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.     

Evaluation of applicability of tryptic peptide maps for "finger printing" mitochondrial membrane protein preparations

A background pattern of intense, polar and basic peptides is generated in a mixture of proteins which limits the applicability of “fingerprinting” by peptide maps as a method of establishing homologies among membrane proteins. In addition, it is observed that in such mixtures of proteins the peptide pattern in the “neutral” portion of the map is characterized by a few, weak, tailing peptides which appear on a smeared background of ninhydrin positive material. It is concluded that several types of control maps must be prepared along with maps of membrane fractions if real homologies are to be identified. Application of such control maps to analysis of a sample of mitochondrial membrane protein and a sample of quasicrystalline protein indicated that both of these preparations are disperse mixtures of proteins.     

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.     

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.     

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%.     

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.     

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.     

Crystallographic analysis of the phytoagglutinin from Abrus precatorius by X-ray diffraction and electron microscopy

The lectin from the seeds of Abrus precatorius has been crystallized and the crystals subjected to study by X-ray diffraction and electron microscopy. Three closely related crystal forms were obtained, of orthorhombic space group P2₁2₁2₁ with $\text{a = 138}\text{A}\text{?}$, $\text{b = 142}\text{A}\text{?}$, and $\text{c = 173}\text{A}\text{?}$, of tetragonal space group P4₁2₁2 with $\text{a = b = 136}\text{A}\text{?}$, $\text{c = 176}\text{A}\text{?}$, and a twinned intermediate of the first two. From electron microscopy and two-dimensional spatial filtering of electron micrographs of the crystals, the molecule appears to consist of four similar domains grouped in a roughly planar diamond-shaped arrangement having a local intramolecular dyad axis. The average diameter of the Abrus lectin molecule is 50 to 60 Å and the individual domains appear to have a diameter of about 25 Å.     

The deacylation of substituted benzol-alpha-chymotrypsins.

An extensive comparison of deacylation rates of mono- and disubstituted benzoyl-α-chymotrypsins indicates that no steric effects on rate or apparent pK_a of deacylation are detectable within this series. Some anomalous effects on deacylation rate appear to be associated with fluoro- and nitro-substituents in particular positions on the ring and may be attributable to specific interactions at the enzyme active site. The extensive series of structurally similar acyl-enzymes prepared has allowed a thorough analysis of the effect of acyl group pK_a on the apparent pK_a of deacylation. The data indicates that polar effects on the apparent pK_a are probably negligible. Rho for the deacylation reaction is in good agreement with model reactions for an imidazole general base-catalyzed model reaction.     

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.     

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.     

The denaturation of ribonuclease A by combinations of urea and salt denaturants.

When urea is added to ribonuclease A that has already been denatured by salt (CaCl₂, LiClO₄ or LiCl were used), a second co-operative transition occurs, supporting the previous demonstration that these salts cause only partial denaturation. Also we have studied the effect of the salts on the urea denaturation, and the effect of urea on the salt denaturation. At low concentrations urea makes the salt transitions occur at lower concentrations, but at higher concentrations it changes the transition so that the completely disordered protein found in urea is produced by the salt. At low concentrations the salts actually stabilize the protein against denaturation by urea, but at higher concentrations they destabilize it. The data are presented in “phase diagrams” which are found to be very useful for such three-component systems.     

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.     

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 action of ethidium bromide upon mitochondrial oxidative phosphorylation and morphology.

Ethidium bromide (23 nmol/mg of protein) was found to be a potent inhibitor of oxidative phosphorylation, as determined by loss of respiratory control through the inhibition of the ADP-induced state-3 rate of oxygen uptake. A time latency for complete loss of respiratory control was noted, after which 2,4-dinitrophenol (DNP) was ineffective in overcoming this inhibition. In the absence of EDTA, ethidium bromide produced an apparent uncoupling, as evidenced by an increase of state-4 rates of oxygen uptake and loss of respiratory control. As low as 8 nmol of ethidium bromide/mg of protein stimulated mitochondrial adenosine triphosphatase (ATPase) for 5 min. Two to three times this amount of ethidium bromide reduced the amount P_i released. Preincubation of mitochondria with ethidium bromide prevented subsequent release of P_i during incubation with ATP. Likewise, preincubation inhibited the DNP-activated ATPase. The uptake of low levels of [¹⁴C]ADP preincubated with ethidium bromide (14 nmol/mg of protein) and succinate or α-ketoglutarate could apparently be reversed, with loss of radioactivity beginning several minutes after addition of the radioactive nucleotide. Inhibition of oxidative phosphorylation by ethidium bromide may be due to modification of the adenine nucleotide transport system in mitochondria. The production of apparently swollen mitochondria treated in vitro with ethidium bromide and substrates necessary for oxidative phosphorylation, as seen in electron micrographs, further indicates that the compound is capable of acting directly upon mouse liver mitochondrial function and structure.     

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.