Molecular modelling of protein-carbohydrate interactions. Understanding the specificities of two legume lectins towards oligosaccharides

By means of a series of new molecular modelling tools, the conformationalbehaviour of mannose-containing di- and trisaccharides boundto either concanavalin A or Lathyrus ochrus isolectin I (LOLI)has been assessed. Tools for estimating and analysing eitherthe ‘rigid’ or the ‘relaxed’ potentialenergy surfaces, representing the conformational space availablefor carbohydrates once interacting with lectins, are reportedfor the first time. Restrictions of conformational space arepredicted to occur with different magnitudes, depending on thenature of the glycosidic linkages, as well as the size of thecarbohydrates. Results from these molecular modelling studiesare compared to existing structural data. Not only could theobserved conformations and orientations of carbohydrates incrystalline lectin–oligosaccharides complexes be reproduced,but several other likely situations were also predicted to occur.Entropy calculations have been performed for comparison withexperimental thermodynamics data. The results of the simulationcan also help giving an explanation of some observed affinityconstants at the molecular level. concanavalin A Lathyrus ochrus lectin-oligosaccharide molecular modelling     

Inhibitory CD161 receptor identified in glioma-infiltrating T cells by single-cell analysis

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Lactose-containing starburst dendrimers: influence of dendrimer generation and binding-site orientation of receptors (plant/animal lectins and immunoglobulins) on binding properties.

Starburst glycodendrimers offer the potential to serve as high-affinity ligands for clinically relevant sugar receptors. In order to define areas of application, their binding behavior towards sugar receptors with differential binding-site orientation but identical monosaccharide specificity must be evaluated. Using poly(amidoamine) starburst dendrimers of five generations, which contain the p-isothiocyanato derivative of p-aminophenyl-beta-D-lactoside as ligand group, four different types of galactoside-binding proteins were chosen for this purpose, i.e., the (AB)(2)-toxic agglutinin from mistletoe, a human immunoglobulin G fraction, the homodimeric galectin-1 with its two binding sites at opposite ends of the jelly-roll-motif-harboring protein and monomeric galectin-3. Direct solid-phase assays with surface-immobilized glycodendrimers resulted in obvious affinity enhancements by progressive core branching for the plant agglutinin and less pronounced for the antibody and galectin-1. High density of binding of galectin-3 with modest affinity increases only from the level of the 32-mer onwards points to favorable protein-protein interactions of the monomeric lectin and a spherical display of the end groups without a major share of backfolding. When the inhibitory potency of these probes was evaluated as competitor of receptor binding to an immobilized neoglycoprotein or to asialofetuin, a marked selectivity was detected. The 32- and 64-mers were second to none as inhibitors for the plant agglutinin against both ligand-exposing matrices and for galectin-1 on the matrix with a heterogeneous array of interglycoside distances even on the per-sugar basis. In contrast, a neoglycoprotein with the same end group was superior in the case of the antibody and, less pronounced, monomeric galectin-3. Intimate details of topological binding-site presentation and the ligand display on different generations of core assembly are major operative factors which determine the potential of dendrimers for applications as lectin-targeting device, as attested by these observations.     

Lipid quantitation in formalin-fixed liver sections

We describe a simple, sensitive, and quantitative procedure for measurement of triglycerides and protein contents in formalin-fixed liver sections. The method can detect as little as 0.27 microgram of triglycerides per mg of protein. It is based on selective binding of Sudan IV and Fast Green FCF to fat and total proteins, respectively, and their sequential elution with solvents. Sudan IV is eluted readily with acetone and Fast Green with NaOH-methanol, and the absorbances obtained at 500 and 610 nm can be used to determine the amount of triglycerides and total protein. The color equivalence for Fast Green was obtained after destaining the sections and measuring the protein contents by micro-Kjeldahl analysis. The color equivalence of Sudan IV was estimated by determining the triglyceride content in liver homogenates by an enzymatic procedure and then measuring the amount of dye bound to multiple fixed sections. There was a strong linear correlation between the triglyceride content as determined chemically and that obtained using the equivalence colors (r2 = 0.98). This method is useful to measure fat content in tissue samples and could be applied to evaluate the progression of liver disease.     

Isolation and characterization of microsatellites in Pacific white shrimp Penaeus (Litopenaeus) vannamei

Five polymorphic microsatellite loci were characterized for Penaeus (Litopenaeus) vannamei. Loci were isolated using a partial Sau3A1 genomic library by the sequencing of randomly selected clones and by a biotinylated (CT)₁₀ and (GT)₁₀ probes screening procedure. The last strategy resulted in the most useful data. About 40% of the clones showed a previously reported satellite/microsatellite (PVS1), reducing the chance of finding new microsatellite regions. Whereas two of the microsatellite loci with more than 10 alleles will be useful for mating analysis in a breeding program, the others might prove useful for population genetic studies.     

Sterilization of Plants for Phytoremediation Studies by Bleach Treatment

Bleach treatment of plants was studied as a simple alternative to axenic tissue cultures for demonstrating phytodegradation of aqueous and gas-phase environmental contaminants. Parrotfeather (Myriophyllum aquaticum), spinach (Spinacia oleracea), and wheat (Triticum aestivum) were exposed to 0.525% NaC10 solutions for 15 s, then rinsed in deionized water. Plate counts indicated that 97 to 100% of viable bacteria were removed from parrotfeather and spinach. Transformation rates for 2,4,6-trinitrotoluene (TNT) by bleached and untreated parrotfeather were virtually identical. Similarly, treated and untreated spinach, wheat heads, and wheat leaves removed methyl bromide (MeBr) from air at the same rates. However, wheat root with attendant adhering soil was rendered inactive by bleach treatment. Parrotfeather roots examined by dissecting microscope and by electron microscope showed no significant damage caused by bleach treatment.