A phycourobilin-containing phycoerythrin from the cyanobacterium Oscillatoria sp.

A filamentous cyanobacterium Oscillatoria sp. was isolated from a thermal spring of the Kamchatka peninsula. It contained a phycoerythrin unusual for cyanobacteria in that it had a phycourobilin prosthetic group. The absorption spectrum of the native purified phycoerythrin displayed maxima at 498 and 567 nm. The phycoerythrin comprised - and -subunits of molecular weights 18,700 and 19,800, respectively, in 1:1 stoichiometry. Polyacrylamide gel isoelectric focusing revealed one protein band at pI 4.6. The - and -subunits differed in their chromophore composition and content: -subunit carried two phycoerythrobilins while the -subunit had three phycoerythrobilins and one phycourobilin. The chromophore composition of all known phycoerythrins of cyanobacteria and red algae were compared, and on the basis of this comparative study designations C₁- to C₅-phycoerythrin were proposed for cyanobacterial red pigments.     

Heme binding by a bacterial repressor protein,the gene product of the ferric uptake regulation (fur) gene ofEscherichia coli

Thefur gene product, Fur, ofEscherichia coli is a repressor when it binds Fe(II). Since heme and iron metabolism are closely linked and Fur is rich in histidine, a ligand for heme, the binding of heme to Fur was investigated. The oxidized Fur-heme complex is stable and low spin with a Soret maximum at 404 nm and no 620-nm band. CO coordinates with the reduced heme-Fur complex, causing a shift from 412 nm to 410 nm, and stabilizes it, increasing the half-life from 5 to 15 min. Circular dichroism (CD) spectra in the Soret region show heme bound in an asymmetric environment in Fur, both in the oxidized and reduced-CO forms. Quenching of tyrosine fluorescence by heme revealed rapid, tight binding (K _d<1μM) with an unusual stoichiometry of 1 heme:1 Fur dimer. Fur binds Mn(II), a model ligand for the endogenous Fe(II), much more weakly (K _d>80μM). Far-ultraviolet CD spectroscopy showed that theα-helix content of apo-Fur decreases slightly with heme binding, but increases with Mn(II) binding. Competition experiments indicated that heme interacts with Fur dimers at the same site as Mn(II) and can displace the metal. In contrast to Mn(II), Zn(II) did not quench the tyrosine fluoroescence of Fur, affected the CD spectrum less than Mn(II), but did bind in a manner which prevented heme from binding. In sum, Fur not only binds heme and Zn(II) with sufficient affinity to be biologically relevant, but the interactions that occur between these ligands and their effects on Mn(II) binding need to be taken into account when addressing the biological function of Fur.     

Crystal structure of Escherichia coli inorganic pyrophosphatase complexed with SO4: Ligand-induced molecular asymmetry

The three-dimensional structure of inorganic pyrophosphatase from Escherichia coli complexed with sulfate was determined at 2.2 Å resolution using Patterson's search technique and refined to an R-factor of 19.2%. Sulfate may be regarded as a structural analog of phosphate, the product of the enzyme reaction, and as a structural analog of methyl phosphate, the irreversible inhibitor. Sulfate binds to the pyrophosphatase active site cavity as does phosphate and this diminishes molecular symmetry, converting the homohexamer structure form (α₃)₂ into α₃′α₃″. The asymmetry of the molecule is manifested in displacements of protein functional groups and some parts of the polypeptide chain and reflects the interaction of subunits and their cooperation. The significance of re-arrangements for pyrophosphatase function is discussed.     

The reconstitution of microsomal redox chains. A comparative analysis of the effectiveness of membrane self-assembly and template binding of electron carriers

The osmotic pressure of solutions of sulphated proteoglycans isolated from the intervertebral discs of animals of various ages was determined. The behaviour of the solutions in salt-added systems was investigated in terms of the Donnan distribution of the mobile ions. It is evident that this effect is the dominating factor in explaining the observed nonidealities. Although marked variations in the compositions of the proteoglycan, with regard to their chondroitin sulphate and keratan sulphate content and hence charge content, occur with increasing age of parent tissue, the osmotic activities of the various preparations are very similar. This is explained by the ;fixation' of the counterions in such a way as to counteract any change in the charge content of the polyion; an ;osmotic buffering' effect. The swelling behaviour of gelatin gels containing the proteoglycan preparations has been measured. In all cases pressures in excess of the sum of the osmotic pressures of the individual components are observed. However, the magnitude of the excess decreases with increasing age of the parent tissue. It is suggested that the age changes, as reflected by a decrease in water content of the gel system, are not the result of changes in the osmotic properties of the individual components but rather reflect changes in the entropic interaction of the proteoglycan with the gelatin matrix. The relevance of this observation to the situation in vivo is discussed.     

Sudies of O-specific polysaccharide chains of Pseudomonas solanacearum lipopolysaccharides consisting of structually different repeating units.

The structure of the O-antigenic ploysaccharide chains of lipopolysaccharides of a number of Pseudomonas solanacearum strains were elucidated mainly with the help of methylation analysis and ¹³CNMR spectroscopy, including a computer-assisted ¹³CNMR-based analysis. Six structually distinct but related polysaccharides were identified. They have a backbone which is built up of three -rhammoyranosyl resides and one 2-acetamido-2-deoxy- -glucopyranosyl residue, and is unsubtituted or substituted with a residue of -xylopyranose or -rhamnopyranose as a monosaccharide side chain. The lipopolysaccharides of most of the strains contain polysaccharide chains consisting of at least two structually different types of repeating units. Three of the polysaccharides are common to more than one strain.     

RNA-hydrolyzing activity of human serum albumin and its recombinant analogue

The comparative analysis of RNA-hydrolyzing activity of albumin from human serum and albumin expressed in methylotrophic yeast Pichia pastoris has been carried out. The rate of polyribonucleotide phosphodiester bond cleavage in the presence of recombinant albumin has been found to be similar to that of the reaction mediated by the native protein. According to ³¹P NMR data, RNA hydrolysis follows the mechanism of intermolecular trans-esterification to yield 2′,3′-cyclophosphodiester reaction products that are further slowly hydrolyzed to form nucleoside-3′- and nucleoside-2′-phosphates. Analysis of pH dependence suggests an acid–base mechanism of catalysis. The catalytic activity and substrate specificity of albumin in RNA hydrolysis distinguish it from human ribonucleases.     

Biomedical ontologies: a functional perspective

The information explosion in biology makes it difficult for researchers to stay abreast of current biomedical knowledge and to make sense of the massive amounts of online information. Ontologies--specifications of the entities, their attributes and relationships among the entities in a domain of discourse--are increasingly enabling biomedical researchers to accomplish these tasks. In fact, bio-ontologies are beginning to proliferate in step with accruing biological data. The myriad of ontologies being created enables researchers not only to solve some of the problems in handling the data explosion but also introduces new challenges. One of the key difficulties in realizing the full potential of ontologies in biomedical research is the isolation of various communities involved: some workers spend their career developing ontologies and ontology-related tools, while few researchers (biologists and physicians) know how ontologies can accelerate their research. The objective of this review is to give an overview of biomedical ontology in practical terms by providing a functional perspective--describing how bio-ontologies can and are being used. As biomedical scientists begin to recognize the many different ways ontologies enable biomedical research, they will drive the emergence of new computer applications that will help them exploit the wealth of research data now at their fingertips.