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Biomedical subjects

D Barra

Publications and source records attributed to D Barra.

At least 91 records · Page 5Linked to original sources
PubMed1991

Assessment of sequence features in internal regions of proteins.

Determination of amino acid replacements or assessment of sequence features localized in internal regions of natural or genetically engineered proteins can be performed in some cases with the expenditure of a minimum amount of work and protein material. The procedure requires fragmentation of a protein sample by a chemical or enzymatic method: one of the fragments should include the sequence tract under investigation, suitably preceded by one or more prolyl residues. Classical Edman degradation can be performed on the whole mixture of fragments, thus avoiding the rate-limiting step of peptide purification. Sequence data become readable after performance of reaction with o-phthalaldehyde at the level of proline residues in the relevant peptide. Two specific cases illustrate the potentiality of the procedure.

Amino Acid Sequence↗
PubMed1990

A tetrameric iron superoxide dismutase from the eucaryote Tetrahymena pyriformis.

An iron-containing superoxide dismutase has been purified from the protozoan Tetrahymena pyriformis. It has a molecular weight of 85,000 and is composed of four subunits of equal size. The tetramer contains 2.5 g atoms of ferric iron. Visible absorption and electron spin resonance spectra closely resemble those of other iron-containing superoxide dismutases. The amino acid sequence of the iron superoxide dismutase was determined. Each subunit is made up of 196 residues, corresponding to a molecular weight of 22,711. Comparison of the primary structure with the known sequences of other iron-containing superoxide dismutases reveals a relatively low degree of identity (33-34%). However, a higher percentage identity is found with mammalian manganese-containing superoxide dismutases (41-42%). The amino acid sequence is discussed in consideration of residues that may distinguish iron from manganese or dimeric from tetrameric superoxide dismutases.

Amino Acid Sequence↗
PubMed1990

Identification of a highly reactive sulphydryl group in human placental glutathione transferase by a site-directed fluorescent reagent.

A fluorescent maleimide derivative, N-(4-anilino-1-naphthyl) maleimide (ANM), a specific probe for thiol groups, reacted with human placental glutathione transferase (GST, EC 2.5.1.18), causing a complete inactivation of the enzyme in a few minutes. The modified enzyme was denatured, alkylated and digested with (L-1-tosylamide-2-phenylethyl chloromethyl ketone)-trypsin. The tryptic digest was analysed by HPLC and a fluorescent peptide was obtained. The sequence of this peptide allowed us, by a comparison with a well known primary structure, to assign the position 47 to the most reactive cysteine of GST enzyme.

Amino Acid Sequence↗
PubMed1990

Purification and characterization of bioactive peptides from skin extracts of Rana esculenta.

The peptide fraction extracted by methanol from the skin of Rana esculenta, a species widely distributed in Western Europe, was investigated. The pharmacological activity found in the extract is attributable to the presence of authentic bradykinin, together with a shorter, partially active version of this molecule, des-Arg9-bradykinin. Also the bradykinin fragment 1-7 has been isolated, but it was inactive in our bioassay system. Moreover, a family of hydrophobic peptides has been purified and characterized, which appeared devoid of pharmacological activities when tested on smooth muscle preparations, but were provided with hemolytic activities.

Amino Acid Sequence↗
PubMed1990

Kunitz-type proteinase inhibitors in sheep and ox.

1. Four protein proteinase inhibitors, belonging to the Kunitz family, were isolated and purified from several sheep organs. 2. Their structural, functional and immunological properties were determined and compared to those of similar inhibitors purified from bovine organs. 3. The Kunitz-type isoinhibitors appear differently distributed in the two species: BPTI, which is the prevailing form in bovids, is found only in minute amounts in sheep organs. 4. The presence of multiple forms of these inhibitors in sheep is discussed on the basis of the same biosynthetic and post-translational processes proposed for the molecules of bovine origin.

Animals↗
PubMed1990

Hemoglobin from the antarctic fish Notothenia coriiceps neglecta. Amino acid sequence of the beta chain.

1. Notothenia coriiceps neglecta is a cold-adapted notothenioid teleost, widely distributed in the Antarctic waters. 2. In comparison with fishes from temperate waters, the blood of this teleost contains a reduced number of erythrocytes and concentration of hemoglobin; the erythrocytes contain two hemoglobins, Hb1 and Hb2, respectively accounting for approximately 90, and 5% of the total. 3. The two components differ by the alpha chain; the amino acid sequence of the beta chain in common to the two hemoglobins has been established, thus completing the elucidation of the primary structure of the major component Hb 1.

Amino Acid Sequence↗
PubMed1990

The amino acid sequence of a ribosome-inactivating protein from Saponaria officinalis seeds.

The complete primary structure of saporin SO-6, a ribosome-inactivating protein extracted from Saponaria officinalis seeds, has been determined. The sequence was reconstructed following purification and analysis of peptides obtained after digestion of the protein with different proteolytic agents. The protein is composed of 253 amino acids, corresponding to a molecular weight of 28,621 Da. Comparison of the primary structure of SO-6 with the sequence deduced from cDNA, shows amino acid substitutions in 11 positions, suggesting a tissue-related genetic variability. When the sequence of saporin is compared to those of two related proteins, ricin A chain and trichosanthin, a low degree of similarity (12%) is found; nevertheless some considerations about structure-function relationships and evolution of RIPs are possible.

Amino Acid Sequence↗
PubMed1989

Scapharca hemoglobins, type cases of a novel mode of chain assembly and heme-heme communication. Amino acid sequence and subunit interactions of the tetrameric component.

The sequences of the A and B chains of the Scapharca inaequivalvis tetrameric hemoglobin (HbII) are reported. They are homologous to the corresponding chains of other Arcid hemoglobins. Moreover, a comparison of the present data with the sequence of the S. inaequivalvis dimeric hemoglobin (HbI), for which high-resolution X-ray data are available, allows the identification of the residues that direct the assembly of the two components and of those that may be involved in the interdimeric contacts.

Allosteric Regulation↗
PubMed1989

Selective oxidation of methionine beta(55)D6 at the alpha 1 beta 1 interface in hemoglobin completely destabilizes the T-state.

When methionine beta(55)D6 in human hemoglobin is oxidized to its sulfoxide derivative, the modified protein appears to maintain most of the chemical and structural properties typical of the native protein. On the contrary, the functional behavior is drastically changed, being characterized (like that of the isolated chains) by high oxygen affinity (p50 = 0.47 torr in 0.1 M Tris (pH 7.3) + 0.1 M NaCl at 25 degrees C), absence of cooperativity (n = 1), and lack of Bohr effect. The complete destabilization of the T-state as a result of this modification is related to a perturbation of the alpha 1 beta 1 subunit interface, which in native hemoglobin remains static during the quaternary ligand-linked transition. Results also suggest that methionyl sulfoxide-containing hemoglobin, obtained under different conditions, assumes functionally different R-states, none of which is exactly comparable with that typical of the native protein.

Amino Acids↗
PubMed1989

Nitrite reductase from Pseudomonas aeruginosa: sequence of the gene and the protein.

The gene coding for nitrite reductase of Pseudomonas aeruginosa has been cloned and its sequence determined. The coding region is 1707 bp long and contains information for a polypeptide chain of 568 amino acids. The sequence of the mature protein has been confirmed independently by extensive amino acid sequencing. The amino-terminus of the mature protein is located at Lys-26; the preceding 25 residue long extension shows the features typical of signal peptides. Therefore the enzyme is probably secreted into the periplasmic space. The mature protein is made of 543 amino acid residues and has a molecular mass of 60,204 Da. The c-heme-binding domain, which contains the only two Cys of the molecule, is located at the amino-terminal region. Analysis of the protein sequence in terms of hydrophobicity profile gives results consistent with the fact that the enzyme is fully water soluble and not membrane bound; the most hydrophilic region appears to correspond to the c-heme domain. Secondary structure predictions are in general agreement with previous analysis of circular dichroic data.

Amino Acid Sequence↗
PubMed1989

Primary structure from amino acid and cDNA sequences of two Cu,Zn superoxide dismutase variants from Xenopus laevis.

A mixture of two different amino acid sequences was discovered in Cu,Zn superoxide dismutase purified from the amphibian Xenopus laevis. No N-terminal post-translational modification was found. The high number of substitutions in the sequence suggested that protein heterogeneity was a product of gene duplication. This was confirmed by isolation of two different cDNA clones. Nucleotide sequence analysis allowed the primary structure of the two peptide chains to be unambiguously assigned. The observed changes (19 in 150 residues) are distributed along the peptide chain to give similar protein net charges although substitutions of the same polarity and/or charge were the exception rather than the rule. The degree of diversity between the two Xenopus variants is comparable to that between mammalian sequences and shows that the putative increase of the rate of mutation for Cu,Zn superoxide dismutase at later evolution stages (Y. M. Lee et al., 1985, Arch. Biochem. Biophys. 241, 577-589; G. J. Steffens et al., 1986, Biol. Chem. Hoppe-Seyler 367, 1017-1024) is observed in amphibians. This is the first time complete sequences for Cu,Zn superoxide dismutase variants from the same organism have been found to be products of divergent genes and not simply allelic mutations.

Amino Acid Sequence↗
PubMed1989

Substitution of arginine for lysine 134 alters electrostatic parameters of the active site in shark Cu,Zn superoxide dismutase.

The complete amino acid sequence was determined for the Cu,Zn superoxide dismutase from the shark Prionace glauca. The active site region shows the substitution of an Arg for Lys at position 134, which is important for electrostatic facilitation of the diffusion of O2- to the catalytically active copper. This change may be related to observed alterations of electrostatic parameters of the enzyme (pK of the pH dependence of the enzyme activity, rate of inactivation by H2O2), although it preserves a high efficiency of dismutation at neutral pH.

Amino Acid Sequence↗
PubMed1989

The amino acid sequence of the alpha- and beta-chains of the two hemoglobins of the Antarctic fish Notothenia coriiceps neglecta.

The blood of the Antarctic fish Notothenia coriiceps neglecta contains two hemoglobins, Hb 1 and Hb 2, which have a beta-chain in common. We have elucidated the primary structure of the beta-chain (146 residues) and of the alpha-chains (142 residues) of the two hemoglobins. The two alpha-chains differ from each other by 51 residues; in comparison with globin sequences of temperate fishes, the alpha-chain of Hb 1 is more similar to that of bluefin tuna than to the alpha-chain of Hb 2 of the same species.

Amino Acid Sequence↗
PubMed1989

N-terminal region of Proteus mirabilis glutathione transferase is not homologous to mammalian and plant glutathione transferases.

The N-terminal amino acid sequence of glutathione transferase, Pm-GST-6.0, purified from Proteus mirabilis [(1988) Biochem. J. 255, 971-975] up to residue 38 and a comparative peptide fingerprint are reported. No obvious homology with the sequences of alpha, pi and mu classes of mammalian glutathione transferases as well as with those of plant glutathione transferases has been noted. These results suggest that the classification so far adopted for glutathione transferases cannot be extended to the bacterial enzyme.

Amino Acid Sequence↗
PubMed1989

The primary structure of rabbit liver mitochondrial serine hydroxymethyltransferase.

The complete amino acid sequence of mitochondrial serine hydroxymethyltransferase from rabbit liver was determined. The sequence was obtained from analysis of peptides isolated from chymotryptic, cyanogen bromide, and limited acid cleavages of the protein. The enzyme consists of four identical subunits, each of 475 residues, i.e. 8 residues shorter than the subunit of the corresponding cytosolic isoenzyme. The sequences of the two rabbit proteins are easily aligned, provided a gap of 5 residues near the amino terminus and a gap of 3 residues near the carboxyl terminus are included in the mitochondrial sequence. The overall degree of identity between the two isoenzymes is 61.9%, whereas the structural identity of each eukaryotic isoenzyme with the corresponding Escherichia coli enzyme is about 40%. The rabbit isoenzymes are about 70 residues longer than the E. coli enzyme, with one-half of these residues accounted for by insertions in both isoenzymes near their carboxyl terminus. Predictions of secondary structure and calculations of hydropathy profiles are also presented, suggesting an even more extensive degree of identity in the three-dimensional folding of the three proteins, in accord with the known similarity of their catalytic properties. Evidence was obtained for the existence of additional molecular forms of the mitochondrial protein, differing in the absence of some amino acid residues at the amino terminus of the polypeptide chain.

Amino Acid Sequence↗
PubMed1989

Tryptic cleavage as a probe of conformational differences between active and inactive forms of ornithine aminotransferase.

Treatment of ornithine aminotransferase with trypsin resulted in rapid and complete loss of enzyme activity in a process that coincided with a reduction in subunit Mr of about 3000. However, electrophoresis showed that a substantial proportion of the enzyme had not been digested. The component of the preparation of ornithine aminotransferase that was insusceptible to trypsin contained a naturally occurring but enzymically inactive form of the enzyme, and when this had been removed, the remaining fully active enzyme was completely digested. Irreversible inactivation with a substrate analogue made all of the enzyme insusceptible to trypsin. The hydrolyzed enzyme still underwent a very slow half-reaction with ornithine. Sequence analysis of the truncated protein, prepared by blotting from electrophoretic gels, showed that hydrolysis had occurred at peptide bond Lys26-Tyr27.

Amino Acid Sequence↗
PubMed1989

Amino acid sequence of alpha-chain of hemoglobin IV from trout (Salmo irideus).

The amino acid sequence of the alpha-chain of trout hemoglobin (Hb) IV is given, thus completing the primary structure of the hemoglobin component of trout's blood characterized by the Root effect. The trout Hb IV alpha-chain consists of 142 amino acid residues; comparison with the corresponding sequences from human and carp hemoglobins shows differences of 50.0 and 35.9%, respectively. A difference of 39.6% is found with the alpha-chain of trout Hb I, the other major hemoglobin component of trout blood, devoid of heterotropic effects.

Amino Acid Sequence↗