Conformation-specific precipitation of human α2-macroglobulin by divalent zinc or calf thymus histone H3

Highly purified native α₂-macroglobulin (α₂M), α₂M-trypsin, and α₂M-methylamine were compared in experiments designed to study protein precipitation. Significant turbidity developed within 30 min in solutions containing histone H3 and either α₂M-methylamine or α₂M-trypsin, as determined by absorbance at λ = 550 nm. No turbidity was detected in solutions that contained histone H3 and native α₂M or histone H3 alone. Experiments with radioiodinated histone H3 or radioiodinated proteinase inhibitor confirmed that both the H3 and the α₂M “fast” forms (α₂M-methylamine, α₂M-trypsin) were present in the precipitates generated. As much as 70% of the ¹²⁵I-α₂M-methylamine was recovered in the precipitate after incubation with a 120-fold molar excess of H3 (concentration of α₂M-methylamine, 0.28 μm). The ratio of histone to proteinase inhibitor by weight in the precipitate was approximately two. Under comparable conditions, somewhat less α₂M-trypsin precipitated from solutions containing H3 than did α₂M-methylamine; however, inactivation of the α₂M-trypsin with phenylmethylsulfonyl fluoride prior to incubation increased the level of precipitation significantly. Solutions containing poly-l-lysine (M_r ~ 13,000) instead of histone did not form precipitates with any of the forms of α₂M studied. In a second set of experiments, radioiodinated native α₂M, α₂M-trypsin, and α₂M-methylamine were incubated in solutions containing ZnCl₂, BaCl₂, CdCl₂, CuSO₄, MgCl₂, or NiCl₂ (concentration of divalent cation between 5 μm and 1.0 mm). Native α₂M was soluble in all of these salts. By contrast, α₂M-methylamine and α₂M-trypsin precipitated extensively from solutions containing greater than 100 μm ZnCl₂. Precipitation was greater than 90% complete at 1 mm ZnCl₂. A similar effect was not observed with any of the other divalent cations.     

Binding of the rat liver 7-8 S dexamethasone receptor to deoxyribonucleic acid

The 7-8 S form of the [3H]dexamethasone (9 alpha-fluoro-11 beta,17,21-trihydroxy-16 alpha-methylpregna-1,4-diene-3, 20-dione) receptor from rat liver cytosol can be converted to the 3-4 S form by RNase treatment or high salt, suggesting a salt-sensitive association between the receptor protein and RNA. In DNA-cellulose column assays, the gradient-purified 3-4 S form bound DNA more efficiently than the 7-8 S form, though the 7-8 S form was also capable of binding to DNA-cellulose to a significant extent. Activated 7-8 S dexamethasone receptor could be released from its association with soluble DNA by treatment with DNase I. Sucrose gradient analysis showed that the released receptor sedimented as the 7-8 S form and was sensitive to RNase treatment, which induced a conversion to the 3-4 S form. Activated RNase-generated 3-4 S receptor again displayed a higher degree of binding to soluble DNA and was recovered in the 3-4 S form following DNase extraction. The fact that the 3-4 S form bound immobilized or soluble DNA more efficiently suggests that the associated RNA of the 7-8 S form interferes directly or indirectly with the receptor association with DNA. The observation that the receptor binds to DNA in its 7-8 S form suggests that the receptor complex is capable of binding RNA and DNA concurrently.     

Molecular organization of 19 S calf thyroglobulin

Controlled freezing and thawing of 19 S calf thyroglobulin resulted in a specific and reproducible breakdown of the protein. Beside the elementary chain (300,000 Da), new, discrete bands are revealed by gel electrophoresis in sodium dodecyl sulfate under reducing conditions. These new species consist of a major peptide of 100,000 Da and several faster-migrating bands. Most of these polypeptides were purified by preparative gel electrophoresis and individually digested in formic acid with CNBr. A comparative gel electrophoresis under denaturating and reducing conditions of (i) the fragments obtained from the native protein, (ii) the electrophoretically purified elementary chain, (iii) the 100,000-Da peptide, and (iv) a smaller fragment (of about 50,000) was performed. It revealed a very close homology among the peptide maps of the intact 19 S, the elementary chain, and the 100,000-Da peptide. Furthermore, it was shown that the digestion products of the smaller fragment, present in the peptide map of the native protein, were absent in both the elementary chain and the 100,000-Da species. These results support the idea that calf thyroglobulin, even though it has an apparently complex molecular organization, contains structural motifs which are repeated in the elementary chain.     

Preferential binding of bacteriophage Mu repressor to supercoiled Mu DNA

It was shown, using a relatively simple assay, that Mu repressor, cI, binds specifically to a region which spans the leftmost HindIII cleavage site on the phage genome. This extends the observations of Kwoh and Zipser [Nature (London) 277, 489-491 (1979)], who were able to define a binding region to the left of this site. These results provide support for the idea that the eight blocks of repeated DNA sequences, which also span the HindIII cleavage site, are involved in repressor binding. These results also indicate that cI repressor has a marked preference for supercoiled DNA.     

Preferential expression of actin genes during oogenesis of Drosophila

The expression of actin genes was examined during oogenesis of Drosophila. Accumulation of actin proteins was quantitated by a two-stage electrophoresis procedure. Egg chambers accumulate actins preferentially, resulting in a twofold enrichment over other nonyolk proteins. RNA gel blot hybridization experiments demonstrated a concomitant twofold selective increase of actin mRNA levels over that of other mRNAs, suggesting regulation of actin genes at the pretranslational level. Despite an abrupt arrest of actin protein accumulation near the end of oogenesis, the bulk of the actin mRNAs remains associated with polysomes of constant size. It appears that this shut-off of actin protein accumulation is due to an overall decrease in translational efficiency, rather than actin mRNA degradation or its dissociation from polysomes.     

Characterization of ellipticine binding to native calf thymus DNA

The binding of [14C]ellipticine to native calf thymus DNA was studied using equilibrium dialysis. A Scatchard polt revealed the presence of high-and low-affinity binding sites in DNA, the former having a K of 4.0 X 10(7) M(-1) and an n (saturation limiting of binding) of 0.078 (1mol ellipticine/13 mol of DNA nucleotides). The forces involved in stabilizing the high-affinity binding, which has been equated with intercalative binding, were due to a combination of hydrophobic interactions and hydrogen bonding. Difference spectra of ellipticine in the presence of the polydeoxynucleotides, poly d(A-T) or poly d(G-C), showed that there was no base specificity involved in the high-affinity binding. Ellipticine binding to the low-affinity sites, which has been equated with surface binding, was due primarily to the participation of electrostatic interactions of ellipticine with the anionic phosphate groups on the double helical surface of DNA.     

N.M.R. spectroscopy and calcium binding of sialic acids: N-glycolylneuraminic acid and periodate-oxidized N-acetylneuraminic acid

N.m.r. spectroscopy (¹H- and ¹³C-) of N-glycolylneuraminic acid, and of its interaction product with Ca²⁺ at pH 7, indicated that a 1:1 complex is formed, with a formation constant of 193 M^?1 [compared to 121 M^?1 for N-acetylneuraminic acid (1)]. From analysis of electric-field shifts, an approximate position of the Ca²⁺ ion in the complex is inferred, with the hydroxyl group of the N-glycolyl group providing the additional binding. Compound 1 was oxidized with sodium periodate, and ¹³C-n.m.r. spectroscopy was applied in an attempt to identify the aldehyde formed, and to demonstrate that the loss of the glycerol-1-yl side-chain (carbon atoms 8 and 9) decreases its Ca²⁺ ion-binding capacity.     

Preferential release of new outer membrane fragments by exponentially growing Escherichia coli

We have examined whether the outer membrane fragments released by normally growing Escherichia coli contain relatively old or new outer membrane.Double-label experiments show that after incorporation of radioactive leucine into E. coli protein, there is a preferential release of outer membrane material which contains a high percentage of newly labeled protein. This implies that outer membrane fragments are preferentially released from those regions where newly synthesized proteins are inserted into the outer membrane. We estimate that these insertion regions cover no more than 13% of the total outer membrane, and that newly inserted proteins diffuse in the plane of the outer membrane with a diffusion constant ? 5 · 10^?13 cm²/s.     

Enzymatic dephosphorylation of endogenous and exogenous dolichyl monophosphate by calf brain membranes

Calf brain membranes have been shown to enzymatically dephosphorylate endogenous and partially purified, exogenous dolichyl [³²P]monophosphate. The properties and specificity of the dolichyl monophosphatase activity have been studied by following the release of [³²P]phosphate from exogenous dolichyl [³²P]monophosphate added in a dispersion with Triton X-100. The calf brain phosphatase (1) is inhibited by Mn²⁺, Mg²⁺, Ca²⁺, fluoride, and phosphate; (2) exhibits a neutral pH optimum; and (3) has an apparent K_m of 200 μm for dolichyl monophosphate. Dolichyl monophosphatase activity can be distinguished from phosphatidate phosphatase on the basis of their responses to fluoride and phosphate. Based on differential thermolability and the effects of divalent cations and EDTA, the calf brain dolichyl monophosphatase can also be discriminated from the general phosphatase activity assayed with p-nitrophenyl phosphate. Dolichyl monophosphatase activity can be solubilized by treating microsomes with Triton X-100. The enzymatic dephosphorylation of exogenous dolichyl [³²P]monophosphate catalyzed by particulate and detergent-solubilized preparations is negligibly affected by equimolar concentrations of ATP and an assortment of phosphomonoesters, including phosphatidic acid and hexadecyl phosphate. A reduction of approximately 40% in dolichyl monophosphatase activity is observed in the presence of equimolar amounts of retinyl monophosphate. Overall, these results represent good evidence for the presence of a neutral polyisoprenyl monophosphatase in central nervous tissue.     

Effects of fatty acids on activity of cGMP-stimulated cyclic nucleotide phosphodiesterase from calf liver

Effects of fatty acids, prostaglandins, and phospholipids on the activity of purified cGMP-stimulated cyclic nucleotide phosphodiesterase from calf liver were investigated. Prostaglandins A2, E1, E2, F1 alpha, and F2 alpha, thromboxane B2, and most phospholipids were without effect; lysophosphatidylcholine was a potent inhibitor. Several saturated fatty acids (carbon chain length 14-24), at concentrations up to 1 mM, had little or no effect on hydrolysis of 0.5 microM [3H]cGMP or 0.5 microM [3H]cAMP with or without 1 microM cGMP. In general, unsaturated fatty acids were inhibitory, except for myristoleic and palmitoleic acids which increased hydrolysis of 0.5 microM [3H]cAMP. The extent of inhibition by cis-isomers correlated with the number of double bonds. Increasing concentrations of palmitoleic acid from 10 to 100 microM increased hydrolysis of [3H]cAMP with maximal activation (60%) at 100 microM; higher concentrations were inhibitory. Palmitoleic acid inhibited cGMP hydrolysis and cGMP-stimulated cAMP hydrolysis with IC50 values of 110 and 75 microM, respectively. Inhibitory effects of palmitoleic acid were completely or partially prevented by equimolar alpha-tocopherol. Palmitelaidic acid, the trans isomer, had only slightly inhibitory effects. The effects of palmitoleic acid (100 microM) were dependent on substrate concentration. Activation was maximal with 1 microM [3H]cAMP and was reduced with increasing substrate; with greater than 10 microM cAMP, palmitoleic had no effect. Inhibition of cGMP hydrolysis was maximal at 2.5 microM cGMP and was reduced with increasing cGMP; at greater than 100 microM cGMP palmitoleic acid increased hydrolysis slightly. Palmitoleic acid did not affect apparent Km or Vmax for cAMP hydrolysis, but increased the apparent Km (from 17 to 60 microM) and Vmax for cGMP hydrolysis with little or no effect on the Hill coefficient for either substrate. These results suggest that certain hydrophobic domains play an important role in modifying the catalytic specificity of the cGMP-stimulated phosphodiesterase for cAMP and cGMP.     

Thermodynamics and kinetics of co-operative protein-nucleic acid binding: II. Studies on the binding between protamine and calf thymus DNA

Unspecific binding of a protamine, namely fluorescein-labelled clupeine Z, to double-stranded calf thymus DNA was studied using fluorescence titration methods and chemical relaxation techniques. Both equilibrium and kinetic data have been analysed using general theoretical approaches discussed in the accompanying paper. The results agree well with the predictions made on the basis of a standard co-operative binding model.Basic parameters evaluated are the co-operative binding constant (K), the coefficient measuring co-operative interaction between nearest neighbours (q), the number of nucleotides occupied by one protamine molecule (n) and the rate constant of dissociation at the ends of bound ligand sequences (K_D). Values obtained at 20 °C, pH 7.5 and 0.4 m-NaCl were K = 5.8 × 10⁷m^?1, q = 1700, n = 20 and K_D = 0.29 s^?1. They have been found to be sensitive to the concentration of added salt (NaCl). This effect apparently reflects the essentially electrostatic nature of the binding process. The results can be satisfactorily described in terms of competitive binding of sodium ions.     

Structural features and some binding properties of proteoheparan sulfate enzymatically labeled by calf brain microsomes

Previous studies established that brain microsomes catalyze the transfer of [35S]sulfate from 3'-phosphoadenosine 5'-phospho[35S]sulfate to an O-linked oligosaccharide chain of a membrane glycoprotein and sulfamino groups of a membrane-associated proteoheparan sulfate (R. R. Miller and C. J. Waechter (1979) Arch. Biochem. Biophys. 198, 31-41). A large fraction of the proteoheparan [35S]sulfate can be released by treating the enzymatically labeled membranes from calf brain with 1 M NaCl. The salt-extracted 35S-labeled proteoglycan has been partially purified by a combination of ion-exchange and gel filtration chromatography. Based on chromatographic analyses, the 35S-labeled proteoglycan labeled in vitro is proposed to be a family of proteoheparan [35S]sulfates having an average molecular weight estimated to be 55,000. Variation in the length of the 35S-labeled polysaccharide chains partially accounts for the differences in molecular size of the proteoheparan [35S]sulfates. Binding studies reveal that the intact proteoheparan [35S]sulfates, as well as the free 35S-labeled polysaccharides released by mild alkali treatment, rapidly reassociate with calf brain membrane preparations. The association with calf brain membranes is saturable and reversible. Consistent with the binding being a specific interaction, only iduronic acid-containing glycosaminoglycans inhibit the association of the 35S-labeled proteoglycan with calf brain membranes and facilitate the disassociation. Neither the binding of the 35S-labeled proteoglycan to membranes nor the displacement was affected by hyaluronic acid, chondroitin 4-sulfate, or chondroitin 6-sulfate. The binding of the enzymatically labeled proteoheparan sulfate is reduced by preincubating membranes with either trypsin or chymotrypsin, but not with neuraminidase or phospholipase D. These results suggest that at least one class of proteoheparan sulfates could be specifically bound to one or more brain membrane proteins. The results also suggest a role for iduronosyl residues, and perhaps the stereochemical relationship of the carboxyl group to the O-sulfate moiety at C-2, in the recognition process.     

Fractionation and molecular weight determination of deoxyribonucleic acid fragments using agarose column chromatography

DNA fragments of several sizes have been produced by shearing E. coli DNA under different pressures. These fragments have been used to demonstrate that column chromatography on agarose Bio-Gel A-15M can provide a rapid, inexpensive fractionation and sizing method for single-stranded nucleic acids having masses between 10⁵ and 10⁶ daltons. Both chromatographic and electrophoretic analysis of the sheared DNA indicated that discrete fragment populations were produced at each shearing pressure and that these fragments were distributed essentially symmetrically around a mean piece size. The average molecular weight of the several DNA fragment distributions was determined electrophoretically by comparison with standard DNA fragments obtained from restriction endonuclease cleavage of SV40 viral DNA. The molecular weights of the denatured, sheared fragments (single-stranded) ranged from 1.25 × 10⁵ to 7.4 × 10⁵. The single-stranded DNA fragments were chromatographed over agarose Bio-Gel A-15M and a linear relationship was found to exist between the mobilities and logarithms of the molecular weights. Readily available tRNA, 5s RNA, and φX174 single-stranded circular DNA chromatographed at the extremes of the linear relationship and could be used to calibrate the column chromatography.     

Mechanism of lactic acid oxidation catalyzed by lactate dehydrogenase from the tail muscle of Homarus americanus.

The mechanism of lactic acid oxidation in the tail muscles of Homarus americanus was studied. In solutions of intermediate ionic strength (0.55) time-course progress curves for lactic acid oxidation as catalyzed by lactate dehydrogenase exhibited a lag period. Evidence is presented which indicates that the lactate dehydrogenase found in the tail muscles of the lobster exists in two distinct physical and kinetic forms. The equilibrium of these forms is dependent upon the ionic strength of the reaction mixture. In low ionic strength solutions, the enzyme exists as a tetrameric species with an apparent K_m for lactic acid of 1.1 m; in high ionic strength solutions, the enzyme exists as a dimer and the corresponding K_m is 0.028 m. At intermediate ionic strengths, an equilibrium between the two physical and kinetic species exists which is modulated by the NADH mole-fraction ($\text{[}\text{NADH}\text{]}\text{[}\text{NADH}\text{+}\text{NAD}{}^{\mathrm{+}}\text{]}$) and, in turn, this modulation results in sigmoidal time-course progress curves. The role of this enzyme is discussed as affected by in vivo ionic strength, temperature and levels of oxidized and reduced nicotine adenine dinucleotides.     

Effect of mercaptopicolinic acid and of transaminase inhibitors on glycogen synthesis by rat hepatocytes.

To explore the mechanism of the stimulation of glycogen synthesis by amino acids (1) we have studied the effects of transaminase inhibitors and of mercaptopicolinic acid, (MPA) an inhibitor of phosphoenol pyruvate carboxykinase. Mercaptopicolinic acid enhanced glycogen synthesis from fructose, dihydroxyacetone and xylitol. Stimulation of glycogen synthesis with hepatocytes from fasted rats by 0.5 mM mercaptopicolinic acid was 50–70% as effective as 10 mM glutamine. With hepatocytes from fed rats, the stimulation of glycogen synthesis by mercaptopicolinic acid was more pronounced, and stimulation by mercaptopicolinic acid and amino acids was additive. Glycogen synthesis as high as 1% in wet weight per hour was attained in hepatocytes with a high initial glycogen content. Over 80% of glycogen synthase was in the active (a) form. Amino oxyacetic acid greatly depressed or abolished the stimulatory effect of glutamine and asparagine and of mercatopicolinic acid, and induced extensive glycogen breakdown in hepatocytes of fed rats.     

Studies of adenosine triphosphate transphosphorylases. XIV. Equilibrium binding properties of the crystalline rabbit and calf muscle ATP--AMP transphosphorylase (adenylate kinase) and derived peptide fragments.

Both a fluorescence-quenching technique and a uv-difference spectral method have been used to study the binding of 1,N⁶-etheno analogs of the adenine nucleotides (?ATP, ?ADP, ?AMP) (J. A. Secrist III, J. R. Barrio, N. J., Leonard, and G. Weber, 1972, Biochemistry, 11, 3499–3506) to crystalline rabbit and calf muscle ATP-AMP transphosphorylase in the presence and absence of Mg²⁺, at 0.16 ($\text{Γ}\text{2}$), 25 °C, and pH 7.4. In addition, the binding of the ?-analogs of the adenine nucleotides has been studied to two S-[¹⁴C]carboxymethylated peptide fragments of the rabbit muscle enzyme (residues 1–44 = MT-I; residues 171–193 = MT-XII), as well as to a synthetic nonapeptide corresponding to residues 32 ? 40 of the rabbit muscle enzyme. In the case of the rabbit and calf enzymes: Mg?ATP^2?, ?ATP^4?, Mg?ADP^?, and ?AMP^2? are bound stoichiometrically (n ～- 1), Mg?AMP is insignificantly bound, and n ～- 2 for ?ADP^3? (n = maximal number of moles bound per mole of protein). In the case of S-carboxymethylated peptide fragments: MT-I binds stoichiometrically to Mg?ATP^2?, ?ATP^4?, Mg?ADP^?, and ?ADP^3? with values of n ～- 1; but MT-I does not bind to ?AMP^2? significantly. MT-XII binds stoichiometrically to uncomplexed ?AMP^2? or to uncomplexed ?ADP^3? (both with n ～- 1); whereas, the binding of Mg?ADP^?, ?ATP^4?, and Mg?AMP to MT-XII are comparatively insignificant. Other peptide fragments in the molecule, viz. fragments MT-IV (residues 77–96) or MT-VI (residues 106–126) did not bind significantly to any of the ethenoanalogs; nor did insulin, nor, e.g., did bo vine serum albumin. The binding of the etheno analogs was also studied to an equimolar mixture of peptides MT-I + MT-XII, which qualitatively duplicated the binding pattern of the entire native molecule, and except for ?ATP^4? or Mg?ATP^2? (which are bound more tightly to the entire native molecule), even quantitatively. The synthetic peptide (residues 32 to 40) was found to bind to Mg?ATP^2?, ?ATP^4?, and Mg?ADP^?, with n ～- 1; but it does not significantly bind to ?AMP^2?, nor to ?ADP^3?. These binding data support the idea that there are two separate sites for the binding of either (a) the complexed nucleotide substrate (MgATP^2? or MgADP^?) residing in the sequence of MT-I (residues 1 to 44) and in the neighborhood of residues 32 to 40, or (b) the uncomplexed nucleotide substrate (AMP^2? or ADP^3?) residing in the sequence of MT-XII (residues 171 to 193) of the rabbit muscle enzyme.