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H Cid

Publications and source records attributed to H Cid.

15 recordsLinked to original sources

Effects of pulp and paper mill effluents on the microplankton and microbial self-purification capabilities of the Biobío River, Chile.

Most studies focus on the ecotoxicity of pulp and paper mill effluents, rather than on how they affect the physicochemical and biological structure and the intrinsic ecological capabilities of the receiving watercourses. We investigated the impact of such effluents on the water quality, microplankton system and microbial self-purification capacity (degradation of polymeric organic compounds via extracellular enzymes) of the Biobío River in Chile. The physicochemical impact on the water quality was indicated by raised conductivity, by the pollution of the water body with nitrate, nitrite and soluble reactive phosphorus, by the appearance of tannin and lignin, and by the steady accumulation of inorganic and organic suspended matter (SPM) along the river. From the biological structure of the microplankton system, very low and declining concentrations of chlorophyll a and heterotrophic flagellate densities were determined. The pulp and paper mill effluents introduced high bacterial abundances and biomass concentrations into the river water. This reflects the effective use made of the abundantly available inorganic and organic nutrients within this industrial and municipal process water by bacteria adapted to these extreme environments, additionally supported by concomitant low grazing pressure derivable from low heterotrophic flagellate abundances. Indeed, in one section of the river affected by a pulp mill, the plant was found to significantly contribute to the self-cleaning capacity of the river. However, this elevated degradation capacity was not enough to compensate for the additionally discharged organic material which, together with the toxic effects of the paper plant effluents, significantly interferes with the ecological status of the Biobío River.

Animals↗

Active-site studies of enzymes by X-ray diffraction methods.

X-Ray diffraction is the only method currently available for the determination of the detailed three-dimensional structure of macromolecules. In this article, the principles behind the use of X-ray crystallography in the study of protein structure are presented. The results obtained in its application to several enzymes are discussed, as well as the limitations of the method.

Binding Sites↗

Interactions that regulate the helical fold in proteins.

Several factors that may contribute to the stabilization of the helical structure in proteins, detected in studies made on short synthetic peptides, have been reported. Some of them are: presence of alanine or leucine, ionic-pair bonding, stabilization of the helical dipole moment by appropriate charges at the helix N- and C-caps, and aromatic interactions of amino acids located at positions i, i + 4. An analysis of 54 helical structures from 12 proteins showed that all these stabilizing factors were also present in proteins, but the influence of any of them had a different weight, according to the distribution of the hydrophobic and hydrophilic amino acid residues in the helical sequence. The role of non-sequence depending interactions in helical stability, such as presence of disulfide bridges, or bonding of helical residues to substrate and/or cofactors, was also analysed.

Alanine↗

Partial DNA sequence of a beta-lactamase produced by a Shigella flexneri strain.

A probe was constructed by radioactive labelling, and enzymatically a DNA fragment of plasmid pMAM-1, which codes for a beta-lactamase in Shigella flexneri UCSM 129, was obtained by amplification of a small part of the gene using the polymerase chain reaction technique (PCR). Since previous published work indicated that this beta-lactamase was of the TEM type, the primers used to amplify the gene were two highly conserved DNA regions in all TEM beta-lactamases. A 500 bp DNA probe was obtained which, by hybridization assays, facilitated the identification of restriction fragments of the plasmid containing the beta-lactamase gene. Two DNA fragments were sequenced by the Sanger method adapted to the PCR technique, and the sequence obtained showed a 100% homology with beta-lactamases TEM-1, TEM-2, TEM-13 and TEM-19. An intragenic restriction site, detected for Pst I, suggested that there is only one copy of the beta-lactamase gene per plasmid copy.

Amino Acid Sequence↗

Characterization of a plasmid codifying the synthesis of a beta-lactamase produced by Shigella flexneri.

The resistance to beta-lactam antibiotics shown by a strain of Shigella flexneri was plasmid-coded. This plasmid, pMAM-1, when transferred to Escherichia coli K-12 by conjugation, presented the same molecular weight (100 kbp) and conferred the same high level of resistance to ampicillin in the transconjugant as in the wild type strains (MIC, 2048-4096). Restriction analysis of the plasmid in transconjugants revealed various restrictive sites to some endonucleases (i.e. Bam HI, Eco RI, Pst I, Nco I, Cla I, Sf I and Sau 3AI, Nhe and Hin dIII), and no restrictive sites at all for other endonucleases (such as Xho I, Dra I, Kpn I, and Sal I). Some restricted DNA fragments were appropriate for cloning and isolation of the beta-lactamase gene present in Shigella flexneri UCSF 129. This work provides the first step in this direction.

Ampicillin Resistance↗

Hydrophobicity and structural classes in proteins.

The bulk hydrophobic character for the 20 natural amino acid residues, has been obtained from a database of 60 protein structures, grouped in the four structural classes alpha alpha, beta beta, alpha + beta and alpha/beta. The hydrophobicity coefficients thus obtained are compared with Ponnuswamy's original values using scales normalized to average = 0.0 and standard deviation = 1.0. Even though most of the amino acid residues do not change their hydropathic character in the different structural classes, their behaviour suggests the convenience that averaging methods should only consider proteins of the same structural class and that this information should be included in the secondary structure methods.

Amino Acids↗

Sagaxine, the protamine from Sardinops sagax. Characterization, sequence and secondary structure prediction.

This paper describes the isolation, purification and full characterization of the protamine from Sardinops sagax. The protein was purified by both gel filtration and ion exchange chromatography and its amino acid composition, electrophoretic behaviour and sequence were determined. We postulate that the protamine exhibits microheterogeneity with a major and a minor component. The molecular weight for the major component is 4377, as calculated from the sequence. The N-terminal amino acid is proline and the C-terminal is arginine. The amino acid composition is: Thr-Ser-Glx-(Pro)2-Gly-(Ala)3-(Val)2-(Lys)2-(Arg)20 The secondary structure for the protamines was also predicted and a revision of our previously published results in this area is discussed. We have called this protamine Sagaxine and an overall comparison with the hitherto described fish protamines is also made.

Amino Acid Sequence↗

Search for a "toxic site" in snake venom phospholipases A2.

Secondary structure predictions on nine snake venom phospholipases A2 by the Chou and Fasman and Cid et al. prediction methods, have led to the location of two possible "toxic sites", responsible for the neurotoxic and myotoxic action of the basic snake venom PLA2, respectively. The accessibility to the neurotoxic site is blocked by the presence of a small helical structure (helix D in the bovine PLA2). The role of lysine residues is found to be decisive in the venom's toxicity.

Amino Acid Sequence↗

The relationship between the structures of four beta-lactamases obtained from Bacillus cereus.

Bacillus cereus has proved to be one of the most interesting microorganisms in the study of beta-lactamases. It secrets these enzymes very efficiently and, frequently, in multiple forms. Three different forms are produced by strain 569/H; mutant 5/B of the same microorganism is constitutive for the secretion of beta-lactamases I and II. The present study, based on secondary structure prediction by two independent methods, states the relationship among the structures of beta-lactamases I, II and III produced by B. cereus 569/H and beta-lactamase I from the strain 5/B of this microorganism. A strong similarity is also established for the enzyme type III of B. cereus and the enzyme type I produced by B. licheniformis which could have an evolutionary explanation. A structural analysis of the leader peptide regions of these enzymes by the method of Mohana and Argos is also reported.

Bacillus cereus↗

Secondary structure prediction of human salivary proline-rich proteins.

Conformations associated with secondary structure in human salivary proline-rich proteins A (PRPA), C (PRPC), P-D and P-E were predicted by analysis of their respective hydrophobicity profiles by computer programming. Structurally, PRPA and PRPC would present a globular head and a tail that consists of type 3(10) polyproline helices. P-D and P-E would be fibrilar molecules with helical zones of the polyproline 3(10) type. Alternatively for PRPA and PRPC, the head and tail would form one globular domain with the tail folding upon itself at places where random coils occur.

Amino Acid Sequence↗

A model for the structure of fructose-1,6-bisphosphatase from pig kidney.

Fructose-1,6-bisphosphatase (EC. 3.1.3.11) is an allosteric enzyme that plays a key role in the gluconeogenesis process. It forms a tetramer of identical subunits, its action is inhibited by AMP, it requires the presence of a divalent cation to be active and it is proteolytically regulated. The prediction of the secondary structure of this enzyme was done by the hydrophobicity profiles' method and by the Chou and Fasman's method with modifications. The predicted structure shows 38% beta-structure, 22% helical structure and 4% beta-turns. The structure can be described in terms of two domains joined by a 17-residues strand of random coiled structure. The location of the active and of the regulatory sites in the model proposed was made by secondary structure analogy with the enzyme obtained from rabbit liver. Domain I contains the AMP binding site and the proteolytic regulation site. Domain II has the active site, which, by appropriate superposition of both domains, can be located close to the AMP binding site and to the hyperreactive SH group. The model proposed meets several structural restrictions, it is thermodynamically stable and can explain the enzymatic behavior of the protein.

Adenosine Monophosphate↗

A model for the secondary structure of beta-lactamases.

A 3-dimensional model, common for the secondary structures of four beta-lactamases obtained from Escherichia coli, Bacillus licheniformis, Bacillus cereus and Staphylococcus aureus, is proposed. The predictions of the structures were made by the hydrophobicity profiles method complemented by the modified Chou and Fasman's method. The model proposed presents 56% constancy and can be described as a 2-domain structure, in agreement with low resolution X-ray data reported for the E. coli enzyme. The model would explain how a common function can be performed by enzymes of very different sizes, composition and sequence.

Bacillus↗

Electrophysiological effects of methyl 3-O-methyl gallate on single muscle fibres.

The electrophysiological changes induced by methyl 3-O-methyl gallate, a substance extracted from Crinodendron hookerianum, have been studied on 32 muscle fibres of Pleurodema thaul. Four concentrations were used: 1 x 10(-5), 2 x 10(-5), 1 x 10(-4), and 2 x 10(-4) mol/l, the results being a reversible dose-dependent reduction of the overshoot and the amplitude of the action potential, a prolongation of the rise and decay times of the spike, as well as a depolarization of the resting membrane potential. An explanation of these results by a blockade of the potassium and possibly the sodium channels in the cellular membrane is discussed.

Action Potentials↗