Aggregation of ferrihaems. Dimerization and protolytic equilibria of protoferrihaem and deuteroferrihaem in aqueous solution

1. The absorption spectra of deutero- and proto-ferrihaem in aqueous solution at 25°C show marked changes with concentration and pH in the Soret band region. Quantitative studies of these phenomena imply that they are associated with ferrihaem dimerization and with protolytic equilibria involving monomeric (M) and dimeric (D) ferrihaem species according to the scheme: [Formula: see text] 2. For deuteroferrihaem we obtain K=1.9×10⁻², pK_a(M)=7.1, pK_a(D)=7.4. Protoferrihaem has a much higher dimerization constant, K=4.5 and pK_a(D)=7.5 (pK_a(M) is not accessible). 3. Possible structural relationships between monomeric and dimeric ferrihaem species in solution are discussed in relation to recent work on the oxo-bridged nature of crystalline ferrihaem dimers.     

Studies on haemin in dimethyl sulphoxide/water mixtures.

The nature of the complexes and equilibria shown by solutions of protohaemin in dimethyl sulphoxide/water mixtures and in the presence of acid and base were studied by u.v.-visible spectrophotometry. In neutral solutions containing from 40 to 100% dimethyl sulphoxide, haemin is present as a monomeric complex in which the Cl-ion is not coordinated. Only a single pH-dependent equilibrium pK12 is observed over the range 40-80% dimethylsulphoxide, corresponding to formation of the mu-oxo dimer. As the dimethyl sulphoxide content is lowered below 35%, so the single equilibrium (pK12) is replaced by two equilibria (pK1 and pK2); with solutions of 5 microM-haemin, pK1 decreases (from pK12 7.55 in 65% dimethyl sulphoxide to pK1 approx. 1.5 in 0.01% dimethyl sulphoxide), whereas pK2 hardly changes (from pK12 7.55 in 65% to pK2 approx. 7.5 in 0.01%).     

Studies on horseradish peroxidase in dimethyl sulphoxide/water mixtures. The activation of hydrogen peroxide and the binding of fluoride.

We studied the variation in spectra and in reactivity towards H2O2 of solutions of horseradish peroxidase in dimethyl sulphoxide/water mixtures, obtained by diluting stock solutions of the enzyme in either water or dimethyl sulphoxide, and assayed the enzyme activity and studied the binding of F- by the peroxidase in 65% (v/v) dimethyl sulphoxide. A broadly similar pattern of changes is observed whether one starts from water or from dimethyl sulphoxide; the changes are essentially reversible, though hysteresis is observed. When the dimethyl sulphoxide content of the solvent mixture is increased, the peroxidase retains its ability to activate H2O2 up to 74% (v/v) dimethyl sulphoxide. The peroxidase in 65% (v/v) dimethyl sulphoxide binds F- together with a proton (or the equivalent loss of HO-), as already established for aqueous solutions. We point out that the occurrence in such solutions of both the ability to activate H2O2 and the inability to bind F- without taking up H+ or losing HO- supports the proposed mechanism for activating H202, whereby the protein binds the substrate in the form of the much more reactive HO2-.     

Isolation of oligomers of 5,6-dihydroxyindole-2-carboxylic acid from the eye of the catfish

The reflecting material of the tapetum lucidum of the sea catfish (Arius felis) was chromatographed on Sephadex LH-20 in methanol–dimethyl sulphoxide–formic acid. Two components were present: one, showing an absorption maximum at 330nm, was tapetal pigment; the other, at 257nm, was an associated nucleoside. The tapetal pigment was extracted in methanol–HCl and isolated by adsorption chromatography on Sephadex LH-20. It yielded a methoxy methyl ester on treatment with diazomethane, and permanganate oxidation gave pyrrole-2,3,5-tricarboxylic acid. From the information provided by u.v. and i.r. spectra of the pigment and its methoxy methyl ester, from elemental analyses and from the oxidation products, we suggest that the tapetal pigment is derived from oxidative coupling of 5,6-dihydroxyindole-2-carboxylic acid. A molecular-weight determination and chromatography of the methoxy methyl ester indicate that the pigment is a mixture of oligomers, among which the tetramers probably predominate. We consider that the monomers are joined mainly by C-C linkages at positions 4 and 7. A synthetic pigment having spectral properties nearly identical with those of the natural pigment was prepared by enzymic oxidation of 5,6-dihydroxyindole-2-carboxylic acid with mushroom tyrosinase. The identity of the tapetal pigment with the synthetic pigment was further confirmed by comparing u.v. and i.r. spectra of their methoxy methyl esters. Formation of the tapetal pigment from tyrosine and relationships of the tapetal pigment to melanin are discussed.     

Biological, proton-magnetic-resonance- and ultraviolet-spectroscopic evidence for a molecular complex of actinomycin D and 10,11-dihydro-3H-naphth[1,2-g]indazol-7-ol (Short Communication)

A proton-magnetic-resonance study of the complex formed between actinomycin D and 10,11-dihydro-3H-naphth[1,2-g]indazol-7-ol strongly suggests that the indazole lies above the phenoxazine ring of actinomycin D. The complex can be destroyed by addition of dimethyl sulphoxide or dimethylformamide. The actinomycin D–indazole complex inhibits growth of Pseudomonas fluorescens and raises the thermal denaturation response of DNA. These data support the hypothesis that a molecular complex is formed which readily inhibits cell growth and interacts with DNA.     

STUDIES IN THE PHYSICAL CHEMISTRY OF THE PROTEINS : VI. THE ACTIVITY COEFFICIENTS OF THE IONS IN CERTAIN OXYHEMOGLOBIN SOLUTIONS.

1. The solvent action of a neutral salt upon a protein, oxyhemoglobin, has been found identical to the solvent action of a neutral salt upon a bi-bivalent or uni-quadrivalent compound. 2. The solubility of oxyhemoglobin in phosphate solutions of varying ionic strength has been defined by the equation: log See PDF for Equation in which µ is the ionic strength, and S ₀ is the solubility in the absence of salt. 3. The values of S ₀ have been calculated to be 12.2, 11.2, and 13.1 gm. per liter respectively at pH 6.4, 6.6, and 6.8. 4. The relatively great solubility of oxyhemoglobin in water has been ascribed to the strong affinity constants for acid and base of certain groups in oxyhemoglobin. 5. The small change in the solubility of oxyhemoglobin effected by neutral salts suggests that but few such groups are dissociated in oxyhemoglobin in the state in which it crystallizes near its isoelectric point. 6. Certain of the other properties of oxyhemoglobin, such as its low viscosity, are considered in the light of its molecular weight and its valence type.     

Rheology and microstructure of solutions of the microbial polysaccharide from Pseudomonas elodea

Rheological studies of solutions and gels of the microbial polysaccharide from the organism Pseudomonas elodea have been combined with X-ray diffraction studies of fibres and pulsed electric-birefringence studies of dilute solutions, to investigate the conformation and interaction of the polymer molecules. Rheological data are suggestive of a locally rigid conformation for the biopolymer in solution. X-Ray diffraction studies suggest that the molecules adopt a three-fold helical structure. O-Acetyl substituents have been shown to inhibit the packing of these helices into crystalline domains. Studies of pulsed electric-birefringence suggest an extended, kinetically rigid structure in solution. Dissolving the polysaccharide in dimethyl sulphoxide inhibits the gelation and shear-thinning characteristics of aqueous solutions. Comparative studies of electric birefringence of solutions in water and dimethyl sulphoxide suggest that the differences in rheological properties may result from a change in molecular conformation.     

Histochemical conditions influencing metachromatic staining. A comparative study by means of a model system of polyacrylamide films

Synopsis The influence of different histochemical conditions on some metachromatic staining reactions has been studied using polyacrylamide films containing pure glycosaminoglycans. The films were incubated in fixatives without staining, and in glycerol, diethylene glycol and other glycols, formamide,N,N-dimethylformamide, dimethyl sulphoxide and ethanol (of several concentrations) after staining and their absorption (metachromatic) spectra recorded. In the case of heparin and heparan sulphate the metachromasy was disturbed when the films were immersed before staining in some fixative solutions containing formaldehyde and acid. After equilibration of stained films in organic solvents, changes in the absorption peaks were found to depend on the type and concentration of solvent, the type of glycosaminoglycan and the type of dye.Films containing glycosaminoglycan plus protein were used to investigate the blocking of the metachromatic reaction as the result of ionic interactions with proteins. The parameters that influence this phenomenon (e.g type of protein, glycosaminoglycan and dye, pH of staining) are discussed and a three-dimensional picture is introduced which can explain some of the results obtained in these experiments.     

Isolation and analysis of lignin-carbohydrate complexes from Lolium multiflorum

Lignin-carbohydrate complexes were extracted from grass cell walls by a variety of solvents. The yield of complexes was greatly enhanced if the sample was finely milled in a ball mill; dimethyl sulphoxide and N alkali extractions gave the highest yields. Hydrolysis showed that the carbohydrate fraction of the alkali-extracted complex contained mainly xylose (ca. 70%) and arabinose (ca. 20 %) whereas the dimethyl sulphoxide extracted complex contained glucose (ca. 50 %), xylose (ca. 30%), arabinose (ca. 12 %) and galactose (ca. 5 %). The UV spectrum of the dimethyl sulphoxide extracted complex showed lignin absorbance at 280 nm, but, in addition, ester bonding was also observed by the presence of a secondary absorbing region near 325 nm. This secondary absorbing region was absent from the spectrum of the alkali-extracted complexes. Fractionation of the complexes by ethanol precipitation gave a major component which appeared homogeneous by molecular sieve chromatography and had a MW of ? 150,000.     

Towards Gene Banking Amphibian Maternal Germ Lines: Short-Term Incubation,Cryoprotectant Tolerance and Cryopreservation of Embryonic Cells of the Frog,Limnodynastes peronii

Gene banking is arguably the best method available to prevent the loss of genetic diversity caused by declines in wild populations, when the causes of decline cannot be halted or reversed. For one of the most impacted vertebrate groups, the amphibians, gene banking technologies have advanced considerably, and gametes from the male line can be banked successfully for many species. However, cryopreserving the female germ line remains challenging, with attempts at cryopreserving oocytes unsuccessful due to their large size and yolk content. One possible solution is to target cryopreservation of early embryos that contain the maternal germ line, but consist of smaller cells. Here, we investigate the short term incubation, cryoprotectant tolerance, and cryopreservation of dissociated early embryonic cells from gastrulae and neurulae of the Striped Marsh Frog, Limnodynastes peronii. Embryos were dissociated and cells were incubated for up to 24 hours in various media. Viability of both gastrula and neurula cells remained high (means up to 40–60%) over 24 hours of incubation in all media, although viability was maintained at a higher level in Ca²⁺-free Simplified Amphibian Ringer; low speed centrifugation did not reduce cell viability. Tolerance of dissociated embryonic cells was tested for two cryoprotectants, glycerol and dimethyl sulphoxide; dissociated cells of both gastrulae and neurulae were highly tolerant to both—indeed, cell viability over 24 hours was higher in media containing low-to-medium concentrations than in equivalent cryoprotectant-free media. Viability over 24 hours was lower in concentrations of cryoprotectant higher than 10%. Live cells were recovered following cryopreservation of both gastrula and neurula cells, but only at low rates. Optimal cryodiluents were identified for gastrula and neurula cells. This is the first report of a slow cooling protocol for cryopreservation of amphibian embryonic cells, and sets future research directions for cryopreserving amphibian maternal germ lines.     

Dimethyl sulphoxide: A review of its applications in cell biology

Dimethyl sulphoxide is a water miscible solvent that has wide applications in cell biology. It acts as a cryoprotective agent in a variety of cells and tissues allowing prolonged storage at subzero temperatures. The action of dimethyl sulphoxide on the stability of the liquid matrix of cell membranes appears to be responsible for its effects and this appears also to be true for related effects on membrane permeability and fusion. Dimethyl sulphoxide is also known to act as an inducer of cellular differentiation and as a free radical scavenger and radioprotectant. A review of the underlying molecular basis of all these effects of dimethyl sulphoxide is presented.     

13C and 1H NMR studies of helix-coil transition of poly(β-benzyl-L-aspartate) and poly(γ-benzyl-L-glutamate): Behavior in nonprotonating solvent mixtures,and origin of solvent-induced chemical shift

From the results of ¹³C-nmr measurement of poly(β-benzyl-L -aspartate) and its model compounds in dimethyl sulphoxide/deuterated chloroform mixtures, it was found that the side chain of poly(β-benzyl-L -aspartate) is solvated by dimethyl sulphoxide in the region more than dimethyl sulphoxide 20% (v/v), where the backbone maintains the α-helix. The chemical shift differences in the benzyl group carbons of poly(γ-benzyl-L -glutamate) (trifluoroacetic acid/deuterated chloroform) accompanied by the helix-coil transition, originate from the interaction between the ester group of the side chain and trifluoroacetic acid. The chemical shift difference in the ester carbon is similar. On the other hand, the chemical shift differences of the side-chain carbons in the alkyl portion (C^β, C^γ) originate not only from the interaction between the ester group of the side chain and trifluoroacetic acid, but also from some other unknown factors. The chemical shift differences of the side-chain carbons of poly(β-benzyl-L -aspartate) originate from the interaction between the ester group of the side chain and trifluoroacetic acid.     

Leakage of Dhurrin and p-Hydroxybenzaldehyde from Young Sorghum Shoots Immersed in Various Solvents

Spectral scanning was used to provide estimates of the leakage of the cyanogenic glucoside, dhurrin (p-hydroxy-[S]-mandelonitrile-β-d-glucoside), and its metabolite, p-hydroxybenzaldehyde (p-HB), from young light-grown shoots of Atlas sorghum (Sorghum bicolor [L.] Moench) when these shoots were immersed in water, toluene, chloroform or mixtures of water and toluene or water and chloroform. Minimal leakage of dhurrin and virtually no leakage of p-HB occurred with water as the solvent. The 0.5% concentration (v/v) of both toluene and chloroform was more effective than either the 1.0 or 2.0% concentrations in effecting leakage of the two solutes. With either 0.5% toluene or 0.5% chloroform as the solvent, 80 to 90% of the total dhurrin was extracted from shoots in a 3-hour period. Breakdown of dhurrin during extraction was much more extensive with 0.5% chloroform than with 0.5% toluene. Some loss of p-HB occurred during 3- or 6-hour extractions in the water-organic solvent mixtures; spectral and chromatographic evidence suggested partial conversion of p-HB to p-hydroxybenzoic acid. With undiluted toluene or chloroform as solvents, extracts contained appreciable amounts of free p-HB but essentially no dhurrin. These solvents were less effective than the water-organic solvent mixtures in extracting the solutes from the shoot issue.     

Kinetics of oxidation of ferrocene by tris-1,10-phenanthrolinecobalt(III) in t-butyl alcoholwater and acetonewater mixtures

Rate constants and activation parameters (ΔH^≠ and ΔS^≠)are reported for the oxidation of ferrocene by the tris-1,10-phenanthrolinecobalt(III) cation in t-butyl alcoholwater and in acetonewater solvent mixtures. Solvent effects on reactivity trends for these systems, for this same reaction in methanolwater mixtures, and for cobalt(II)-catalysed racemisation of Co(phen)_3³⁺ in t-butyl alcoholwater solvent mixtures are analysed into initial state and transition state contributions. The dependences of solubilities on solvent composition for ferrocene and for [Co(phen)₃](ClO₄)₃ in methanol, t-butyl alcohol, and acetonewater mixtures are also reported; these results are needed in order to establish solvent effects on the initial states of the reactions studied.     

BOUND WATER IN MUSCLE

1. The amount of free unfrozen water, i.e. water acting as normal solvent, in frog''s muscle at temperatures below the initial freezing-point has been calculated from the vapour pressure isotherm of the muscle. 2. Significant amounts of free water are present at –20°C. The total amount of unfrozen water at –20°C. cannot, therefore, be taken as a measure of the bound water in muscle. 3. The calculated values of free water, when compared with experimentally determined values of total unfrozen water, indicate that the amount of bound water in muscle at various temperatures is small. 4. A temperature considerably below –20°C., roughly between –40° and –60°C., is required to freeze completely the free water in muscle.     

Aggregation of Aβ40/42 chains in the presence of cyclic neuropeptides investigated by molecular dynamics simulations

Alzheimer’s disease is associated with the formation of toxic aggregates of amyloid beta (Aβ) peptides. Despite tremendous efforts, our understanding of the molecular mechanisms of aggregation, as well as cofactors that might influence it, remains incomplete. The small cyclic neuropeptide somatostatin-14 (SST₁₄) was recently found to be the most selectively enriched protein in human frontal lobe extracts that binds Aβ₄₂ aggregates. Furthermore, SST₁₄’s presence was also found to promote the formation of toxic Aβ₄₂ oligomers in vitro. In order to elucidate how SST₁₄ influences the onset of Aβ oligomerization, we performed all-atom molecular dynamics simulations of model mixtures of Aβ₄₂ or Aβ₄₀ peptides with SST₁₄ molecules and analyzed the structure and dynamics of early-stage aggregates. For comparison we also analyzed the aggregation of Aβ₄₂ in the presence of arginine vasopressin (AVP), a different cyclic neuropeptide. We observed the formation of self-assembled aggregates containing the Aβ chains and small cyclic peptides in all mixtures of Aβ₄₂–SST₁₄, Aβ₄₂–AVP, and Aβ₄₀–SST₁₄. The Aβ₄₂–SST₁₄ mixtures were found to develop compact, dynamically stable, but small aggregates with the highest exposure of hydrophobic residues to the solvent. Differences in the morphology and dynamics of aggregates that comprise SST₁₄ or AVP appear to reflect distinct (1) regions of the Aβ chains they interact with; (2) propensities to engage in hydrogen bonds with Aβ peptides; and (3) solvent exposures of hydrophilic and hydrophobic groups. The presence of SST₁₄ was found to impede aggregation in the Aβ₄₂–SST₁₄ system despite a high hydrophobicity, producing a stronger “sticky surface” effect in the aggregates at the onset of Aβ₄₂–SST₁₄ oligomerization.     

Spectrofluorimetric method for the determination of large chlorophyll a/b ratios

A practical spectrofluorimetric calibration method at room temperature is described for determining large chlorophyll a/b ratios on direct extracts from plant material of pigments in 80% aqueous acetone, dimethyl sulfoxide, and N,N-dimethylformamide. The method is based on the work of Boardman and Thorne [Boardman NK and Thorne SW (1971) Biochim Biophys Acta 253: 222–231] who used diethyl ether as solvent. We repeated the calibration in diethyl ether and find significantly different parameters for the calibration curve. The range of standards in this work included solutions with chlorophyll a/b ratios of 10–125 in dimethyl sulfoxide, and of 10–220 in the other solvents. Fluorescence emission spectra were found to be a highly sensitive method for assessing chlorophyll purity. We determined the limits of sensitivity for each solvent from the calibration data. The empirically determined slope of the calibration curve was shown to be related to intrinsic properties of the chlorophylls in solution; this allows predictions of the performance of the method in other solvents.     

A water molecule participates in the secondary structure of hyaluronan.

The structure of hyaluronan was investigated in water/dimethyl sulphoxide mixtures by using high-field n.m.r. and space-filling molecular models. The secondary structure previously established in detail in 'dry' dimethyl sulphoxide [Heatley, Scott & Hull (1984) Biochem. J. 220, 197-205] undergoes changes on addition of water, compatible with the incorporation of a water bridge between the uronate carboxylate and acetamido NH groups. Molecular models show that such a configuration is highly probable, and saturation-transfer experiments yield rates of NH proton exchange that support this proposed structure. The existence of two distinct stable configurations for hyaluronan, in water-rich and water-poor conditions respectively, may have biological implications, e.g. during its biosynthesis in cell membranes. There are extensive hydrophobic regions in both forms, which may be important for interactions with e.g., membranes, proteins and itself.     

Amyloid Fibrillation of Insulin under Water-Limited Conditions

Amyloid fibrillation in water-organic mixtures has been widely studied to understand the effect of protein-solvent interactions on the fibrillation process. In this study, we monitored insulin fibrillation in formamide and its methyl derivatives (formamide, N-methyl formamide, N,N-dimethyl formamide) in the presence and absence of water. These model solvent systems mimic the cellular environment by providing denaturing conditions and a hydrophobic environment with limited water content. Thioflavin T (ThT) assay revealed that binary mixtures of water with formamide and its methyl derivatives enhanced fibrillation rates and β-sheet abundance, whereas organic solvents suppressed insulin fibrillation. We utilized solution small-angle x-ray scattering (SAXS) and differential scanning calorimetry (DSC) to investigate the correlation between protein-solvent interactions and insulin fibrillation. SAXS experiments combined with simulated annealing of the protein indicated that the degree of denaturation of the hydrophobic core region at residues B11–B17 determines the fibrillation rate. In addition, DSC experiments suggested a crucial role of hydrophobic interactions in the fibrillation process. These results imply that an environment with limited water, which imitates a lipid membrane system, accelerates protein denaturation and the formation of intermolecular hydrophobic interactions during amyloid fibrillation.     

Chromatographic behaviour of rat-liver monophosphoinositide

1. Chromatography of rat-liver lipids on a column of silicic acid or a mixture of silicic acid and Hyflo Super-Cel, with chloroform–methanol mixtures, gave monophosphoinositide-containing fractions which were invariably contaminated by the presence of nitrogen-containing phospholipids. The behaviour of the inositide was extremely sensitive to column loading and the results with different batches of silicic acid were not reproducible. 2. However, when chromatography on an alumina column was used, the solvent system chloroform–methanol–water (23:23:4, by vol.) completely eluted the neutral lipids, choline-containing phospholipids and phosphatidylethanolamine. An increase of the water content of the solvent to 14% (by vol.) then led to the elution of the monophosphoinositide component, now free from nitrogen-containing phospholipids, but still contaminated by the presence of a phospholipid, which from its properties was taken to be polyglycerophosphatide. 3. Most of the polyglycerophosphatide could be removed from a rat-liver lipid extract by silicic acid chromatography with chloroform–methanol (19:1, v/v). The other phospholipids were then eluted and applied to an alumina column, whereby a monophosphoinositide fraction of much greater purity was obtained. 4. Further purification of the monophosphoinositide was achieved by chromatography on a mixture of silicic acid and cellulose powder. The final product was virtually pure by thin-layer chromatography and gave the expected analysis for monophosphoinositide.