The subunit interface of the Escherichia coli ribosome. Crosslinking of 30 S protein S9 to proteins of the 50 S subunit.

Purified 50 S ribosomal subunits were found to contain significant amounts of protein coincident with the 30 S proteins S9 and/or S11 on two-dimensional polyacrylamide/urea electropherographs. Peptide mapping established that the protein was largely S9 with smaller amounts of S11. Proteins S5 and L6 were nearly coincident on the two-dimensional polyacrylamide/urea electropherographs. Peptide maps of material from the L6 spot obtained from purified 50 S subunits showed the presence of significant amounts of the peptides corresponding to S5. Experiments in which ³⁵S-labelled 30 S subunits and non-radioactive 50 S subunits were reassociated to form 70 S ribosomes showed that some radioactive 30 S protein was transferred to the 50 S subunit. Most of the transferred radioactivity was associated with two proteins, S9 and S5. Sulfhydryl groups were added to the 50 S subunit by amidination with 2-iminothiolane (methyl 4-mercaptobutyrimidate). These were oxidized to form disulfide linkages, some of which crosslinked different proteins of the intact 50 S ribosomal subunit. Protein dimers were partially fractionated by sequential salt extraction and then by electrophoresis of each fraction in polyacrylamide gels containing urea. Slices of the gel were analysed by two-dimensional polyacrylamide/sodium dodecyl sulfate diagonal gel electrophoresis. Final identification of the constituent proteins in each dimer by two-dimensional polyacrylamide/urea gel electrophoresis showed that 50 S proteins L5 and L27 were crosslinked to S9. The evidence suggests that proteins S5, S9, S11, L5 and L27 are located at the interface region of the 70 S ribosome.     

Biogenesis of erythrocyte membrane proteins in vivo studies in anemic rabbits

To study the process of red cell membrane protein synthesis we have followed the time course of [³H]leucine appearance in total protein and individual peptides of the erythrocyte membrane following injection of the amino acid into phenylhydrazine-anemic rabbits. Multiple peripheral blood samples were taken from single animals over a 5-week period. Erythrocyte membrane proteins were separated by polycrylamide gel electrophoresis in sodium dodecylsulfate and dithiothreitol; incorporation of radioactivity was determined by gel slicing and liquid scintillation spectrometry. Appearance of [³H]leucine in circulating erythrocytes reached a peak at 1–3 days, with a steady decline thereafter. The radioactive amino acid appeared first in the lowest molecular weight peptides and last in the largest peptides; at the earliest time point (8 h), little radioactivity was observed in any of the four largest peptides present in the membranes (bands A, 1, 2 and 3). Certain smaller peptides (bands 4, 5 and 9) were the predominant species labeled at this time. By 24 h all peptides showed significant incorporation. With maturation of the red cells, label largely disappeared from bands A, 9 and several smaller peptides; this was confirmed by finding that the peptides are virtually absent from mature circulating erythrocytes. These data are interpreted as showing that red cell membrane proteins are synthesized asynchronously during the life cycle of the erythrocyte; the largest peptides are made predominantly in the earlier marrow stages of development, while certain of the smaller peptides are still being synthesized in the reticulocyte stage. Several membrane proteins appear to be specific to the reticulocyte and are lost during the process of cell maturation in the circulation.     

Microfingerprints of proteins through labeling acetylation of their proteolytic peptides

Microgram amounts of proteins applied to polyacrylamide gel electrophoresis were subjected to a fingerprinting procedure using a combined proteolysis-acetylation method with the aid of ¹⁴C-labeled acetic anhydride of high specific activity. After staining, gel slices were partially dried and were resoaked in a solution of a protease. After elution and acetylation, the resulting peptides were resolved in fingerprints on cellulose thin-layer chromatography plates and subjected to autoradiography with or without sensitization. Yields, completeness of fingerprinting, and possible artefacts were investigated.     

A survey of peptides containing sites of phosphorylation in nonhistone nuclear proteins

³²P-labeled peptides obtained by pronase digestion of unfractionated nonhistone nuclear proteins were resolved on columns of Dowex 50, DEAE-Sephadex, Bio-Gel P2, and paper electrophoresis at pH 1.8. Each of 30 peptides analyzed contained predominantly glycine, glutamic acid and proline. The chain length ranged from 7 to 19 residues, including 1 to 4 phosphorylated residues per peptide. These results suggest phosphorylation sites in nonhistones involve a high negative charge density in non-helical regions of these proteins.     

Mass spectrometric characterization of isoform variants of peanut (Arachis hypogaea) stem lectin (SL-I)

Matrix assisted laser desorption/ionization–time-of-flight (MALDI–TOF) mass spectrometric (MS) analysis of purified Arachis hypogaea stem lectin (SL-I) and its tryptic digests suggested it to be an isoformic glucose/mannose binding lectin. Two-dimensional gel electrophoresis of SL-I indicated six isoforms (A1–A6), which were confirmed by Western blotting and MALDI–TOF MS analysis. Comparative analysis of peptide mass spectra of the isoforms matched with A. hypogaea lectins with three different accession numbers (Q43376_ARAHY, Q43377_ARAHY, Q70DJ5_ARAHY). Tandem mass spectrometric (MS/MS) analysis of tryptic peptides revealed these to be isoformic variants with altered amino acid sequences. Among the peptides, the peptide T12 showed major variation. The ¹⁹⁹Val–Ser–Tyr–Asn²⁰² sequence in peptide T12 of A1 and A2 was replaced by ¹⁹⁹Leu–Ser–His–Glu²⁰² in A3 and A4 (T12′) while in A5 and A6 this sequence was ¹⁹⁹Val–Ser–Tyr–Val²⁰² (T12″). Peptide T1 showed the presence of ¹⁰Asn in the isoforms A1–A5 while in A6 this amino acid was replaced by ¹⁰Lys (T1′). Overall amino acid sequence as identified by MS/MS showed a high degree of similarity between A1, A2 and among A3, A4, A5. Carbohydrate binding domain and adenine binding site seem to be conserved.     

Biochemical characterization of enkephalin-like immunoreactive peptides of adrenal glands

The total enkephalin-like immunoreactive peptide content of adrenal glands from dog, cattle, guinea pig and rat was investigated by radioimmunoassay using a (met⁵)-enkephalin antiserum. Dog adrenals contain the highest amount of peptides, cattle and guinea pig adrenals contain lesser amounts, and the rat adrenals had the least amount (0.05% that of the dog). Comparison of the (met⁵)-enkephalin content of the adrenal cortex and medulla with that of whole bovine adrenal gland indicates that the peptides are concentrated in the medulla. Analysis of the chromaffin granules from bovine adrenal medulla indicates this to be the primary storage site for (met⁵)-enkephalin-like peptides. Gel chromatography reveals a molecular heterogeneity of the immunoreactive peptides in all species tested; high molecular weight peptides account for a larger proportion of the immunoreactivity when compared with the low molecular weight peptides.     

Acid Soluble Peptides in Rat Skeletal Muscle

The acid soluble peptide fraction was prepared from rat skeletal muscle, and the amino acid composition of the fraction was analyzed. The peptide fraction was rich in glutamic acid (or glutamine) and glycine and was poor in branched chain or aromatic amino acids. Since the peptide fraction contained N^τ-methylhistidine, the fraction or at least a part of it was presumed to be composed of intermediate peptides of protein degradation in skeletal muscle. At least 31 spots were detected in the fraction by one dimensional paper electrophoresis.     

Identical 110,000 dalton phosphoproteins in nuclei and polyribosomes of a rapidly growing rat hepatoma

Nuclei and free polyribosomes from rat hepatoma tissue were incubated $\text{in vitro}$ in the presence of [³²P] ATP. 0.2 N HCl-soluble nuclear proteins and polyribosomal proteins binding to oligo (dT) cellulose were prepared. A 110 kd phosphoprotein was separated by SDS polyacrylamide gel electrophoresis from each of the samples. The phosphoprotein was analysed using limited digestion with protease V8 in a second SDS gel. The patterns obtained for stained peptides and phosphopeptides were completely identical for both preparations. Thus significant amounts of the 110 kd protein appear to be present, as genuine constituents, in both nuclei and polyribosomes.     

Determination of amino acid compositions and NH2-terminal sequences of peptides electroblotted onto PVDF membranes from tricine-sodium dodecyl sulfate-polyacrylamide gel electrophoresis: application to peptide mapping of human complement component C3

The combination of high-resolution Tricine-Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (H. Sch?gger and G. von Jagow (1987) Anal. Biochem. 166, 368-379) and electroblotting onto polyvinylidene difluoride (PVDF) membranes represents a powerful technique for the isolation of small amounts of peptides and protein fragments (Mr 1000-20,000) in a suitable form for amino acid sequencing, directly on the blotting membrane. Conditions for electrophoresis and electroblotting were optimized with respect to high transfer yield and suitability for both amino acid analysis and sequence determination of stained PVDF-bound peptides. Transfer yields were 50-80%, amino acid compositions including Cys were correct, and picomole quantities were sequenced with initial and repetitive yields as high as those we normally obtain for peptides in solution. The method was used for peptide mapping of polymorphic forms of human complement component C3.     

The peptides of chloroplast membranes: I. The soluble coupling factor (Ca2+-ATPase)

The chloroplast coupling factor (CF₁) was analyzed by gel electrophoresis in SDS and found to contain two major bands in equal amounts with mobilities corresponding to molecular weights of 62,000 and 57,000 and three minor bands of molecular weights 38,000, 21,000, and 14,000. The peptides were present in comparable amounts in many different preparations of the protein and, therefore, were thought not to be tightly bound contaminants. The interaction between these five peptides was shown to be noncovalent.Incubation of the enzyme with trypsin, under conditions which activate the latent ATPase, was found to cause selective digestion of the five peptides; the 62,000 M_r peptide was the most susceptible to digestion, while the 57,000 M_r peptide was most stable to trypsin. When chloroplast membranes were exposed to trypsin in the light to activate the postillumination Mg²⁺-dependent ATPase activity, EDTA extraction solubilized a protein fraction which contained the normal CF₁ peptide pattern. Also, the membranes, when solubilized and chromatographed on SDS-gels did not show the disappearance of any band.The ATPase activity of the protein was highly susceptible to ionic strength, being 50% inhibited by monovalent salts at a concentration of 0.05 m.     

Separation of cyanogen bromide-cleaved peptides of the vesicular stomatitis virus glycoprotein and analysis of their carbohydrate content.

The purified glycoprotein of vesicular stomatitis virus was cleaved at methionine residues with cyanogen bromide, and the resultant peptides were analyzed by two-dimensional electrophoresis in sodium dodecyl sulfate-polyacrylamide gels. Five peptide bands were resolved in cylindrical gels run under nonreducing conditions. After reduction and electrophoresis in the second dimension, 11 peptides were resolved, indicating that several were originally linked by disulfide bonds. Double-label experiments indicated that at least 8 of the 11 peptides were unique. The major oligosaccharide chains were attached to two different cyanogen bromide peptides. In addition, six other peptides contained small amounts of sialic acid, fucose, and mannose, indicating that the glycoprotein contains more carbohydrate chains than the two major ones which have been reported previously.     

Anti-peptide antibodies specific for the gastrin/cholecystokinin-B receptor

Summary Seven synthetic peptides, between 7–22 residues long, corresponding to six different parts of the gastrin/CCK_B receptor molecule which are conserved among the species, were used for raising antibodies. The peptides were coupled to keyhole limpet hemocyanine and injected into rabbits. ELISA analysis demonstrated that all peptides produced an immune response after three to six injections given at biweekly intervals. The titer ranged from 1:10⁴ to 1:10⁵. All antibodies recognized a 78 kDa protein on immunoblots of NIH 3T3 cells stably transfected with human gastrin/CCK_B receptor cDNA, as well as human and guinea pig stomach mucosal extracts. Preincubation of the sera with the corresponding peptides abolished the staining. Indirect immunofluorescence staining revealed that four antibodies out of the seven tested recognized the receptor in fixed COS-7 cells transiently transfected with human gastrin/CCK_B receptor cDNA. The reactive antibodies were raised against the peptides corresponding to receptor residues 40–58, 153–160, 288–294 and 356–372. Immunohistochemical staining of guinea pig stomach using these antisera resulted in intense staining of parietal cells in the fundus and cardia regions.Abbreviations CCK cholecystokinin - GR gastrin/CCK_B receptor - TFA trifluoroacetic acid - BSA bovine serum albumin - PBS phosphate-buffered saline - PAGE polyacrylamide gel electrophoresis - ELISA enzyme-linked immunosorbent assay - EDTA ethylenediamino tetraacetic acid - CLSM confocal laser scanning microscopy - KLH keyhole limpet hemocyanine     

Active center and subunit structure of transaldolase from Candida utilis.

Crystalline transaldolase (type III) isolated from Candida utilis is composed of two identical subunits, as shown by the following lines of evidence. 1. Tryptic digestion of the performic acid oxidized enzyme yields the number of ninhydrin- and arginine-positive peptides expected for identical subunits. 2. All attempts to separate both subunits by molecular weight or charge differences have failed. 3. Cyanogen bromide cleavage and sodium dodecyl sulfate gel electrophoresis of S-carboxymethylated transaldolase revealed four distinct peptides designated C₂ to C₅ according to their decreasing molecular weight and one additional peak, C₁, in low yield, presumably an aggregate or partially degraded peptide.By chromatography on Sephadex G-100 the maleylated cyanogen bromide digest from ¹⁴C-labeled β-giyceryl-transaldolase could be separated into four peptide peaks which have been analyzed for their amino acid composition. The largest peptide C₂ with a molecular weight of 16,800 was identified as the active site containing fragment. The four fragments together account for all amino acid residues in the entire protein.From transaldolase (type I) containing four methionine residues three cyanogen bromide peptides could be identified. By addition of the individual peptides a molecular weight of 37,100 ± 3500 could be calculated, which is half the molecular weight of the native enzyme. From experimental data presented so far both isoenzymes of transaldolase can be regarded as “half-of-the-sites” enzymes.     

Further studies on the peptido-galactomannan from the yeast form of Cladosporium werneckii. Identification of O-acetyl substituents and isolation of the peptide components following beta-elimination.

The pathogenic yeast Cladosporium werneckii produces a surface peptido-phosphogalactomannan (PPGM) with a peptide backbone rich in serine and threonine to which three types of carbohydrate chains are linked. These chains are: Type a, glactomannan units linked through phosphodiester bonds to produce long chains of molecular weight about 50,000; type b more numerous short mannosyl oligosaccharide units, and type c, more infrequent, long galactomannan chains. The first two are linked to the peptide through alkali-labile bonds to serine and threonine of the peptide whereas type c chains are linked through alkali-stable bonds (Lloyd, K. O. (1972) Biochemistry, 11, 3884–3890). The PPGM sample can be separated into three or four major components by diethylaminoethyl (DEAE-) Sephadex chromatography. By means of sequential degradations with alkali and acid, the structural basis for this heterogeneity has been demonstrated. It is due to the presence of different proportions of the three types of chains in the various fractions. The presence of O-acetyl groups, mainly on the a chains, was demonstrated in PPGM by chemical analysis and by proton and ¹³C nuclear magnetic resonance spectroscopy. Purified a chains were isolated from PPGM following Pronase digestion. By taking advantage of the alkali lability of the carbohydrate-protein linkages it has been possible to cleave the peptide moiety away from the carbohydrate. By sequential chromatography on Bio-Gel P-100, Dowex 1 and Bio-Gel P-100, five modified peptide fractions were isolated. The molecular weights of these fractions varied from 9,500 to 18,500 as judged by polyacrylamide-gel electrophoresis. Unlike the original peptide, the modified peptides contained low amounts of serine and threonine. The predominant amino acids were alanine, glycine, aspartic acid and glutamic acid which together make up between 51 and 55% of the peptides. The high content of the last two amino acids accounts for the acidic nature of the peptides. It appears that each fraction consists of a slightly heterogeneous population of peptides very similar in amino acid composition. It is not clear whether the compositional and size heterogeneity exists in the original peptide or whether it arose during the isolation procedure.     

Analysis of the major polypeptides of spectrin by tryptic digestion

The two major polypeptides of erythrocyte membrane spectrin have been isolated by preparative polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate. The tryptic peptide maps of the two polypeptides have been prepared by thin-layer chromatography and electrophoresis. Radioactive peptides have been prepared by ¹⁴C-carboxymethylation and chloramine T-catalysed ¹²⁵I iodination. Maps of both sets of peptides demonstrate a marked similarity between the two parent polypeptides.     

Structural similarities between the major polypeptides of thylakoid membranes from Chlamydomonas reinhardtii

The major polypeptides of thylakoid membranes from Chlamydomonas reinhardtii were purified by preparative gel electrophoresis and examined for structural similarities. The largest of these polypeptides has an apparent molecular mass of 29,500 ± 500 daltons, whereas the other two both have an apparent mass of 26,000 ± 500 daltons. The amino acid compositions and uv-absorption spectra of the 29K- and 26K-dalton polypeptides are very similar. The same pattern of release of amino acids was obtained from both fractions by digestion with carboxypeptidase Y. Endoproteolytic digestion with trypsin, chymotrypsin, staphylococcal protease, and mild acid yielded identical patterns of N-terminal amino acids from both the 29K- and 26K-dalton polypeptides. However, different patterns of peptides were found after electrophoresis of fragments generated by digestion with staphylococcal protease. Conditions of electrophoresis were defined that permitted separation of the 26K-dalton fraction into two components, designated as polypeptides 16 and 17 in the identification system of Chua and Bennoun (1975, Proc. Nat. Acad. Sci. USA72, 2175–2179). Amino acid compositions of these two polypeptides are nearly identical. Polypeptide 16 contained N-terminal isoleucine, but no free N-terminal amino group was detected in polypeptide 17. Electrophoretic analysis of staphylococcal protease digests of these two polypeptides revealed significant differences in the patterns of peptides. These data confirm that there are three distinct major polypeptides in these membranes, which are present at nearly equal amounts. However, the data also suggest that significant similarities in amino acid sequence exist between these polypeptides.     

Self-association and solubility of peptides: solvent-titration study of N alpha-protected C-terminal sequences of substance P

Self-association of N^α-protected peptides related to C-terminal sequences of substance P in methylene chloride was disrupted by adding increasing amounts of various polar organic solvents. This process was monitored by the disappearance of the amide I C?O stretching band (1630 cm^?1) of strongly intermolecularly H-bonded molecules in the irabsorption spectra. The effects induced by main-chain length, incorporation at position 9 of a residue promoting folding (α-aminoisobutyric acid), the nature of solvent, and peptide concentration were established. A corollary ¹H-nmr investigation provided detailed information on the NH protons involved in the self-association process as H-bonding donors. The increasing propensity to aggregate exhibited by these peptides is paralleled by a decrease in their solubility. The impact of these results on the synthesis of substance P short sequences is briefly outlined.     

Purification of a multiphosphorylated peptide from canine cardiac myosin heavy chains labeled in tissue culture

Partial acid hydrolysis of canine cardiac myosin heavy chains labeled with [³²P]orthophosphate in myocardial cell culture yielded a peptide having a molecular weight between 700 and 1500 and containing phosphothreonine and phosphoserine. The phosphate-rich peptide of myosin heavy chains produced by partial acid hydrolysis was purified first by Sephadex gel filtration, followed by elution with a gradient of formic acid from a Dowex ion-exchange chromatograph. Further identification of the multiphosphorylated peptide was made using high voltage electrophoresis and amino acid analyses. The data described here demonstrate that partial acid hydrolysis (time dependent) can be used to produce partially acid-stable peptides in a good yield.     

Fatty Acid Induced Leaking of Organic Compounds from Boletus variegatus

Addition of octanoic acid (2· 10^-3M) to the suspending medium (final pH 4.85) of Boletus variegatus mycelium induced a marked leaking of UV absorbing substances from the cells. The material had an absorption maximum at 260 nm, a minimum at 240 nm, and the absorption ratios 250: 260 and 280:260 were 0.81 and 0.49. The material released immediately after addition of the acid consisted mainly of low molecular weight substances. These substances, listed according to decreasing rates of leaking, were identified as pentoses, pentosephosphates, nucleosides, and mono- and di-nucleotides. Also, purine and pyrimidine bases were released at this early stage of treatment. After 90 minutes' treatment, an outflux of oligoribonucleotides was observed. The oligoribonucleotides did not occur as single substances, but were forming complexes with peptides. Minor amounts of ribonucleic acid were also leaking out from the cells. Deoxyribose containing substances were never observed in the filtrates. The compounds were subjected to enzymatic degradation after they had left the cells. This was shown by a marked increase with time of inorganic phosphorus, pentose/pentosephosphates, and nucleosides in the filtrate. The leaking of low molecular weight substances immediately after acid addition is correlated to seriously reduced growth. However, the growth was wholly restored after a three days' lag period. On the other hand, when considerable amounts of oligoribonucleotide peptides had been released from the cells, growth could not be re-established.     

Differences in iodinated peptides and thyroid hormone formation after chemical and thyroid peroxidase-catalyzed iodination of human thyroglobulin

The distribution of iodine among the polypeptides of human goiter thyroglobulin (Tg) was examined. Tg was iodinated in vitro with ¹³¹I to levels of 2 to 84 gram atoms (g.a.)/mol using thyroid peroxidase (TPO) or a chemical iodination system. The samples were reduced, alkylated, and subjected to sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Two low-molecular-weight peptides appeared preferentially in radioautograms of the sodium dodecyl sulfate (SDS) gels of TPO-iodinated samples. Iodination of these peptides increased sharply in the TPO-treated Tg as the level of total iodine/ molecule rose. Radioiodine was incorporated into these same gel regions in the chemically treated Tg, but only after much higher levels of total iodination were reached. Differences in iodoamino acid distribution were also noted between the chemically and enzymatically iodinated thyroglobulins. In the chemically iodinated samples, little thyroxine (T₄) was synthesized, even at high iodine levels. In the TPO-treated samples only small amounts of T₄ were seen below 14 g.a. total I/mol, while at or above that level of iodination T₄ formation increased sharply. To examine the coupling process, Tg was chemically iodinated, excess I^? removed, and the samples treated with TPO and a H₂O₂-generating system in the absence of iodide. Radioautograms obtained from SDS-polyacrylamide gels of reduced and alkylated protein from such coupling assays showed an increase in the level of iodine in the low-molecular-weight peptides after TPO treatment. Thyroxine production also increased with TPO treatment. The addition of free DIT (a known coupling enhancer) to the [¹³¹I]Tg/TPO incubation increased both the production of T₄ and the amount of iodine in the smaller polypeptides. Two-dimensional maps prepared from CNBr-digested TG showed differences between the coupled and uncoupled samples. Our observations confirm the importance of the lowmolecular-weight peptides derived from Tg in thyroid hormone synthesis. At total iodine levels above 14 g.a./mol Tg in enzymatically treated samples there is selective incorporation of iodine into both the low-molecular-weight polypeptides and into thyroid hormone.