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A Colosimo

Publications and source records attributed to A Colosimo.

At least 55 records · Page 3Linked to original sources
PubMed1993

An improved method for detection of words with unusual occurrence frequency in nucleotide sequences.

A statistical analysis designed to deal with the problem of identifying rare or abundant "words" of arbitrary length in genomic fragments is presented. Our approach has the novelty of taking into account the statistical role of the presence of shorter words nested into longer ones and of introducing a Bayesian correction to minimize the effects of statistical fluctuations and of possible mistakes in genomic data. The method is successfully used in a thorough analysis of the abundance of short nucleotide sequences in the Escherichia coli genome.

Base Sequence↗
PubMed1993

Human elongation factor EF-1 beta: cloning and characterization of the EF1 beta 5a gene and assignment of EF-1 beta isoforms to chromosomes 2,5,15 and X.

We report here the isolation and characterization of a novel human elongation factor-1 beta (EF-1 beta) gene by cDNA selection from YAC mapping on chromosome 5q12-q14. This gene is specifically transcribed in fetal brain and in skeletal muscle and is characterized by a complete sequence homology with previously described EF-1 beta cDNAs. We also assigned the loci for three other EF-1 beta isoforms, to human chromosomes 2, 15 and X. The multiple chromosomal assignments of EF-1 beta loci demonstrates the genetic heterogeneity of human EF-1 beta peptides.

Base Sequence↗
PubMed1993

Plasmid DNA and low-frequency electromagnetic fields.

Physico-chemical and biological properties were studied in recombinant plasmids exposed to electric and magnetic fields (EMFs). The absence of slow-migrating DNA species and failure to identify induced DNA conformers, suggests that EMFs do not have any obvious genotoxic effect in any of the experimentally tested conditions.

DNA Damage↗
PubMed1991

A Hypercard program for the identification of biological specimens.

A Hypercard-based software tool developed to provide help in the identification of biological specimens is presented. The package implements a matching algorithm that compares alphanumeric strings and runs on Macintosh computers, though its simple architecture can be transferred to other computers and/or other programming environments. The overall performance of the program and its easy customization to specific problems are demonstrated by discussing at length one application in the field of earthworm identification.

Algorithms↗
PubMed1990

Interaction of hemoglobin with chloride and 2,3-bisphosphoglycerate. A comparative approach.

The equilibrium oxygen-binding properties of hemoglobins from reindeer (Rangifer tarandus tarandus), musk ox (Ovibos muschatos) and a bat (Rousettus aegyptiacus) have been investigated with special reference to the effect of heterotrophic ligands such as chloride and 2,3-bisphosphoglycerate [Gri(2,3)P2]. The results obtained with hemoglobins from reindeer and musk ox indicate that their low oxygen affinity and their insensitivity to Gri(2,3)P2 are not only an intrinsic property of the molecule, as proposed in the case of ruminant hemoglobins, but also the results of the interplay between chloride and Gri(2,3)P2 interactions. In other words, insensitivity of reindeer and musk ox hemoglobins to Gri(2,3)P2 is mainly due to a decreased affinity constant for this cofactor and to an increased affinity constant for chloride anions; this renders more effective the competition of chloride for th anion-binding site. On the other hand bat hemoglobin behaves in a completely different way and could be regarded as a type case of low-affinity hemoglobin since its functional properties are modulated neither by chloride nor by Gri(2,3)P2. The results are discussed in the light of the amino acid residues which are known to be involved in the binding of organic phosphates.

Allosteric Regulation↗
PubMed1990

What the intermediate compounds in ligand binding to hemoglobin tell about the mechanism of cooperativity.

The populations of the intermediates in concentrated solutions of hemoglobin A0 equilibrated at various PCO values, pH 7.0, 0.1 M KCl, and 20 degrees C, have been determined using cryogenic methods. Data on CO saturations and distributions of intermediates were analysed in terms of the free energies of dimer-tetramer assembly of the intermediates (G.K. Ackers and F.R. Smith, Annu. Rev. Biophys. Chem. 16 (1987) 583). The cooperative free energy value of the singly ligated species was approximately one-half the total cooperative energy. The cooperative free energy value of the doubly ligated species was not significantly different from that of carboxyhemoglobin. Because of experimental error, the observed difference in concentrations among the populations of the doubly ligated species cannot be taken as indicative of their functional heterogeneity. Additional studies on some NO intermediates have emphasized that (alpha 1 beta 1)(alpha 2 beta 2)X, a key intermediate in the formulation of the 'third-state' hypothesis in the deoxy/cyanomethemoglobin system, has a free energy value for dimer-tetramer assembly which is critically dependent on the nature of the ligand X as suggested by Ackers and Smith (reference as cited above).

Carboxyhemoglobin↗
PubMed1990

SIMFIT: a microcomputer software-toolkit for modelistic studies in biochemistry.

A software package suitable for personal computers and designed to handle simulation and fitting problems related to the study of biomolecules under pre-steady and steady state conditions is presented, and its overall architecture as well as the implemented algorithms illustrated. The peculiar features of the package are: (i) integrated capability of simulating dynamic models and fitting to them experimental data; (ii) handling of stiff problems; (iii) free use of algebraic as well as differential equations; (iv) objective comparison of models of different complexity. The above features are discussed through a number of examples taken from the direct experience of the authors in enzyme kinetics and ligand binding.

Biochemical Phenomena↗
PubMed1990

Microcomputer-assisted periodic pattern recognition in the primary structure of proteins.

Some relevant problems concerning the computational methods able to predict the higher structures of biopolymers from the sequence of their monomers will be introduced and a software package, LAPS (Look At Primary Structures) able to tackle many of those problems even on microcomputers, will be illustrated in its architecture and performances. In discussing some exemplary applications, special emphasis will be given to the recognition of repetitive patterns.

Amino Acid Sequence↗
PubMed1989

Allosteric formulation of thermal transitions in macromolecules, including effects of ligand binding and oligomerization.

We examine the effects of concentration (aggregation), buffers, and ligation, under conditions of either constant ligand activity or limited total amount of ligand, upon thermal denaturation of macromolecules as measured by scanning calorimetry. In doing so we utilize and extend an earlier generalized allosteric treatment [S. J. Gill, B. Richey, G. Bishop, and J. Wyman (1985) Biophys. Chem. 21, 1-14], applicable to ligand binding, enthalpy changes, and volume changes in a macromolecular system. The approach is contrasted with formulations based on the idea of structural domains. We show how information from the full scanning calorimetric curves can be utilized in arriving at and testing appropriate models for observed behavior in selected examples.

Allosteric Regulation↗
PubMed1987

A kinetic model for lipoxygenases based on experimental data with the lipoxygenase of reticulocytes.

A comprehensive kinetic model for lipoxygenase catalysis is proposed which includes the simultaneous occurrence of dioxygenase and hydroperoxidase activities and is based on the assumption of a single binding site for substrate fatty acid and product. The aerobic reaction of purified lipoxygenase from rabbit reticulocytes with 9,12(Z,Z)-octadecadienoic acid (linoleic acid) as substrate was studied. The rate constants and the dissociation constants of this enzyme were calculated for the model from progress curves; the model describes correctly the experimental data. The following kinetic features of the reticulocyte enzyme are assumed to apply generally to lipoxygenases. (a) The enzyme shows autoactivation by its product. (b) The rate-limiting step is the hydrogen abstraction. (c) Both substrate fatty acid and its product are competitive inhibitors of the lipoxygenase. (d) Lowering the oxygen concentration enhances the degree of substrate inhibition, whereas product inhibition is not influenced. (e) If substrate is in excess the oxygen concentration determines the share of dioxygenase and hydroperoxidase activities of the enzyme. As predicted from the model it was found that at low concentrations of oxygen the regio- and stereo-specificities of the dioxygenation are diminished. During the autoactivation phase the steady-state approximation does not hold.

Animals↗
PubMed1985

Cytochrome c-551 and azurin oxidation catalysed by Pseudomonas aeruginosa cytochrome oxidase. A steady-state kinetic study.

The kinetics of oxidation of azurin and cytochrome c-551 catalysed by Pseudomonas aeruginosa cytochrome oxidase were re-investigated, and the steady-state parameters were evaluated by parametric and non-parametric methods. At low concentrations of substrates (e.g. less than or equal to 50 microM) the values obtained for Km and catalytic-centre activity are respectively 15 +/- 3 microM and 77 +/- 6 min-1 for azurin and 2.15 +/- 0.23 microM and 66 +/- 2 min-1 for cytochrome c-551, in general accord with previous reports assigning to cytochrome c-551 the higher affinity for the enzyme and to azurin a slightly higher catalytic rate. However, when the cytochrome c-551 concentration was extended well beyond the value of Km, the initial velocity increased, and eventually almost doubled at a substrate concentration greater than or equal to 100 microM. This result suggests a 'half-hearted' behaviour, since at relatively low cytochrome c-551 concentrations only one of the two identical binding sites of the dimeric enzyme seems to be catalytically active, possibly because of unfavourable interactions influencing the stability of the Michaelis-Menten complex at the second site. When reduced azurin and cytochrome c-551 are simultaneously exposed to Ps. aeruginosa cytochrome oxidase, the observed steady-state oxidation kinetics are complex, as expected in view of the rapid electron transfer between cytochrome c-551 and azurin in the free state. In spite of this complexity, it seems likely that a mechanism involving a simple competition between the two substrates for the same active site on the enzyme is operative. Addition of a chemically modified and redox inactive form of azurin (Hg-azurin) had no effect on the initial rate of oxidation of either azurin and cytochrome c-551, but clearly altered the time course of the overall process by removing, at least partially, the product inhibition. The results lead to the following conclusions: (i) reduced azurin and cytochrome c-551 bind at the same site on the enzyme, and thus compete; (ii) Hg-azurin binds at a regulatory site, competing with the product rather than the substrate; (iii) the two binding sites on the dimeric enzyme, though intrinsically equivalent, display unfavourable interactions. Since water is the product of the reduction of oxygen, point (iii) has important implications for the reaction mechanism.

Apoproteins↗
PubMed1985

Circular dichroism observations on the lipoxygenase from reticulocytes.

CD spectra of reticulocyte lipoxygenase were recorded at various times during aerobic incubation, which leads to loss of catalytic activity, and after inactivation by the reaction product, 13-LS-hydroperoxylinoleic acid. Neither process showed any correlation with a decrease in the alpha-helix content, which was only observed over much longer times. It is concluded that inactivation of reticulocyte lipoxygenase by the suicidal reaction with 13-LS-hydroperoxylinoleic acid is not accompanied by gross structural alterations.

Animals↗
PubMed1985

Mechanism of control of cytochrome oxidase activity by the electrochemical-potential gradient.

Cytochrome c oxidation by bovine cytochrome oxidase embedded into liposomal vesicles with high respiratory control ratio (RCR = 6-10) has been studied by rapid-mixing experiments in the presence and absence of different ionophores. Kinetic analysis of the reaction indicates a linkage between the intrinsic activity of the enzyme, the efficiency of coupling and the electrochemical potential across the membrane. A simple model, based on two allosteric states with different catalytic properties in rapid equilibrium, is presented and successfully applied in the simulation of the observed time-course.

Animals↗
PubMed1985

Kinetics of redox-linked proton pumping activity of native and subunit III-depleted cytochrome c oxidase: a stopped-flow investigation.

The kinetics of oxidation of reduced cytochrome c by cytochrome c oxidase reconstituted into unilamellar vesicles (COV) has been followed by stopped-flow method in the time range 3 msec-1 sec. In the presence of valinomycin, the oxidation of cytochrome c is linked to proton ejection in the external medium, with an apparent stoichiometry (H+/e-) of 0.93 +/- 0.22, under conditions in which the enzyme is in the more active "pulsed" state (i.e., having undergone oxidation-reduction cycles). The time course of reaction indicates that the conformational change(s) involved in coupling the redox reaction to proton translocation is fast. Similar experiments carried out with cytochrome c oxidase depleted of subunit III show that proton-pumping is maintained, although with a lower efficiency (H+/e- = 0.5). The number of protons ejected per electron appears to be correlated to the value of the respiratory control ratio; although this result is partly due to an increase in the rate of diffusion back into the vesicles, a relationship between the respiratory control ratio and the efficiency of the proton pump may be inferred, suggesting a control of the H+/e-ratio.

Animals↗
PubMed1984

A re-examination of the reactions of cyanide with cytochrome c oxidase.

Experiments were performed to examine the cyanide-binding properties of resting and pulsed cytochrome c oxidase in both their stable and transient turnover states. Inhibition of the oxidation of ferrocytochrome c was monitored as a function of cyanide concentration. Cyanide binding to partially reduced forms produced by mixing cytochrome c oxidase with sodium dithionite was also examined. A model is presented that accounts fully for cyanide inhibition of the enzyme, the essential feature of which is the rapid, tight, binding of cyanide to transient, partially reduced, forms of the enzyme populated during turnover. Computer fitting of the experimentally obtained data to the kinetic predictions given by this model indicate that the cyanide-sensitive form of the enzyme binds the ligand with combination constants in excess of 10(6) M-1 X s-1 and with KD values of 50 nM or less. Kinetic difference spectra indicate that cyanide binds to oxidized cytochrome a33+ and that this occurs rapidly only when cytochrome a and CuA are reduced.

Cyanides↗
PubMed1984

Circular-dichroic properties and secondary structure of Pseudomonas aeruginosa soluble cytochrome c oxidase.

The c.d. spectra of Pseudomonas aeruginosa cytochrome c oxidase in the oxidized state and the reduced state are reported in the visible- and u.v. absorption regions. In the visible region the comparison between the spectra of reduced cytochrome c oxidase and ferrocytochrome c-551 allows the identification of the c.d. bands mainly due to the d1 haem chromophore in cytochrome c oxidase. In the near-u.v. region the assignment of some of the observed peaks to the haem groups and to the aromatic amino acid residues is proposed. A careful analysis of the data in the far-u.v. region leads to the determination of the relative amounts of alpha-helix and beta-sheet in the enzyme, giving for the first time a picture of its secondary structure. A significant difference in this respect between the reduced and the oxidized species is observed and discussed in the light of similar conclusions reported by other workers.

Circular Dichroism↗