A modified assay of 3':5'-cyclic-AMP phosphodiesterase.

A modification of the assay of cyclic nucleotide phosphodiesterase involving batch use of Dowex 1 anion exchange resin is described which allows for quantitative recovery of adenosine, guanosine, and their metabolites from the resin slurry. The assay described is suitable for use in crude preparations containing purine catabolizing enzymes. A standardized procedure for determining kinetic parameters of cyclic AMP hydrolysis is also discussed. This procedure was used in the partial characterization of the kinetics of cyclic AMP hydrolysis by rat and rabbit heart supernatant fractions.     

Modification of rat liver iodothyronine 5'-deiodinase activity with diethylpyrocarbonate and rose bengal; evidence for an active site histidine residue

Iodothyronine 5'-deiodinase activity of rat liver microsomes was rapidly and completely lost by treatment with diethylpyrocarbonate (DEP) and by photo-oxidation with Rose Bengal (RB). In both cases inactivation followed pseudo first order reaction kinetics. Inactivation by DEP was diminished in the presence of substrate or competitive inhibitors, and was reversed by hydroxylamine treatment. In addition to photo-oxidation, deiodinase activity was also inhibited by RB in the dark. This inhibition was reversible and competitive with substrate (Ki 60 nM). These results suggest the location of an essential histidine residue at or near the active site of rat liver iodothyronine deiodinase.     

Polysaccharides with sulfate groups are human T-cell mitogens and murine polyclonal B-cell activators (PBAs). I. Fucoidan and heparin

We reported previously that dextran sulfate and carrageenan (kappa, lambda, and iota), which are sulfated polysaccharides, were human T-cell mitogens and mouse polyclonal B-cell activators (PBA). To clarify our working hypothesis further, we used fucoidan and heparin, both sulfated polysaccharides. The following results were obtained: (1) fucoidan is human T-cell mitogen and a mouse PBA; (2) heparin is also a human T-cell mitogen and a mouse PBA, but the degree of the responses by heparin is lower than that by fucoidan; (3) helper T-cell-dependent B-cell differentiation was not observed, since both fucoidan and heparin activate OKT4⁺ cells and OKT8⁺ cells nonspecifically and suppressor T cells (OKT8⁺ cells) may inhibit the helper function of B-cell differentiation by helper T cells (OKT4⁺ cells); and (4) our working hypothesis that polysaccharides with sulfate groups are human T-cell mitogens and mouse PBAs was further strengthened. The relationship between molecular weight and sulfate groups of the polysaccharides is discussed in detail.     

Biosynthesis of ergosta-4,6,8(14),22-tetraen-3-one. A novel oxygenative pathway

Specifically (tritium) labeled precursors (VIII, X, XIV, XV, and XVI), upon feeding to Penicillium rubrum, are incorporated into ergosta-4,6,8(14),22-tetraen-3-one (IV) to the extent of 14.2, 4.5, 11.4, 16.3, and 5.5% respectively. Proof that the ergostane skeleton was incorporated intact was afforded by a chemical-biosynthetic cycle, the latter stages of which entailed reduction of isolated (IV) to ergosterone (VIII), followed by removal of the label through base-catalyzed exchange. A search of the growth medium of P. rubrum revealed the presence of nonartefactual ergosterol epidioxide (XIII) and ergosta-6,22-dien-3β,5α,8α-triol (XVIII). The incorporation data are consistent with a set of multiple pathways with no unique biosynthetic sequence apparent.     

Separation of dipeptides by high-resolution gas chromatography on a fused silica capillary column after trimethylsilylation

Separation of trimethylsilyl derivatives of over 50 dipeptides was achieved by high-resolution gas chromatography using a fused silica capillary column coated with methyl silicone liquid phase. Excellent peak symmetry and reproducibility were obtained. Several pairs of sequence isomeric dipeptides could also be well separated. Application of this approach to peptide sequencing by means of the dipeptidyl aminopeptidase-gas chromatography/mass spectrometry method is also discussed.     

Solvent and solute effects on “inside-outside” conformations and rotation about the peptide bond in a miniature protein model

The physicochemical parameters affecting protein unfolding in relation to peptide bond rotations are briefly reviewed. As a suitable model for the study of solvent and solute effects on amide rotation and inside-outside conformations, the 2,2′-biphenyl analog of N-benzoyl-l-phenylalanine methyl ester (I) was synthesized and resolved enzymatically with α-chymotrypsin. The optically pure substance exists as conformer I_a (R,S configuration) with an axial methoxycarbonyl in the crystalline state. Rotation about the biphenyl axis leads to the equatorial conformer I_b (S,S configuration) in various solvents. In polar solvents, rotation about the amide is rate limiting. Accurate measurements of this rotation were accomplished by following the rate of change in the maximum amplitude of the biphenyl Cotton band at 256 nm. The high sensitivity of the method allowed rate and equilibrium measurements at 10^?3M in the absence of intermolecular association. Small differences of the order of 100 cal/mole in ΔG^≠ or ΔG_eq could thus be detected accurately. It was found that k_obs or k₁ (forward step) for equilibration was linearly related (correlation coefficient of 0.96 for k_obs) with E_T, the solvent polarity index on Reichardt and Dimroth's scale. Rotation was slowest in water and fastest in carbon tetrachloride, δΔG^≠, being 2.4 kcal/mole. Chaotropic anions, cations, and guanidinium chloride accelerated the rate in water. However, the inside-outside (axial-equatorial; I_aI_b) ratio at equilibrium did not correlate in any simple manner with the solvent E_T values. Rather, correlation within groups of solvents appeared to exist. It was suggested that solvent association with the amide differs quantitatively in the inside and outside conformations. The position of the equilibrium in water was affected by chaotropic ions but not by urea or quanidinium chloride. Some possible mechanisms are briefly outlined.     

Kinetic identification of component X as P430: a primary electron acceptor of Photosystem I

Kinetics of dark recoveries of Component X, Center A, and Center B at 20 and 0 °C after a 30-s illumination were studied in membrane fragments from a blue-green alga by using low temperature electron paramagnetic resonance spectroscopy in combination with a quick-freeze method. These kinetics were compared with those obtained by spectrophotometry under the same conditions. Contrary to the currently popular view, the result strongly suggests that Component X, rather than Center A or Center B, is P430.     

Regulation of exocellular protease in Neurospora crassa: induction and repression under conditions of nitrogen starvation.

Exponential-phase cells of Neurospora crassa require the continued presence of a protein inducer and nitrogen starvation to induce exocellular protease under conditions where protein is the sole nitrogen source. The nature of the protein inducer appears relatively unimportant, since both soluble proteins (e.g., myoglobin) and insoluble proteins (e.g., corn zein) will effect induction. Nonstarved cells of N. crassa appear to have small nitrogen pools, since nitrogen starvation of exponential cells prior to transfer into a medium where protein is the sole nitrogen source effects starvation-time-dependent decreases in protease biosynthesis. Ammonium ion represses protease synthesis, with apparent specificity at low concentrations. The amino acids arginine, tryptophan, and threonine effect repression of protease biosynthesis under conditions of nitrogen starvation. Under conditions of sulfur starvation, the amino acids cysteine, methionine, and cystine repress protease biosynthesis. In carbon-starved cells, all of the above amino acids, plus histidine, isoleucine, leucine, lysine, phenylalanine, and valine, effect repression. Examination of amino acid pools formed when cells are grown on protein as the sole nitrogen source demonstrated that the amino acids which repress protease biosynthesis under conditions where protein is the sole carbon source accumulate in significant amounts during the course of protease induction, with kinetics consonant with the induction process.     

A method for predicting the location of particles sedimenting in sucrose gradients

A theory was developed for the calculation of the positions of zones of particles sedimenting through a sucrose gradient. Equations were derived for particles sedimenting through gradients in which the sucrose concentration is (a) a linear function of radius, or (b) a hyperbolic function of radius. Computations were made for both swing-out and zonal rotors. The theory, which is based on direct integration of the sedimentation equation, exploits equations relating (a) the density of sucrose solutions to sucrose concentration and (b) the viscosity of sucrose solutions to sucrose concentration, and also the concept of reduced time (T/2 = S20.w integral of t to w2dt) of Fujita. The required computations may be made using a scientific calculator. Experimental support for the theory was obtained.     

Direct determination of UDP-glucuronic acid in cell extracts by high-performance liquid chromatography

A simple and sensitive method for the direct determination of UDP-glucuronic acid by high-performance liquid chromatography with simultaneous measurement of UDP-glucose was developed. Optimal resolution and separation of UDP-glucuronic acid was attained under isocratic conditions with the ion-pairing agent n-octylamine. Quantitation was sensitive down to 5 pmol for standards and for liver cell extracts. Because this method directly measures UDP-glucuronic acid, it can be used for quantitation in the presence of drugs that interfere with enzymatic methods.     

Equilibrium isoelectric focussing in acrylamide gel slabs--reduction of cathodic drift.

A simple, economical method for counting acrylamide gel slices on solid filter paper supports in a toluene-based scintillation cocktail is described. Major advantages of the system include no requirement for either dissolution of the gel or elution of the radioactive material prior to emulsion counting and the direct reutilization of scintillation cocktail and vials. Additionally, ³²P-labeled RNA samples can be counted with better relative efficiencies and those labeled with ¹⁴C or ³³P can be determined at equivalent efficiencies. Tritium was detected less readily, with an absolute efficiency of approximately 10%.     

A model study of ergot alkaloid biosynthesis

A hypothesis of the mechanistic mode of prenylation of tryptophan, an early phase of ergot alkaloid biosynthesis, occurring by way of 3-(α,α-dimethylally)indolenine and its ring-tautomer indoline intermediates and a Cope rearrangement of the latter has been tested in a model study. 3-(α,α-Dimethylallyl)indolines derived from tetrahydrocarbazole and its cyclopentano equivalent have been synthesized by a five-step procedure. The compounds are stable up to ca. 200°C and liberate no benz-prenylated products even on pyrolysis beyond this temperature, thus diminishing the viability of the above biosynthetic hypothesis. The chemistry of the thermolyses is described.     

Alternative methods of preparation and analysis of quasicrystalline protein from Neurospora crassa

Quasicrystalline protein from Neurospora crassa, prepared by three different methods, was analyzed for the presence of free N-terminal groups. It was found that quasicrystalline protein prepared with alkali treatment, but not material prepared without alkali, had free terminal amino groups. It was concluded that use of alkali to digest uv-absorbing material normally associated with quasicrystalline protein also caused hydrolysis of peptide bonds. An alternative method using short exposures to perchloric acid is suggested as an alternative step for the preparation of this protein fraction.     

Disposition of polar and nonpolar residues on outer surfaces of transmembrane helical segments of proteins involved in proton translocation

"Helical wheel" projections of transmembrane helical segments of membrane proteins involved in proton translocation were constructed. The particular proteins studied were the uncF protein subunit of the Escherichia coli proton-ATPase, the uncE protein subunit of the E. coli proton-ATPase, and cytochrome oxidase subunit III. Clear demarcation of polar and nonpolar regions on surfaces of transmembrane helical segments was seen in the uncF protein and in uncE protein helical segment two, but not in uncE protein helical segment one. The transmembrane segment of cytochrome oxidase subunit III which includes the dicyclohexylcarbodiimide (DCCD)-reactive residue was very similar to E. coli uncE protein helical segment two. The DCCD-reactive residue in both was clearly located on a nonpolar surface.     

Solvent interactions with the active site of the pig heart cytosolic aspartate aminotransferase.

Aqueous solvent interactions with the chromophoric pyridoxal phosphate prosthetic group of aspartate aminotransferase (EC 2.6.1.1) were analyzed quantitatively with ethylene glycol, glycerol, dimethylsulfoxide (DMSO), sucrose, and xylitol as cosolvents. The smaller cosolvents perturb the visible absorption and visible dichroic spectra of the free enzyme, but this solvent perturbation is not observed with the acidic enzymeglutarate complex. Addition of cosolvents caused an increase in the enzyme's affinity for glutarate. This increase in affinity resulted from an increase in the acidic dissociation constant (pK₂) of the enzyme-glutarate complex. The changes in the acidic dissociation constant of the enzyme-glutarate complex, upon addition of cosolvents, correlate well with the changes observed in the pK_a's of carboxylic acids in comparable solvents. Since these solvents have little effect on the pK_a of the enzyme itself, it is concluded that the increase in affinity is due to a specific solvation effect on a carboxyl group of the enzymebound glutarate, rather than resulting from a conformational change in the protein.     

Quantitative in situ hybridization of ribosomal RNA species to polytene chromosomes of Drosophila melanogaster.

In situ hybridization of ¹²⁵I-labelled 5 S and 18 + 28 S ribosomal RNAs to the salivary polytene chromosomes of Drosophila melanogaster was successfully quantitated. Although the precision of the data is low, it is possible to compare the hybridization reaction between an RNA sample and chromosomes in situ with the reaction between the same RNA sample and Drosophila DNA immobilized on nitrocellulose filters. The in situ hybrid dissociates over a narrow temperature range with a midpoint similar to the value expected for the filter hybrid. The kinetics of the in situ hybridization reaction can be fit with a single first-order rate constant that has a value from three to five times smaller than the corresponding filter hybridization reaction. Although the reaction saturates at longer times or higher RNA concentrations, the saturation value does not correspond to an RNA molecule bound to every available DNA sequence. With the acid denaturation procedure most commonly used to preserve cytological quality, only 5 to 10% of the complementary DNA in the chromosomes is available to form hybrids in situ. This hybridization efficiency is a function of how the slides are prepared and the conditions of annealing, but is approximately constant with a given procedure for both 5 S RNA and 18 + 28 S RNA over a number of different cell types with different DNA contents. The results provide further evidence that the formation of RNA-DNA hybrids is the sole basis of in situ hybridization, and show that the properties of the in situ hybrids are remarkably similar to those of filter hybrids. It is also suggested that for reliable chromosomal localization using the in situ hybridization technique, the kinetics of the reaction should be followed to ensure that the correct rate constant is obtained for the major RNA species in the sample and an impurity in the sample is not localized instead.