were tested against Argas persicus ticks in a test of susceptibility and in a multiple choice test in bioassay. A mixture of guanine hydrochloride and diatomaceous earth in saline was used as an attractant in bioassays, causing 53.1–95.7% assembly. The attractant was mixed with acaricides to reduce their repellency and enhance their efficiency in bioassays. Permethrin was the most toxic (LC95 at day 7=0.5–1.4mg m–2 depending on the developmental stage) and most repellent acaricide. The mortality of males in the bioassay was significantly higher (76.7–94.3%, p<0.01) when acaricide in amounts of 16 and 160 g of active ingredient per filter paper disc were mixed with attractant (0.5 mg per filter paper disc) instead of acaricide alone (20–45.7% mortality only). The mean permethrin residue on the tick body at the end of bioassay with the acaricide– attractant mixture was significantly higher (13.62±11. 64 ng) than in experiments without the attractant (less than 1 ng). Propoxur was less toxic (LC95 at day 7=0.9–1.9 mg –2) and diazinon the least toxic (LC95 at day 7=2– 9.4 mg m–2), both being not or only slightly repellent. Males and females also assembled on filter paper discs treated with propoxur without an attractant. Diazinon displayed significant mortality only in amounts of 0.1 and 1 mg of active ingredient per filter paper disc with or without the attractant. Therefore, the repellency of permethrin can be reduced and its effectiveness enhanced when used in a mixture with an attractant. No similar effect was observed with propoxur or diazinon.     

Prediction of IgE(Lb4)–ligand complex structures by automated docking

A mouse monoclonal anti-2,4,6-trinitrophenyl IgE (clone Lb4) was screened with a random set of over 2000 compounds, and several ligands were found to bind with affinities comparable to that of the immunizing hapten (K_D in the μM range). An automated docking algorithm was used for the prediction of complex structures formed by 2,4-dinitrophenyl (DNP) and non-DNP ligands in the fragment variable region of IgE(Lb4). All ligands were found to dock in an L-shaped cavity of 15 × 16 × 10 Å, surrounded by complementary-determining regions L1, L3, H2 and H3. The ligands were found to occupy the same binding site in different orientations. For rigid ligands the most stable orientation could be predicted with high probability, based on the calculated energy of binding and the occurrence frequencies of identical complexes obtained by repeated simulations. The localization of a flexible ligand (cycrimine-R) was more ambiguous, but it still docked in the same site. The results support a model for heteroligating antibody (Ab) binding sites, where different ligands utilize the total set of available contacts in different combinations. It is suggested that although pseudoenergies calculated by the docking algorithm do not correlate with experimentally measured binding energies, the screening-and-docking procedure can be useful for the mapping of Ab and other receptor binding sites ligating small molecules.     

The effects of cortisol and amino acids on the metabolic activity of rat skin stored in dimethyl sulfoxide buffer at −196 °C

Addition of amino acids to the DMSO buffer reduces the intracellular amino acid depletion of rat skin tissue frozen and stored at ?196 °C.Although prolonged exposure to DMSO progressively inhibits the [2-¹⁴C]glycine and l-[U-¹⁴C]leucine incorporation into the proteins, cortisol and amino acid additions to the buffer medium protect the protein-synthesizing activity. These factors also stimulate the incorporation of [6-³H]-thymidine into DNA. The stimulatory characteristics of cortisol and of amino acids separately are enhanced when both components are added together to the preserving buffer. These effects are noticeable in tissue only exposed to the DMSO buffer without freezing as well as in skin frozen and stored at ?196 °C and subsequently thawed at 40 °C.A stimulatory effect of cortisol and of a free amino acid, supplement to the medium on the α-amino-[1-¹⁴C]isobutyric acid uptake by the cells is only observed in skin exposed for a short period of time to the DMSO buffer, but it is not detectable after longer exposure and after freezing.     

Pathways of methanol conversion in a thermophilic anaerobic (55 °C) sludge consortium

The pathway of methanol conversion by a thermophilic anaerobic consortium was elucidated by recording the fate of carbon in the presence and absence of bicarbonate and specific inhibitors. Results indicated that about 50% of methanol was directly converted to methane by the methylotrophic methanogens and 50% via the intermediates H₂/CO₂ and acetate. The deprivation of inorganic carbon species [(HCO₃^–+CO₂)] in a phosphate-buffered system reduced the rate of methanol conversion. This suggests that bicarbonate is required as an electron (H₂) sink and as a co-substrate for the efficient and complete removal of the chemical oxygen demand. Nuclear magnetic resonance spectroscopy was used to investigate the route of methanol conversion to acetate in bicarbonate-sufficient and bicarbonate-depleted environments. The proportions of [1,2-¹³C]acetate, [1-¹³C]acetate and [2-¹³C]acetate were determined. Methanol was preferentially incorporated into the methyl group of acetate, whereas HCO₃^– was the preferred source of the carboxyl group. A small amount of the added H¹³CO₃^– was reduced to form the methyl group of acetate and a small amount of the added ¹³CH₃OH was oxidised and found in the carboxyl group of acetate when ¹³CH₃OH was converted. The recovery of [¹³C]carboxyl groups in acetate from ¹³CH₃OH was enhanced in bicarbonate-deprived medium. The small amount of label incorporated in the carboxyl group of acetate when ¹³CH₃OH was converted in the presence of bromoethanesulfonic acid indicates that methanol can be oxidised to CO₂ prior to acetate formation. These results indicate that methanol is converted through a common pathway (acetyl-CoA), being on the one hand reduced to the methyl group of acetate and on the other hand oxidised to CO₂, with CO₂ being incorporated into the carboxyl group of acetate.     

Menadione sodium bisulfite inhibits the toxic aggregation of amyloid-β(1–42)

Protein misfolding and aggregation are associated with amyloidosis. The toxic aggregation of amyloid-β 1–42 (Aβ42) may disrupt cell membranes and lead to cell death and is thus regarded as a contributing factor in Alzheimer's disease (AD). 1,4-naphthoquinone (NQ) has been shown to exhibit strong anti-aggregation effects on amyloidogenic proteins such as insulin and α-synuclein; however, its high toxicity and poor solubility limit its clinical application. Menadione sodium bisulfite (MSB, also known as vitamin K3), is used clinically in China to treat hemorrhagic diseases caused by vitamin K deficiency and globally as a vitamin K supplement. We hypothesized that MSB could inhibit amyloid formation since its backbone structure is similar to NQ. To test our hypothesis, we first investigated the effects of MSB on Aβ42 amyloid formation in vitro. We found that MSB inhibited Aβ42 amyloid formation in a dose dependent manner, delayed the secondary structural conversion of Aβ42 from random coil to ordered β-sheet, and attenuated the ability of Aβ42 aggregates to disrupt membranes; moreover, the quinone backbone rather than lipophilicity is esstial for the inhibitory effects of MSB. Next, in cells expressing a pathogenic APP mutation (Osaka mutation) that results in the formation of intraneuronal Aβ oligomers, MSB inhibited the intracellular aggregation of Aβ. Moreover, MSB treatment significantly extended the life span of Caenorhabditis elegans CL2120, a strain that expresses human Aβ42. Together, these results suggest that MSB and its derivatives may be further explored as potential therapeutic agents for the prevention or treatment of AD.     

Relative binding affinities of chlorophylls in peridinin–chlorophyll–protein reconstituted with heterochlorophyllous mixtures

Peridinin–chlorophyll–protein (PCP), containing differently absorbing chlorophyll derivatives, are good models with which to study energy transfer among monomeric chlorophylls (Chls) by both bulk and single-molecule spectroscopy. They can be obtained by reconstituting the N-terminal domain of the protein (N-PCP) with peridinin and chlorophyll mixtures. Upon dimerization of these “half-mers”, homo- and heterochlorophyllous complexes are generated, that correspond structurally to monomeric protomers of native PCP from Amphidinium carterae. Heterochlorophyllous complexes contain two different Chls in the two halves of the complete structure. Here, we report reconstitution of N-PCP with binary mixtures of Chl a, Chl b, and [3-acetyl]-Chl a. The ratios of the pigments were varied in the reconstitution mixture, and relative binding constants were determined from quantification of these pigments in the reconstituted PCPs. We find higher affinities for both Chl b and [3-acetyl]-Chl a than for the native pigment, Chl a.     

Partial purification of penicillin acylase from Escherichia coli in poly(ethylene glycol)–sodium citrate aqueous two-phase systems

Studies on the partition and purification of penicillin acylase from Escherichia coli osmotic shock extract were performed in poly(ethylene glycol)–sodium citrate systems. Partition coefficient behavior of the enzyme and total protein are similar to those described in other reports, increasing with pH and tie line length and decreasing with PEG molecular weight. However, some selectivity could be attained with PEG 1000 systems and long tie line at pH 6.9. Under these conditions 2.6-fold purification with 83% yield were achieved. Influence of pH on partition shows that is the composition of the system and not the net charge of the enzyme that determines the behaviour in these conditions. Addition of NaCl to PEG 3350 systems significantly increases the partition of the enzyme. Although protein partition also increased, purification conditions were possible with 1.5 M NaCl where 5.7-fold purification and 85% yield was obtained. This was possible due to the higher hydrophobicity of the enzyme compared to that of most contaminants proteins.     

Resonance energy transfer and competing processes in donor–acceptor of sodium zinc (II)-2,9,16,23-phthalocyanine tetracarboxylate molecule

An important issue that should be taken into consideration when applying the molecules in photodynamic therapy (PDT) of cancer is the occurrence of homo-resonance energy transfer process between them. We have determined the probability of energy transfer for sodium zinc (II)-2,9,16,23-phthalocyanine tetracarboxylate (ZnPc(COONa)₄) molecules in aqueous NaOH solution. The homo-quenching effect of the molecule was also measured by calculating the diffusion controlled bimolecular rate constant of k _q = 6.5?×?10⁹ M^?1s^?1, which did not show a significant competition with the rate constant of homo-resonance energy transfer process at the applied concentration of the molecules (6 μM). The Förster radius (R? ₀) for ZnPc(COONa)₄ molecules was calculated to be 42 Å. The availability of these calculations should facilitate the potential application of ZnPc(COONa)₄ molecule as an anticancer drug in PDT.