Molecular modeling and analysis of human and plant endo-β-N-acetyl- glucosaminidases for mutations effects on function

Endo- β-N-acetylgucosaminidases (ENGases) are the enzymes that catalyze both hydrolysis and transglycosylation reactions. It is of interest to study ENGases because of their ability to synthesize glycopeptides. Homology models of Human, Arabidopsis thaliana and Sorghum ENGases were developed and their active sites marked based on information available from Arthrobacter protophormiae (PDB ID: 3FHQ) ENGase. Further, these models were docked with the natural substrate GlcNAc-Asn and the inhibitor Man₃GlcNAc-thiazoline. The catalytic triad of Asn, Glu and Tyr (N171, E173 and Y205 of bacteria) were found to be conserved across the phyla. The crucial Y299F mutation showing 3 times higher transglycosylation activity than in wild type Endo-A is known. The hydrolytic activity remained unchanged in bacteria, while the transglycosylation activity increased. This Y to F change is found to be naturally evolved and should be attributing higher transglycosylation rates in human and Arabidopsis thaliana ENGases. Ligand interactions Ligplots revealed the interaction of amino acids with hydrophobic side chains and polar uncharged side chain amino acids. Thus, structure based molecular model-ligand interactions provide insights into the catalytic mechanism of ENGases and assist in the rational engineering of ENGases.     

The Movement of Zinc through Excised Stems of Seedlings of Pinus radiata D. Don.

Radioactive Zn solns were drawn through 10 cm stem sectionsexcised from seedlings of P. radiata to determine the locationand quantity of ⁶⁵Zn remaining in the stems and the concn of⁶⁵Zn in the exudate. Zinc was removed from solns passing through the excised stemsby processes which appeared to be non-metabolic because coolingthe inflow solns did not decrease the proportion of Zn removedand non-specific because Ca competed with Zn for ‘exchangesites’. The formation of anionic or uncharged complexes between Zn andEDTA, or citrate resulted in more Zn passing through the excisedstems. Consistent with the greater stability of Zn-EDTA complexesmore Zn passed through stems treated with EDTA than with citrate.Decreasing the pH of solns containing Zn, Ca and potassium citrateincreased the amount of Zn deposited in the basal (inflow) endof the stems, probably by decreasing the amount of Zn boundto citrate. Increasing the conen of Zn in test solns containingZn, Ca and potassium citrate did not change the distributionof ⁶⁵Zn in the stems as the capacity of the stems to removeZn from soln was large enough to remove all the free Zn in allthe solns Pinus radiata D. Don, pine, zinc, movement, stems     

Technical comment on Boersma et al. (2016) Temperature driven changes in the diet preference of omnivorous copepods: no more meat when it's hot? Ecology Letters, 19, 45–53

A recent study concluded that omnivorous plankton will shift from predatory to herbivorous feeding with climate warming, as consumers require increased carbon:phosphorous in their food. Although this is an appealing hypothesis, we suggest the conclusion is unfounded, based on the data presented, which seem in places questionable and poorly interpreted.     

Topological studies on the enzymes catalyzing the biosynthesis of Glc-P- dolichol and the triglucosyl cap of Glc3Man9GlcNAc2-P-P-dolichol in microsomal vesicles from pig brain: use of the processing glucosidases I/II as latency markers

In the current model for Glc3Man9GlcNAc2-P-P-Dol assembly, Man5GlcNAc2- P-P-Dol, Man-P-Dol, and Glc-P-Dol are synthesized on the cytoplasmic face of the ER and diffuse transversely to the lumenal leaflet where the synthesis of the lipid-bound precursor oligosaccharide is completed. To establish the topological sites of Glc-P-Dol synthesis and the lipid-mediated glucosyltransfer reactions involved in Glc3Man9GlcNAc2-P-P-Dol synthesis in ER vesicles from pig brain, the trypsin-sensitivity of Glc-P-Dol synthase activity and the Glc-P- Dol:Glc0-2Man9GlcNAc2-P-P-Dol glucosyltransferases (GlcTases) was examined in sealed microsomal vesicles. Since ER vesicles from brain do not contain glucose 6-phosphate (Glc 6-P) phosphatase activity, the latency of the lumenally oriented, processing glucosidase I/II activities was used to assess the intactness of the vesicle preparations. Comparative enzymatic studies with sealed ER vesicles from brain and kidney, a tissue that contains Glc 6-P phosphatase, demonstrate the reliability of using the processing glucosidase activities as latency markers for topological studies with microsomal vesicles from non-gluconeogenic tissues lacking Glc 6-P phosphatase. The results obtained from the trypsin-sensitivity assays with sealed microsomal vesicles from brain are consistent with a topological model in which Glc-P-Dol is synthesized on the cytoplasmic face of the ER, and subsequently utilized by the three Glc-P-Dol-mediated GlcTases after "flip-flopping" to the lumenal monolayer.      

The Growth and Carbon Economy of Selection Lines of Lolium perenne cv. S23 with Differing Rates of Dark Respiration: 2. Grown as Young Plants from Seed

Young plants of two selection lines of Lolium perenne cv. S23with ‘fast’ and ‘slow’ rates of ‘maturetissue’ respiration were individually grown from seed,together with plants of S23, their common parent, in 9.2 cmpots in a controlled environment at 20/15 °C day/night temperatures. No significant differences were found between the genotypesin leaf extension and tiller production during this early stageof their growth. They did differ however, by an average of 26%,in the rate of dark respiration of fully expanded leaf laminae.The use of a simple model demonstrated that such a differencein respiration could alone account for the different rates ofdry matter production shown by the selection lines when grownas young crops from seed. Possible penalties of ‘slow’respiration are also considered. Lolium perenne L., ryegrass, respiration, maintenance respiration, stimulated swards, leaf growth, tiller production, carbon economy     

A feature selection approach for identification of signature genes from SAGE data

Background  

One goal of gene expression profiling is to identify signature genes that robustly distinguish different types or grades of tumors. Several tumor classifiers based on expression profiling have been proposed using microarray technique. Due to important differences in the probabilistic models of microarray and SAGE technologies, it is important to develop suitable techniques to select specific genes from SAGE measurements.