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D Barra

Publications and source records attributed to D Barra.

At least 55 records · Page 3Linked to original sources
PubMed1994

Human acylpeptide hydrolase. Studies on its thiol groups and mechanism of action.

The presence of a cysteine residue(s) near the active site of acylpeptide hydrolase was suggested by inactivation of the enzyme with sulfhydryl-modifying agents and by the substantial protection against inactivation afforded by the competitive inhibitor acetylmethionine. 5,5'-dithiobis-(2-nitrobenzoate) titrations of the native and the denatured enzyme together with analysis for cysteic acid after performic acid oxidation showed that the enzyme contained 12 free SH groups and three disulfide bonds/monomer. Chemical modification with radiolabeled iodoacetamide led to the labeling of Cys-30 and Cys-64 suggesting that one or both of these Cys residues are close to the active site. Modification of one or both of them probably inhibits the enzyme either because of a distortion of the active site or because the adducts present a barrier to the efficient diffusion of substrates into and products out of the active site. Studies on the mechanism of action of acylpeptide hydrolase have employed p-nitrophenyl-N-propyl carbamate as a potent active site-directed inhibitor. Enzyme inactivation, which follows pseudo first-order kinetics, is diminished by the competitive inhibitor acetylmethionine. The inhibited enzyme slowly regains activity at a rate that is increased in the presence of the nucleophile hydroxylamine. A general mechanism involving an acyl-enzyme intermediate is supported by evidence for the formation of acetyl-alanyl hydroxamate during hydrolysis of acetyl-alanine p-nitroanilide in the presence of hydroxylamine. The effect on Vmax and Km during this reaction indicate that hydrolysis of the acyl-enzyme intermediate is rate-limiting.

Amino Acid Sequence↗
PubMed1994

Antimicrobial peptides from skin secretions of Rana esculenta. Molecular cloning of cDNAs encoding esculentin and brevinins and isolation of new active peptides.

Three cytolytic peptides, termed brevinin-1E, brevinin-2E, and esculentin, were isolated from skin secretions of the European frog Rana esculenta (Simmaco, M., Mignogna, G., Barra, D., and Bossa, F. (1993) FEBS Lett. 324, 159-161). Nucleotide sequence analysis of cDNAs coding for the corresponding precursors revealed that in all of them a single copy of the sequence of the mature peptide is present preceded by a dibasic cleavage site and followed by a stop codon. The signal peptides of these precursors show a clear homology to the corresponding region of the precursor of dermorphin, a neuropeptide occurring in the skin of amphibians of the subfamily Phyllomedusinae. Ten new peptides, ranging in size from 24 to 46 residues, all possessing an intramolecular disulfide bridge located at the carboxyl-terminal end, were isolated from skin secretions of R. esculenta. These peptides can be grouped into four subfamilies on the basis of their distinctive structural and/or functional properties. All of these new peptides have antimicrobial and/or hemolytic activities typical for the respective subfamily. In addition, we demonstrate that esculentin-1 also inhibits the growth of Pseudomonas aeruginosa, Candida albicans, and Saccharomyces cerevisiae.

Amino Acid Sequence↗
PubMed1994

In vivo incorporation of copper into the iron-exchangeable and manganese-exchangeable superoxide dismutase from Propionibacterium shermanii. Amino acid sequence and identity of the protein moieties.

Propionibacterium shermanii, an aerotolerant anaerobe, produces an iron-containing or a manganese-containing superoxide dismutase, depending on the metal supplied in the culture medium [Meier, B., Barra, D., Bossa, F., Calabrese, L. & Rotilio, G. (1982) J. Biol. Chem. 257, 13977-13980]. In this study, we demonstrate in vivo incorporation of copper into an active superoxide-dismutase protein when iron and manganese are absent from the growth medium. Superoxide dismutases containing either iron, manganese or copper were isolated from P. shermanii, their complete amino acid sequences were determined and the identity of their protein moieties was established. The polypeptide chain is made up of 201 amino acid residues, corresponding to a molecular mass of 22.6 kDa. From sedimentation equilibrium experiments, the native protein shows a molecular mass of approximately 86 kDa and therefore consists of four identical subunits. The primary structure was compared with the structure of other Fe-superoxide dismutases and Mn-superoxide dismutases, in particular those possessing a strict metal cofactor specificity.

Amino Acid Sequence↗
PubMed1994

Selective oxidation of methionyl residues in the human recombinant secretory leukocyte proteinase inhibitor. Effect on the inhibitor binding properties.

Binding of the human recombinant secretory leukocyte proteinase inhibitor (SLPI) [native and with the methionyl residues at positions 73, 82, 94 and 96 of domain 2 oxidized to the sulfoxide derivative (Met(O) SLPI)] to bovine alpha-chymotrypsin (alpha-chymotrypsin) [native and with the Met192 residue converted to the sulfoxide derivative (Met(O) alpha-chymotrypsin)] as well as to native bovine beta-trypsin (beta-trypsin), which does not contain methionyl residues, has been investigated between pH 4.0 and 8.0, and between 10.0 degrees C and 30.0 degrees C, from thermodynamic and/or kinetic viewpoints. By increasing the number of oxidized methionyl residues present at the proteinase:inhibitor contact interface (from 0 to 3), the adducts investigated are increasingly destabilized and the relaxation time of the complexes into conformers less stable is enhanced. On the other hand, the selective oxidation of methionyl residues of SLPI and alpha-chymotrypsin, by reaction with chloramine T, does not affect the proteinase inhibition recognition mechanism. Therefore, even though conformational changes may occur in the conversion of native SLPI and native alpha-chymotrypsin to their Met(O) derivatives, a localized steric hindrance can be considered as the main structural determinant accounting for the reported results.

Amino Acid Sequence↗
PubMed1994

Binding of native and [homoserine lactone-52]-52,53-seco-bovine basic pancreatic trypsin inhibitor (Kunitz inhibitor) to porcine pancreatic beta-kallikrein-B and bovine alpha-chymotrypsin: thermodynamic study.

Values of the association equilibrium constant (Ka) for the binding of the native and of the cyanogen bromide-cleaved bovine basic pancreatic trypsin inhibitor (native BPTI and [Hse lactone-52]-52,53-seco-BPTI, respectively) to neuraminidase-treated porcine pancreatic beta-kallikrein-B (kallikrein) and bovine alpha-chymotrypsin (chymotrypsin) have been determined between pH 4.0 and 9.0, at 20.0 degrees C. Over the whole pH range explored, native BPTI and [Hse lactone-52]-52,53-seco-BPTI show the same affinity for kallikrein. On the other hand, the affinity of [Hse lactone-52]-52,53-seco-BPTI for chymotrypsin is higher, around neutrality, than that found for native BPTI by about one order of magnitude, converging in the acidic pH limb. The simplest mechanism accounting for the observed data implies that, on lowering the pH from 9.0 to 4.0, (i) the decrease in affinity for the binding of native BPTI to kallikrein and chymotrypsin, as well as for the association of [Hse lactone-52]-52,53-seco-BPTI to kallikrein, reflects the acidic pK shift, upon inhibitor association, of a single ionizing group; and (ii) the decrease of Ka values for [Hse lactone-52]-52,53-seco-BPTI binding to chymotrypsin appears to be modulated by the acidic pK shift, upon inhibitor association, of two non-equivalent proton-binding residues. On the basis of the stereochemistry of the serine proteinase/inhibitor contact region(s), these data indicate that long-range structural changes in [Hse lactone-52]-52,53-seco-BPTI are energetically linked to the chymotrypsin:inhibitor complex formation. This observation represents an important aspect for the mechanism of molecular recognition and regulation in BPTI.

Animals↗
PubMed1994

The amino acid sequence of glutamate dehydrogenase from Pyrococcus furiosus, a hyperthermophilic archaebacterium.

The complete amino acid sequence of glutamate dehydrogenase from the archaebacterium Pyrococcus furiosus has been determined. The sequence was reconstructed by automated sequence analysis of peptides obtained after cleavage with cyanogen bromide, Asp-N endoproteinase, trypsin, or pepsin. The enzyme subunit is composed of 420 amino acid residues yielding a molecular mass of 47,122 D. In the recently determined primary structure of glutamate dehydrogenase from another thermophilic archaebacterium, Sulfolobus solfataricus, the presence of some methylated lysines was detected and the possible role of this posttranslational modification in enhancing the thermostability of the enzyme was discussed (Maras, B., Consalvi, V., Chiaraluce, R., Politi, L., De Rosa, M., Bossa, F., Scandurra, R., and Barra, D. (1992), Eur. J. Biochem. 203, 81-87). In the primary structure reported here, such posttranslational modification has not been found, indicating that the role of lysine methylation should be revisited. Comparison of the sequence of glutamate dehydrogenase from Pyrococcus furiosus with that of S. solfataricus shows a 43.7% similarity, thus indicating a common evolutionary pathway.

Amino Acid Sequence↗
PubMed1994

[D-Leu2]deltorphin, a 17 amino acid opioid peptide from the skin of the Brazilian hylid frog, Phyllomedusa burmeisteri.

A novel 17 amino acid peptide, having a D-leucine in position 2 of its sequence, has been isolated from methanol extracts of the skin of the Brazilian frog, Phyllomedusa burmeisteri. The sequence of the peptide is: Tyr-D-Leu-Phe-Ala-Asp-Val-Ser-Thr-Ile-Gly-Asp-Phe-Phe-His-Ser-Ile-NH2. It displays a poor affinity for delta-opioid binding sites, both in the periphery and in the central nervous system. However, the shorter synthetic amidated analogue (1-10) possess both on the central and peripheral delta binding sites an agonistic potency equalling in affinity and exceeding in selectivity that of the enkephalins. The shorter amidated analogue (1-7) is virtually inactive on opioid binding sites in the periphery, but displays a clear-cut affinity for both delta and mu binding sites on rat brain membranes. To date six different D-amino acid residues have been found, always in position 2 of the sequence, in as many as 11 natural peptide molecules of animal origin.

Amino Acid Sequence↗
PubMed1993

Novel antimicrobial peptides from skin secretion of the European frog Rana esculenta.

Three antimicrobial peptides were isolated from skin secretion of the European frog, Rana esculenta. Two of them show similarity to brevinin-1 and brevinin-2, respectively, two antimicrobial peptides recently isolated from a Japanese frog [Morikawa, N., Hagiwara, K. and Nakajima, T. (1992) Biochem. Biophys. Res. Commun. 189, 184-190]. The third one, named esculentin, is 46 residues long and represents a different type of peptide. All these peptides have as a common motif an intramolecular disulfide bridge located at the COOH-terminal end. The peptides from R. esculenta show distinctive antibacterial activity against representative Gram-negative and Gram-positive bacterial species. In particular, esculentin is the most active against Staphylococcus aureus, and has a much lower hemolytic activity.

Amino Acid Sequence↗
PubMed1993

Selective oxidation of Met-192 in bovine alpha-chymotrypsin. Effect on catalytic and inhibitor binding properties.

Catalytic and inhibitor binding properties of bovine alpha-chymotrypsin, in which the Met-192 residue has been converted by treatment with chloramine T to the sulfoxide derivative (Met(O)192 alpha-chymotrypsin), have been examined relative to the native enzyme (alpha-chymotrypsin), between pH 4.5 and 8.0 (mu = 0.1), and/or 5.0 degrees C and 40.0 degrees C. Values of kcat, k+2 and/or k+3 for the hydrolysis of all the substrates examined (i.e., tMetAcONp, ZAlaONp, ZLeuONp, ZLysONp and ZTyrONp) catalyzed by native and Met(O)192 alpha-chymotrypsin are similar, as well as values of Km for the hydrolysis of ZLeuONp, ZLysONp and ZTyrONp. On the other hand, Ks and Km values for the hydrolysis of ZAlaONp and tMetAcONp are decreased by about 5-fold. Met-192 oxidation does not affect the kinetic and thermodynamic parameters for the (de)stabilization of the complex formed between the proteinase and the bovine basic pancreatic trypsin inhibitor. On the other hand, the recognition process between between alpha-chymotrypsin and the recombinant proteinase inhibitor eglin c from the leech Hirudo medicinalis is influenced by the oxidation event. Considering known molecular models, the observed catalytic and inhibitor binding properties of native and Met(O)192 alpha-chymotrypsin were related to the inferred stereochemistry of the proteinase-substrate and proteinase-inhibitor contact region(s).

Animals↗
PubMed1993

The amino acid sequence of glutathione transferase from Proteus mirabilis, a prototype of a new class of enzymes.

The complete amino acid sequence of glutathione transferase from Proteus mirabilis was determined. The sequence was reconstructed by analysis of peptides obtained after cleavage by trypsin, Glu-C and Asp-N endoproteinases. The enzyme subunit is composed of 203 amino acid residues corresponding to a molecular mass of 22856 Da. Comparison of this sequence with other known primary structures of the corresponding enzyme from different sources shows a low level of identity (17-26%) with only seven conserved residues in all the sequences considered. This novel glutathione transferase could represent the prototype of a new class, possibly including other bacterial enzymes.

Amino Acid Sequence↗
PubMed1993

Antibacterial and haemolytic peptides containing D-alloisoleucine from the skin of Bombina variegata.

A family of bombinin-related peptides is present in the skin of Bombina variegata. These peptides contain 27 residues with Gly as N-terminus and display antimicrobial activity. From sequence analysis of the cDNAs encoding for the corresponding peptide precursors, the presence of a novel 20-residue peptide with Ile as N-terminus was predicted. We have now purified a family of hydrophobic peptides named H1-H5, whose sequences correspond to the predicted peptide with some variability in positions 1, 2 and 8. In particular, H3-H5 contain a D-alloisoleucine residue in the second position. All these peptides display antibacterial and haemolytic activity.

Amino Acid Sequence↗
PubMed1993

Pharmacological studies of 'sapo' from the frog Phyllomedusa bicolor skin: a drug used by the Peruvian Matses Indians in shamanic hunting practices.

The dried skin secretion from Phyllomedusa bicolor, 'sapo', is used by the Matses Indians of the Northern Peru, in shamanic rites mainly designed to improve luck in hunting. When rubbed into burned, exposed areas of the skin, the drug causes the prompt appearance of violent peripheral gastrointestinal and cardiovascular effects soon followed by remarkable central effects (increase in physical strength, heightening of senses, resistance to hunger and thirst, exalted capacity to face stress situations). All the peripheral and most of the central effects of 'sapo' can be ascribed to the exceptionally high content of the drug (up to 7% of its weight) in potently active peptides, easily absorbed through the burned, inflamed areas of the skin. The concentration in 'sapo' of the single peptides (phyllocaerulein, phyllomedusin, phyllokinin, demorphins and deltorphins) has been determined by bioassay, and peptide contents were correlated with the different symptoms of the 'sapo' intoxication.

Amino Acid Sequence↗
PubMed1993

Sequence studies on pyridoxal phosphate-dependent enzymes.

The amino acid sequences of two pyridoxal phosphate-dependent enzymes, namely glutamate decarboxylase and 4-aminobutyrate aminotransferase, were solved by a combination of direct protein sequencing and cDNA sequencing. In the case of glutamate decarboxylase from Escherichia coli, correct ordering of three internal peptides was achieved by sequencing a fragment of DNA generated by PCR. In the case of 4-aminobutyrate aminotransferase from pig liver, chemical studies on the reaction of the enzyme with a suicide inhibitor allowed a detailed description of the mechanism of inactivation and collection of partial sequence information on the protein. The sequence of the protein was completely reconstructed after analysis of further peptide fragments derived by proteolytic and chemical cleavages, with the help of the information from the cDNA-deduced sequence of pig brain 4-aminobutyrate aminotransferase performed by another group (Kwon, Park and Churchich [1992] J. Biol. Chem. 267, 7215-7216).

4-Aminobutyrate Transaminase↗
PubMed1992

Protein structure of pig liver 4-aminobutyrate aminotransferase and comparison with a cDNA-deduced sequence.

The amino acid sequence of pig liver 4-aminobutyrate aminotransferase has been determined by gas-phase sequencing of proteolytically derived peptide fragments. The sequence differs substantially from that predicted for the same enzyme on the basis of the sequence of cDNA derived from pig brain in recently published work [Kwon, O., Park, J. & Churchich, J. E. (1992) J. Biol. Chem. 267, 7215-7216]. Apart from a few minor differences, the two sequences are completely different in the segment of protein comprising the 36 residues at positions 107-142. Insertion of a cytosine between bases 402 and 403 in the cDNA sequence, together with deletion of the guanine at position 510, results in a DNA sequence which predicts exactly the amino acid sequence determined by peptide analysis in the present work. The mammalian enzyme has approximately 44% sequence identity with the same enzyme from two unicellular eukaryotes (Saccharomyces cerevisiae, Aspergillus nidulans) and 22% identity with that from Escherichia coli.

4-Aminobutyrate Transaminase↗
PubMed1992

Chemical modification of human placental glutathione transferase by pyridoxal 5'-phosphate.

Incubation of GST pi from human placenta with 8 mM PLP resulted in a rapid loss of activity during the first 10 min, concomitant with a Schiff base formation. This inactivation was probably due to the formation of a reversible adduct between PLP and the enzyme. After sodium borohydride treatment this adduct was reduced and stabilized. Stoichiometry and peptide isolation studies showed that three lysine residues were modified during reaction of GST and PLP. Protection of the enzyme against inactivation was achieved in the presence of 4 mM GSH suggesting that at least one lysyl residue is associated with the substrate binding site. Peptide mapping by digesting the enzyme with trypsin revealed that lysine shielded by GSH is Lys-127. Our results suggest that this residue may play an important role in enzymatic activity.

Amino Acid Sequence↗