The liganding of glycolipid transfer protein is controlled by glycolipid acyl structure

Glycosphingolipids (GSLs) play major roles in cellular growth and development. Mammalian glycolipid transfer proteins (GLTPs) are potential regulators of cell processes mediated by GSLs and display a unique architecture among lipid binding/transfer proteins. The GLTP fold represents a novel membrane targeting/interaction domain among peripheral proteins. Here we report crystal structures of human GLTP bound to GSLs of diverse acyl chain length, unsaturation, and sugar composition. Structural comparisons show a highly conserved anchoring of galactosyl- and lactosyl-amide headgroups by the GLTP recognition center. By contrast, acyl chain chemical structure and occupancy of the hydrophobic tunnel dictate partitioning between sphingosine-in and newly-observed sphingosine-out ligand-binding modes. The structural insights, combined with computed interaction propensity distributions, suggest a concerted sequence of events mediated by GLTP conformational changes during GSL transfer to and/or from membranes, as well as during GSL presentation and/or transfer to other proteins.     

Genetic diversity of the Pacific walrus (<Emphasis Type="Italic">Odobenus rosmarus divergens</Emphasis>) in the western part of the Chukchi Sea

We study 117 Pacific walrus samples from three rookeries within the western part of Chukchi Sea (Cape Vankarem, Cape Serdtse-Kamen, and Kolyuchin Island). We analyze the variability of nuclear (20 microsatellite loci) and mitochondrial DNA (three fragments). Two microsatellite loci which are described as microsatellites for the first time are used in this study: repeated sequences within introns of Coro1c and Plod2 genes. A high degree of genetic diversity is demonstrated for both nuclear and mitochondrial markers compared to Atlantic walrus. A high degree of genetic diversity is preserved within populations of Pacific walrus, despite a strong decline in the recent past. We discover the absence of significant differentiation for microsatellite loci and the presence of weak differentiation for mtDNA (mainly for a D-loop fragment). Walrus specimens that use the rookeries of the western part of Chukchi Sea are thought to belong to a single reproductive group.     

Analysis of the DNA joining repertoire of Chlorella virus DNA ligase and a new crystal structure of the ligase-adenylate intermediate

Chlorella virus DNA ligase is the smallest eukaryotic ATP-dependent DNA ligase known; it suffices for yeast cell growth in lieu of the essential yeast DNA ligase Cdc9. The Chlorella virus ligase–adenylate intermediate has an intrinsic nick sensing function and its DNA footprint extends 8–9 nt on the 3′-hydroxyl (3′-OH) side of the nick and 11–12 nt on the 5′-phosphate (5′-PO₄) side. Here we establish the minimal length requirements for ligatable 3′-OH and 5′-PO₄ strands at the nick (6 nt) and describe a new crystal structure of the ligase–adenylate in a state construed to reflect the configuration of the active site prior to nick recognition. Comparison with a previous structure of the ligase–adenylate bound to sulfate (a mimetic of the nick 5′-PO₄) suggests how the positions and contacts of the active site components and the bound adenylate are remodeled by DNA binding. We find that the minimal Chlorella virus ligase is capable of catalyzing non-homologous end-joining reactions in vivo in yeast, a process normally executed by the structurally more complex cellular Lig4 enzyme. Our results suggest a model of ligase evolution in which: (i) a small ‘pluripotent’ ligase is the progenitor of the much larger ligases found presently in eukaryotic cells and (ii) gene duplications, variations within the core ligase structure and the fusion of new domains to the core structure (affording new protein–protein interactions) led to the compartmentalization of eukaryotic ligase function, i.e. by enhancing some components of the functional repertoire of the ancestral ligase while disabling others.     

Flavonoid oxidation kinetics in aqueous and aqueous organic media in the presence of peroxidase,tyrosynase, and hemoglobin

The kinetics of oxidation reactions of flavonoids, quercetin, dihydroquercetin, and epicatechin has been studied in the presence of biocatalysts of different natures: horseradish peroxidase, mushroom tyrosinase, and hemoglobin from bull blood. Comparison of the kinetic parameters of the oxidation reaction showed that peroxidase appeared to be the most effective biocatalyst in these processes. The specificity of the enzyme for quercetin increased with increasing the polarity of the solvent in a series of ethanol–acetonitrile–dimethyl sulfoxide.     

Behaviour of DNA-RNase A complex in the presence of formaldehyde]

A formaldehyde-produced fixation of defects caused by a despiralizing action of a protein was studied in the case of DNA-RNAase A complex. The concentration of the defects fixed was measured by kinetic formaldehyde method (KF-method). It was shown that following processes take place in the complex in the presence of formaldehyde: (a) fixation of defects; (b) unwinding of DNA; (c) inactivation of the protein. The rates of all these processes depend on the concentration of formaldehyde, phi. At formaldehyde concentrations above some critical value phic the protein is inactivated before the defects are fixed. At phi less than phic the protein inactivation proceeds more slowly than the fixation of defects; at sufficiently low formaldehyde concentration no inactivation of protein occurs practically during the fixation time (20 min). The number of new defects formed during the time of fixation is linear with the formaldehyde concentration in the region where no inactivation of the protein occurs. Therefore the initial concentration of defects can be determined through an extrapolation to zero concentration of formaldehyde. On the basis of the data obtained a method is proposed for the evaluation of the number of defects in DNA caused by the despiralizing action of proteins. A model is proposed describing the behaviour of the complexes of DNA with despiralizing proteins in the presence of formaldehyde.     

Influence of formaldehyde on the melting temperature of DNA]

It has been shown that formaldehyde has no marked physical effect upon DNA resulting in lowering of its melting temperature. The effect of lowering of DNA melting temperature observed earlier by other authors resulted from the process of unwinding of DNA due to chemical reactions of formaldehyde with reactive base groups.