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D Barra

Publications and source records attributed to D Barra.

At least 127 records · Page 7Linked to original sources

The primary structure of ornithine aminotransferase. Identification of active-site sequence and site of post-translational proteolysis.

Tentative assignments of functional residues in rat liver mitochondrial ornithine aminotransferase have recently been made using the amino acid sequence deduced from a cDNA clone [(1985) J.Biol.Chem. 260, 12993-12997]. Partial sequences obtained using the pure mature protein demonstrate that one of these assignments, that of Lys 292 as the residue that binds the coenzyme pyridoxal phosphate, is correct. However, the identification of the Glu 34-Gln 35 bond as the site of post-translational proteolysis is in error. This cleavage occurs instead at Ala 25-Thr 26.

Amino Acid Sequence↗

Thiol proteins in chromatin.

Total half-cystine residues in proteins of pig liver chromatin have been measured. About half of them are present in the reduced state. Thiol groups of non-histone chromatin proteins, which amount to about 40 nmol/mg of protein, are preferentially located in chromatin fragments which are more easily solubilised either by DNAse I or by DNAse II. The data obtained are compatible with an involvement of SH and SS groups in chromatin structure and function.

Amino Acids↗

The complete amino acid sequences of cytosolic and mitochondrial aspartate aminotransferases from horse heart, and inferences on evolution of the isoenzymes.

We report here the complete amino acid sequences of the cytosolic and mitochondrial aspartate aminotransferases from horse heart. The two sequences can be aligned so that 48.1% of the amino acid residues are identical. The sequences have been compared with those of the cytosolic isoenzymes from pig and chicken, the mitochondrial isoenzymes from pig, chicken, rat, and human, and the enzyme from Escherichia coli. The results suggest that the mammalian cytosolic and mitochondrial isoenzymes have evolved at equal and constant rates whereas the isoenzymes from chicken may have evolved somewhat more slowly. Based on the rate of evolution of the mammalian isoenzymes, the gene-duplication event that gave rise to cytosolic and mitochondrial aspartate aminotransferases is estimated to have occurred at least 10(9) years ago. The cytosolic and mitochondrial isoenzymes are equally related to the enzyme from E. coli; the prokaryotic and eukaryotic enzymes diverged from one another at least 1.3 X 10(9) years ago.

Amino Acid Sequence↗

The primary structure of mitochondrial aspartate aminotransferase from human heart.

The complete amino acid sequence of the mitochondrial aspartate aminotransferase (L-aspartate:2-oxoglutarate aminotransferase, EC 2.6.1.1) from human heart has been determined based mainly on analysis of peptides obtained by digestion with trypsin and by chemical cleavage with cyanogen bromide. Comparison of the sequence with those of the isotopic isoenzymes from pig, rat and chicken showed 27, 29 and 55 differences, respectively, out of a total of 401 amino acid residues. Evidence for structural microheterogeneity at position 317 has also been obtained.

Amino Acid Sequence↗

Primary structure and antiproteolytic activity of a Kunitz-type inhibitor from bovine spleen.

The amino acid sequence of protease inhibitor II, previously isolated from bovine spleen, has been completely elucidated and reveals a high homology (approximately 90%) with that of bovine pancreatic trypsin inhibitor (BPTI), the well-known Kunitz inhibitor. The secondary and tertiary structure of this new inhibitor appears similar to that of BPTI. Whereas its affinity for bovine trypsin, chymotrypsin, and trypsinogen is almost identical to that of BPTI, the affinity for porcine pancreatic kallikrein is decreased, as expected on the basis of the amino acid substitutions. Analysis of the pH dependence of the affinity constant confirms the previous assignment of the ionizable groups, whose pK values are perturbed on complex formation, to kallikrein and not to the inhibitor molecule.

Amino Acid Sequence↗

Primary structure of porcine Cu,Zn superoxide dismutase.

The complete amino acid sequence of Cu,Zn superoxide dismutase from porcine erythrocytes has been determined. Comparison of the sequence with that of the bovine enzyme shows an overall high degree of homology with conservation of the crucial residues and the presence of two regions prone to variation. In one of these hypervariable regions the insertion of one residue with respect to the bovine enzyme and evidence of structural microheterogeneity has been observed. On the basis of the three-dimensional structure of the bovine enzyme no obvious relationship is apparent between a specific amino acid replacement and the unique pH-dependence pattern of the activity of the porcine enzyme.

Amino Acid Sequence↗

Amino acid sequence of the cooperative homodimeric hemoglobin from the mollusc Scapharca inaequivalvis and topology of the intersubunit contacts.

The dimeric hemoglobin (HbI) from Scapharca inaequivalvis is highly homologous to the other known dimeric Acid hemoglobins. The sequence has a distinctive hydrophobicity profile in the region corresponding to the E and F helices with respect to both the hemoglobin and myoglobin chains from vertebrates due to the presence of several additional hydrophobic residues. The characteristic topology of the E and F helices is conserved in all the known sequences of Arcid hemoglobins including that of the so-called alpha chain of the tetrameric component from Anadara trapezia. The rationale for this conservation lies in the unusual assembly of Arcid hemoglobins where the E and F helices are involved in the interdimeric contact. It is suggested that the extra hydrophobic residues play a major role in the assembly of the basic dimeric unit in these hemoglobins.

Allosteric Regulation↗

An essential arginine residue at the binding site of pig kidney 3,4-dihydroxyphenylalanine decarboxylase.

Pig kidney 3,4-dihydroxyphenylalanine (Dopa) decarboxylase is inactivated by the arginine-specific reagent phenylglyoxal. Under these experimental conditions, the reaction follows pseudo-first-order kinetics with a second-order rate constant of 25 m-1 min-1. Holo- and apo-enzyme were inactivated at the same rate. However, inactivation seems to be related to modification of 1 and 2 arginyl residues per mol of holo- and apo-enzyme, respectively. Only one of these two residues was essential to decarboxylase activity of the enzyme. Phenylglyoxal-modified apo-Dopa decarboxylase retained the capacity to bind pyridoxal-P. Neither this reconstituted species nor the phenylglyoxal-modified holoenzyme were able to form Schiff base intermediates with aromatic amino acids in L and D forms. These data together with protection experiments suggest that the susceptible arginine residue in holoenzyme may somehow perturb the substrate binding site. However, unlike in other pyridoxal-P enzymes, this critical arginine in Dopa decarboxylase does not seem to behave as an anionic recognition site for the phosphate group of the coenzyme or the carboxy group of the substrate. It is speculated that this guanidyl group could function in hydrogen bonding of substrate side chain.

Animals↗

Rohdei-litorin: a new peptide from the skin of Phyllomedusa rohdei.

The bombesin-litorin family of peptides is characterized by the common amino acid sequence-Gly-His-X-Met-NH2 at the C-terminus, where X is a hydrophobic or aromatic residue. A new member of this family, rohdei-litorin, has been isolated from amphibian skin and its structure shown to be: Glp-Leu-Trp-Ala-Thr-Gly-His-Phe-Met-NH2. This new peptide displayed a greater affinity than other members of the family for rat urinary bladder receptors. A litorin-like peptide, with high affinity for this kind of receptor, has already been described in mammalian spinal cord and named neuromedin B. Rohdei-litorin shares with neuromedin B the entire C-terminal octrapeptide and may be considered the amphibian counterpart of this mammalian neuropeptide.

Amino Acid Sequence↗

Identity of the metal ligands in the manganese- and iron-containing superoxide dismutases.

Alignment of the amino acid sequence of peptides obtained following digestion of Photobacterium leiognathi iron superoxide dismutase with the known sequence of Bacillus stearothermophilus manganese superoxide dismutase shows that the residues found to form ligands to the manganese are conserved in the iron enzyme. This indicates that the metal ligands in both proteins are identical.

Amino Acid Sequence↗

Assay of pyroglutamyl aminopeptidase by high-performance liquid chromatography and its use in peptide sequencing.

Assay of pyroglutamyl aminopeptidase by HPLC methodology allows determination of the kinetic parameters of the enzyme for a variety of natural peptide substrates. Moreover, by this method it is possible both to evaluate the extent of the enzymatic reaction by determining the amount of pyrrolidone carboxylic acid released and to obtain the unblocked peptide for structural and functional characterization.

Amino Acid Sequence↗

Protease inhibitors from the parasitic worm Parascaris equorum.

Two proteic inhibitors (I and II) of serine proteases have been purified from the parasitic worm Parascaris equorum by affinity chromatography on immobilized trypsin followed by preparative electrophoresis. They have an apparent relative molecular mass of 9000 and 7000 as determined by gel filtration, a slightly acid isoelectric point (5.5 and 6.1) and a similar amino acid composition. Both inhibitors lack serine, methionine and tyrosine. They bind bovine trypsin extremely strongly with an association constant, Ka, larger than 10(9) M-1, and form a 1:1 complex with this protease. The Ka values for the binding to bovine chymotrypsin are approximately 3.3 X 10(8) M-1 (inhibitor I) and approximately 2 X 10(6) M-1 (inhibitor II). Inhibitor I interacts also with porcine elastase (Ka approximately 5 X 10(7) M-1), while inhibitor II is inactive towards this enzyme.

Animals↗

The primary structure of human liver manganese superoxide dismutase.

The complete amino acid sequence of manganese superoxide dismutase from human liver was determined. The sequence was deduced following characterization of the peptides obtained from tryptic, chymotryptic, and Staphylococcus aureus digests of the apoprotein. Chemical cleavage with dimethyl sulfoxide-hydrobromic acid was also carried out. The amino acid sequence listed below is made up of 196 amino acids and the two subunit polypeptides in the native enzyme appear to be identical. No homology was observed with copper/zinc containing class of superoxide dismutase. Lys-His-Ser-Leu-Pro-Asp-Leu-Pro-Tyr-Asp-Tyr-Gly-Ala-Leu-Glu-Pro-His-Il e -Asn-Ala-Gln-Ile-Met-Gln-Leu-His-His-Ser-Lys-His-His-Ala-Ala-Tyr-Val-Asn -Asn-Leu-Asn-Val-Thr-Gln-Glu-Lys-Tyr-Gln-Glu-Ala-Leu-Ala-Lys-Gly-Asp-Val -Thr-Ala-Gln-Ile-Ala-Leu-Gln-Pro-Ala-Leu-Lys-Phe-Asn-Gly-Gly-Gly-His-Ile -Asn-His-Ser-Ile-Phe-Trp-Thr-Asn-Leu-Ser-Pro-Asn-Gly-Gly-Gly-Gln-Pro-Lys -Gly-Glu-Leu-Leu-Glu-Ala-Ile-Lys-Arg-Asp-Phe-Gly-Ser-Phe-Asp-Lys-Phe-Lys -Gln-Lys-Leu-Thr-Ala-Ala-Ser-Val-Gly-Val-Gln-Gly-Ser-Gly-Trp-Leu-Gly-Phe -Asn-Lys-Gln-Arg-Gly-His-Leu-Gln-Ile-Ala-Ala-Cys-Pro-Asn-Gln-Asp-Pro-Leu -Gln-Gly-Thr-Thr-Gly-Leu-Ile-Pro-Leu-Leu-Gly-Ile-Asp-Val-Trp-Glu-His-Ala -Tyr-Tyr-Leu-Gln-Tyr-Lys-Asn-Val-Arg-Pro-Asp-Tyr-Leu-Lys-Ala-Ile-Trp-Asn -Val-Ile-Asn-Trp-Glu-Asn-Val-Thr-Glu-Arg-Tyr-Met-Ala-Cys-Lys-Lys.

Amino Acid Sequence↗

Partial amino-acid sequence and cysteine reactivities of cytosolic aspartate aminotransferase from horse heart.

Cytosolic aspartate aminotransferase (L-aspartate:2-oxoglutarate aminotransferase, EC 2.6.1.1) from horse heart has five cysteine residues, two of which can be titrated with 5,5'-dithiobis(2-nitrobenzoid acid) in the native enzyme with no impairment of catalytic activity. The rate of modification is unaffected by the presence of substrates. Reaction with N-ethylmaleimide leads to loss of catalytic activity, the rate of inactivation being increased by the presence of substrates. Peptides containing 361 amino-acid residues (about 88% of the total number in the protein) have been isolated and aligned by comparison with the known sequence of the isotopic isoenzyme from pig heart. In the regions compared, 342 of the residues are identical. Hence, assuming that those regions are representative of the whole, then the cytosolic isoenzymes from horse and from pig have about 95% identity of structure. Uniquely among the mammalian cytosolic aspartate aminotransferases so far examined, the enzyme from horse heart is acetylated at the N-terminus.

Amino Acid Sequence↗

Structural and genetic relationships between cytosolic and mitochondrial isoenzymes.

The most common type of genetic relationship between cytosolic and mitochondrial isoenzymes will probably be found to be divergent evolution from a common ancestral form. This is firmly established for the aspartate aminotransferases and less directly so in other cases. The two isoenzymes of aspartate aminotransferase have evolved at roughly equal rates at the level of total amino acid sequence but certain limited surface regions of the mitochondrial form have been much more highly conserved than corresponding regions in the cytosolic protein; these regions probably play a role in topogenesis of the mitochondrial isoenzyme. It is of interest that nearly all mitochondrial proteins are initially synthesised as precursors of molecular weight greater than the mature forms. In the case of aspartate aminotransferase, and possibly of other such isoenzymes, the N-terminus of the mature protein is nearly coincident with that of the cytosolic isoenzyme. Hence during evolution either the gene for the mitochondrial isoenzyme has gained an extra coding region for this N-terminal extension or, less likely, the structural gene for the cytosolic form has suffered a sizeable terminal deletion. Cytosolic and mitochondrial superoxide dismutases have not shared a common ancestral form as shown by the fact that their primary structures are completely unrelated. On the other hand, the mitochondrial and prokaryotic enzymes are clearly related. There is now, however, evidence to suggest that some prokaryotes possess a copper/zinc enzyme related to the eukaryotic cytosolic form. Hence the possibility arises that primitive prokaryotes possessed both proteins. The copper/zinc superoxide dismutase has been retained in the cytosol of eukaryotic cells and a few bacterial species.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗