The use of the acetylenic function for direct chemical modification of proteins

The possibility of using the acetylenic function for chemical modification of proteins was tested on chlorotetrolic acid and methyl chlorotetrolate. These compounds react under mild conditions with different functional groups analogous to those present in proteins. The ease with which the same nucleophile adds to the triple bond and substitutes the chlorine was compared, and the stability of the addition products was checked. The modification of amino groups by addition across the triple bond can be reversed in acidic medium. In reactions with small model molecules and with proteins, the tested compounds behave like bifunctional protein reagents.     

Light-dependent chemical modification of thylakoid membrane proteins with carboxyl-directed reagents

Spinach chloroplast thylakoid membranes were chemically modified with membrane penetrating reagents reactive toward protein carboxyl groups, a carbodiimide and the nucleophiles [¹⁴C]glycine ethyl ester or [³H]serotonin. The reagents, being weak bases, were accumulated within the inner aqueous space in the light, due to the low pH inside. Both the accumulation and the low pH stimulating effect on the carbodiimide activation step contributed to a greater labeling in the light compared to dark, and uncouplers inhibited most of the light-dependent increase. Hence, it is likely that the proteins showing the light-dependent, uncoupler-sensitive labeling have those parts located within the inner aqueous space or within the membrane itself. While many membrane proteins which separated on sodium dodecyl sulfate-polyacrylamide gels (12.5–25% gradient) showed some increased labeling in the light, the most conspicuous were the four polypeptides of the chlorophyll $\text{a}\text{b}$ light-harvesting complex. The light-harvesting complex was purified from dark- and light-treated, labeled membranes. The resultant preparation showed about a sixfold, light-dependent, uncoupler-sensitive labeling increase compared to dark conditions. Polypeptides near 6 and 8 kdalton showed light-dependent, uncoupler-resistent increases in carboxyl group modification, which could be due to localized acidic conditions near sites of proton release.     

Inactivation of Salmonella phosphoribosylpyrophosphate synthetase by specific chemical modification of a lysine residue.

Phosphoribosylpyrophosphate synthetase from Salmonella typhimurium contains nine lysine residues per subunit and can be inactivated by reagents specific for this amino acid. Pyridoxal-P reversibly inhibited the enzyme by about 70% by forming a Schiff base derivative with lysine. Reduction with NaBH₄ made this inactivation irreversible. Kinetic experiments indicated that the failure to inactivate the enzyme completely in a single treatment with pyridoxal-P reflects a reversible equilibrium between inactive Schiff base and a noncovalent complex. Modification of one lysine residue per subunit correlated with apparently total loss of activity. The rate of inactivation of the enzyme was decreased fourfold by saturating concentrations of ATP and was decreased at least 20-fold by formation of a quaternary complex of the enzyme with Mg²⁺, α,β-methylene ATP, and ribose-5-P. Trinitrobenzenesulfonate also irreversibly inactivated the enzyme, but this reagent was less specific in that the loss of activity corresponded to the modification of four to five lysine residues. These results suggest that an essential lysine is near the active site of Phosphoribosylpyrophosphate synthetase.     

Stability of 70S ribosomes in relation to misreading and antibacterial activity of aminoglycosides.

The anomeric aminoglycosides, RU 21886 and RU 23468, which both have a 2-deoxystreptamine residue, stabilize 70S ribosomes to similar extents at low magnesium ion concentrations. Only RU 21886, however, has marked antibacterial and bactericidal activity and gives rise to a high level of misreading in cell-free protein synthesizing systems. It would thus appear that the ability to stabilize the association of the two ribosomal subunits does not necessarily lead to errors in translation.     

Identification of vitelline membrane proteins in Drosophila melanogaster

In Drosophila melanogaster, proteins involved in vitelline membrane production are secreted by ovarian follicle cells during stages 9 and 10 of oogenesis. We have used SDS-PAGE and two-dimensional electrophoresis to identify six major size classes of radiolabeled components in purified vitelline membrane preparations. Analyses of in vivo labeled proteins from egg chambers of different developmental stages and stage 10 follicle cells show that components of five of these size classes are synthesized by follicle cells during the period of vitelline membrane deposition. Immunological analysis of eggshell antigens utilizing complex antisera raised to purified eggshell fragments has confirmed the identity of components of three size classes.     

Identification of a peptide sequence involved in association of subunits of yeast hexokinases

The chemistry of the proteolytic conversion of the native yeast hexokinases P-I and P-II to the respective modified forms S-I and S-II was studied in detail. The conversion of P-I to S-I was found to involve the removal of one six and one five residue peptide from P-I; these peptides were isolated and sequenced, and a comparison with the partial sequence of native P-I demonstrated that they were cleaved from the amino terminal end. Since results indicated that exactly the same peptides were cleaved from P-II during conversion to S-II, it is concluded that the first 11 amino acids in P-I and P-II have the same sequence. That sequence is: val · his · leu · gly · pro · lys · lys · pro · gln · ala · arg The basicity of these peptides was reflected in the decrease in isolectric point observed when a P-form is converted to an S-form. The peptides are clearly involved in the association of the subunits of yeast hexokinase, since their removal greatly weakens the tendency of the subunits to dimerize.     

Fluorine chemical shifts in complexes of sodium trifluoralkylsulfates with reduced proteins

Equilibrium dialysis experiments were carried out for several proteins, reduced with dithioerythritol, in aqueous buffer and the anionic surfactants, sodium 12,12,12-trifluorododecylsulfate or sodium 13,13,13-triflourotridecylsulfate, with surfactant concentrations above the critical micelle concentration. Fluorine chemical shifts were determined for each retentate and dialysate solution. The results show that most of the proteins bind 3.2 ± 0.4 millimoles of fluorinates surfactant per gram. In every case the chemical shift of the bound detergent ions is very near that found for micelles, suggesting that the bound ions form micelle-like aggregates.     

Identification of cyclic guanosine monophosphate-binding proteins in Drosophila by direct photoaffinity labeling

A procedure for direct photoaffinity labeling with [³²P]cGMP has been used to identify cGMP-binding proteins in Drosophila. This method provides better sensitivity and resolution than previously described direct methods, because the proteins can be visualized by autoradiography following sodium dodecyl sulfate-gel electrophoresis. Labeling is observed with cGMP concentrations as low as 4 × 10^?8m and is specific for cGMP. The sensitivity of the technique is sufficient to permit detection of cGMP-binding proteins in crude extracts. With this technique a single cytoplasmic cGMP-binding protein of subunit M_r 108,000 has been identified in Drosophila embryos and cultured cells.     

Study of the internal structure of Escherichia coli ribosomes by neutron and x-ray scattering.

Neutron scattering curves of the small and large subparticles of Escherichia coli ribosomes are presented over a wide range of scattering angles and for several contrasts. It was verified that the native ribosome structure was not affected by ²H₂O in the buffer. The reliability of the neutron scattering curves, obtained in H₂O buffer, was established by X-ray scattering experiments on the same material.The non-homogeneous distribution of RNA and protein in the subparticles of E. coli ribosomes is confirmed, with RNA predominantly within the particle and protein predominantly on its periphery. The distances between the centres of gravity of the RNA and protein components do not exceed 25 Å and 30 Å, in the large and small subparticles, respectively.The volume occupied by the RNA within the large and small subparticles is determined. The ratio of the “dry” volume of the RNA to the occupied volume is found to be 0.56; it is the same in both subparticles. Such packing of RNA is characteristic of single helices of ribosomal RNA at their crystallization and of the helices in transfer RNA crystals. A conclusion is drawn that RNA in ribosomes is in a similar state.Experimental scattering curves for the small subparticle depend significantly on the contrast in the angular region in which the scattering is mainly determined by the particle shape. The scattering curve, as infinite contrast is approached, is similar to that calculated for the particle as observed by electron microscopy. Thus, the long-existing contradiction between electron microscopy data (an elonggated particle with an axial ratio 2:1) and X-ray data (an oblate particle with an axial ratio 1:3.5), concerning the overall shape of the 30 S subparticle, is settled in favour of electron microscopy. The experimental neutron scattering curve of RNA within the small subparticle is well-described by the V-like RNA model proposed recently by Vasiliev et al. (1978).Experimental data are given to support the hypothesis that the maxima in the X-ray scattering curves, in the region of scattering angles corresponding to Bragg distances of 90 to 20 Å, arise from the ribosomal RNA component alone. It is shown that the prominence of the peaks in this region of the scattering curve depends only on the scattering fraction of the RNA component. The scattering fraction can be changed both by using the “native contrast” (ribosomal particles containing different amounts of protein) and by varying the solvent composition. The maxima are most pronounced where the RNA scattering fraction is highest or in solvents where the protein density is matched by the solvent. The scattering vectors of the maxima in the X-ray and neutron scattering curves, however, remain unchanged. This allows us to propose the tight packing of RNA as a common principle for the structural arrangement of RNA in ribosomes.     

Dissociation of eukaryotic ribosomes by purified initiation factor EIF-3

Purified eukaryotic initiation factor, EIF-3, prepared from ascites cells dissociated rat liver 80S ribosomes into subunits. Ribosomes bearing endogenous mRNA and nascent peptide were not dissociated by EIF-3. When 80S ribosomes reconstituted from subunits were used as substrate the reaction had the following characteristics: Dissociation was rapid--the reaction being completed within 2 min at 30°. The extent of dissociation was directly proportional to the amount of EIF-3; with 21 μg of EIF-3 about 70% (or 10.5 μg) of the 80S monomers were dissociated. The dissociation of 80S monomers by EIF-3 decreased with increasing concentrations of magnesium. The reaction was not catalytic: 28 moles of EIF-3 were required to dissociate 1 mole of 80S ribosomes. The characteristic of the dissociation reaction promoted by EIF-3 and by $\text{E. coli}$ initiation factor IF-3 are remarkably similar. The dissociation reaction provides a practical assay for EIF-3 independent of complimentation of other initiating factors.     

Inactivation of purine nucleoside phosphorylase by modification of arginine residues.

Treatment of purine nucleoside phosphorylase (EC 2.4.2.1), from either calf spleen or human erythrocytes, with 2,3-butanedione in borate buffer or with phenylglyoxal in Tris buffer markedly decreased the enzyme activity. At pH 8.0 in 60 min, 95% of the catalytic activity was destroyed upon treatment with 33 mM phenylglyoxal and 62% of the activity was lost with 33 mm 2,3-butanedione. Inorganic phosphate, ribose-1-phosphate, arsenate, and inosine when added prior to chemical modification all afforded protection from inactivation. No apparent decrease in enzyme catalytic activity was observed upon treatment with maleic anhydride, a lysine-specific reagent. Inactivation of electrophoretically homogeneous calf-spleen purine nucleoside phosphorylase by butanedione was accompanied by loss of arginine residues and of no other amino acid residues. A statistical analysis of the inactivation data vis-à-vis the fraction of arginines modified suggested that one essential arginine residue was being modified.     

Identification of a carbon-oxygen lyase activity cleaving the ether linkage in carboxymethyloxysuccinic acid

Cell-free extracts of an organism capable of degrading the synthetic ether carboxymethyloxysuccinic acid were used to study the mechanism of degradation of this compound. The initial degradation products were acidic and could be separated by high-voltage electrophoresis. Extended incubation of [¹⁴C]carboxymethyloxysuccinate with the cell-free extracts gave rise to radioactive carbon dioxide and to glycolic, malic, fumaric, and pyruvic acids which were identified by electrophoresis. Identification of the malic and glycolic acids was confirmed by the addition of non-radioactive carrier malic and glycolic acids and recrystallization to constant specific radioactivity. The identification of pyruvate was substantiated by thin-layer chromatography of the 2,4-dinitrophenylhydrazine derivative. The presence of fumaric acid was substantiated by its ultraviolet absorbance.Shorter incubations give rise to only malic, glycolic, and fumaric acids. When the time course of the reaction was followed carefully over the first 15 min of the reaction, it was found that initially nearly equimolar quantities of glycolic and fumaric acids were produced. The early production of fumaric acid was also demonstrated by following the increase in 245-nm absorbance of the degradation mixture. The fumaric acid was subsequently hydrated to malic acid, and the quantity of fumaric acid present decreased slightly until it reached a steady-state level. The presence of fumarase in the extract was demonstrated. It was concluded that the initial attack on the carboxymethyloxysuccinic acid was a cleavage of the ether linkage by an elimination mechanism catalyzed by a carbon-oxygen lyase giving rise to glycolic and fumaric acids.     

Thermodynamic investigations of proteins. II. Calorimetric study of lysozyme denaturation by guanidine hydrochloride.

The thermodynamic parameters of the denaturation of lysozyme are determined at various temperatures (25-60 degrees C) by isothermal calorimetric titrations with guanidine hydrochloride (GuHCl) and by scanning calorimetry in the presence of GuHCl. An approach for the determination of the enthalpy of preferential binding of GuHCl is proposed. It has been shown from GuHCl denaturation experiments that the net enthalpies of denaturation and the denaturational change in the heat capacity of protein can be obtained if preferential binding is taken into consideration. These results are nearly the same as in the case of thermal denaturation in the absence of denaturants. It is concluded that the states of both heat- and GuHCl-denatured lysozyme are thermodynamically indistinguishable.     

Acyltransferase systems involved in phospholipid metabolism in Saccharomyces cerevisiae.

Membrane preparations from Saccharomyces cerevisiae OC-2 catalyzed the acylation of glycerophosphate, 1-acyl and 2-acyl isomers of monoacylglycerophosphate, and 1-acyl and 2-acyl isomers of monoacylglycerylphosphorylcholine. The acyl-CoA:glycerophosphate acyltransferase system (EC 2.3.1.15) showed a broad specificity for acyl-CoAs when the maximal velocities were compared under optimized conditions. The acyl-CoA:2-acylglycerophosphate acyltransferase activity was much lower than the 1-acyl-glycerophosphate acyltransferase activity. Although the 1-acylglycerophosphate acyltransferase system utilized saturated and unsaturated acyl-CoAs at comparable rates, the acylations at the 1- and 2-positions were relatively more selective for palmitate and oleate, respectively, when assayed in the presence of palmitoyl-CoA, oleoyl-CoA, 1-acylglycerophosphate, and 2-acylglycerophosphate. The acyl-CoA:1-acylglyceryl-phosphorylcholine acyltransferase system (EC 2.3.1.23) was relatively more specific for unsaturated acyl-CoAs, while the acyl-CoA:2-acylglycerylphosphorylcholine acyltransferase system (EC 2.3.1.23) utilized both palmitoyl-CoA and oleoyl-CoA at a comparable rate. Although various acyltransferase systems showed a different degree of specificity for acyl-CoAs, the positional distribution of fatty acids in the phospholipid molecules could not be explained simply by the observed specificities. Zymolyase, β-1,3-glucanase from Arthrobacter luteus, was used successfully for the protoplast formation. Subcellular fractionation of the protoplast revealed that these acyltransferase activities were localized mainly in the microsomal fraction. However, the glycerophosphate and 1-acylglycerophosphate acyltranferase activities in the mitochondrial fraction could not be explained by the contamination of microsomes in this fraction. These observations are apparently inconsistent with a current concept that the mitochondrial fraction is the major site of phospholipid synthesis in yeast.     

Choline acetyl transferase activity in chick embryo neuroretinas during development in ovo and in monolayer cultures

The specific activity of the enzyme choline acetyl transferase (CAT) in chick neuroretinas was investigated during in ovo development and in monolayer cultures. The enzyme activity was barely detectable on the 6th day of incubation but increased markedly between the 7th and 11th days. The activity increased sharply between the 15th and 17th days and then slowly until hatching. When cell suspensions from 6- to 7-day neuroretinas were cultured as monolayers, CAT specific activity increased rapidly. After 4–5 days in culture, the activity of the enzyme was identical to that found in the neuroretina on the 11th day of incubation. Cells from 9-day neuroretinas also differentiate in monolayer cultures, but with a more irregular pattern. These data show that cholinergic neurons from chick embryo neuroretina differentiate in monolayer cultures without a lag and at the same rate as in vivo.     

A complex of acidic ribosomal proteins. Evidence of a four-to-one complex of proteins in the Bacillus stearothermophilus ribosome

Two acidic proteins from the 50 S subunit of Bacillus stearothermophilus ribosomes, namely B-L13 (homologous to Escherichia coli protein $\text{L}\text{7}\text{L}\text{12}$) and B-L8, form a complex. Radioactive B-L13, added to ribosomes before dissociation, does not appear in the complex after electrophoresis, so the (B-L13 · B-L8) complex must exist in the ribosome before dissociation. Digestion of B. stearothermophilus ribosomes with polyacrylamide-bound trypsin causes the appearance of new B-L8 and B-L13 spots on two-dimensional polyacrylamide gel electrophoresis, in a pattern which suggests that single molecules of B-L13 are being sequentially cleaved from a four-to-one complex of B-L13 and B-L8.     

Covalent modification as the cause of the anomalous kinetics of aryl sulfatase A.

Mammalian aryl sulfatase A enzymes are known to exhibit an anomalous kinetic behavior in which the enzyme becomes inactivated as it catalyzes the hydrolysis of substrate. Part of the activity of this inactive, turnover-modified form of the enzyme can apparently be restored by the simultaneous presence of substrate and sulfate ion. The present experiments, conducted with 2-hydroxy-5-nitrophenyl [³⁵S]sulfate (nitrocatechol sulfate), establish that the turnover-modified enzyme is covalently labeled. The stoichiometry of the incorporation of radioactivity corresponds to 2 g atom of ³⁵S per mole of enzyme monomer (each monomer of rabbit liver aryl sulfatase consists of two equivalent subunits). It is also shown that isolated, turnover-modified enzyme has lost 80% of its secondary structure when compared to the native enzyme. A commonly used sulfating agent, pyridine-sulfur trioxide complex brings about a similar loss of activity and of secondary structure.