Rational Enzyme Design without Structural Knowledge: A Sequence-Based Approach for Efficient Generation of Transglycosylases

Glycobiology is dogged by the relative scarcity of synthetic, defined oligosaccharides. Enzyme-catalysed glycosylation using glycoside hydrolases is feasible but is hampered by the innate hydrolytic activity of these enzymes. Protein engineering is useful to remedy this, but it usually requires prior structural knowledge of the target enzyme, and/or relies on extensive, time-consuming screening and analysis. Here, a straightforward strategy that involves rational rapid in silico analysis of protein sequences is described. The method pinpoints 6–12 single-mutant candidates to improve transglycosylation yields. Requiring very little prior knowledge of the target enzyme other than its sequence, the method is generic and procures catalysts for the formation of glycosidic bonds involving various d /l -, α/β-pyranosides or furanosides, and exo or endo action. Moreover, mutations validated in one enzyme can be transposed to others, even distantly related enzymes.     

Ordinary and penalized minimum power-divergence estimators in two-way contingency tables

Basu and Basu (Statistica Sinica 8:841–860, 1998) have proposed an empty cell penalty for the minimum power-divergence estimators which can lead to improvements in the small sample properties of these estimators. In this paper, we study the small and moderate sample performances of the ordinary and penalized minimum power-divergence estimators in terms of efficiency and robustness for the log-linear models in two-way contingency tables under the assumptions of multinomial sampling. Calculations made by enumerating all possible sample combinations show that the penalized estimators are competitive with the ordinary estimators for the moderate samples and definitely better for the smallest sample considered for both efficiency and robustness under the considered models. The results also reveal that the bigger the main effects the more need for penalization.     

GSK-3-selective inhibitors derived from Tyrian purple indirubins

Gastropod mollusks have been used for over 2500 years to produce the "Tyrian purple" dye made famous by the Phoenicians. This dye is constituted of mixed bromine-substituted indigo and indirubin isomers. Among these, the new natural product 6-bromoindirubin and its synthetic, cell-permeable derivative, 6-bromoindirubin-3'-oxime (BIO), display remarkable selective inhibition of glycogen synthase kinase-3 (GSK-3). Cocrystal structure of GSK-3beta/BIO and CDK5/p25/indirubin-3'-oxime were resolved, providing a detailed view of indirubins' interactions within the ATP binding pocket of these kinases. BIO but not 1-methyl-BIO, its kinase inactive analog, also inhibited the phosphorylation on Tyr276/216, a GSK-3alpha/beta activation site. BIO but not 1-methyl-BIO reduced beta-catenin phosphorylation on a GSK-3-specific site in cellular models. BIO but not 1-methyl-BIO closely mimicked Wnt signaling in Xenopus embryos. 6-bromoindirubins thus provide a new scaffold for the development of selective and potent pharmacological inhibitors of GSK-3.     

Use of pseudo-sample extraction and the projection technique to estimate the chemical rank of three-way data arrays

Determining the rank of a trilinear data array is a first step in subsequent trilinear component decomposition. Different from estimating the rank of bilinear data, it is more difficult to decide the significant number of component to fit the trilinear decompositions exactly. General methods of rank estimation utilize the information contained in the singular values but ignore information from eigenvectors. In this paper, a rank estimating method specifically for trilinear data arrays is proposed. It uses the idea of direct trilinear decomposition (DTLD) to compress the cube matrix into two pseudo sample matrices which are then decomposed by singular value decomposition. Two eigenvectors combined with the projection technique are used to estimate the rank of trilinear data arrays. Simulated trilinear data arrays with homoscedastic and heteroscedastic noise, different noise levels, high collinearity, and real three-way data arrays have been used to illustrate the feasibility of the proposed method. Compared with other factor-determining methods, for example use of the factor indication function (IND), residual percentage variance (RPV), and the two-mode subspace comparison approach (TMSC), the results showed that the new method can give more reliable answers under the different conditions applied.      

Synthesis of a library of xylogluco-oligosaccharides for active-site mapping of xyloglucan endo-transglycosylase

Complex oligosaccharides containing alpha-D-xylosyl-(1-->6)-beta-D-glucosyl residues and unsubstituted beta-(1-->4)-linked D-glucosyl units were readily synthesized using enzymatic coupling catalyzed by the Cel7B E197A glycosynthase from Humicola insolens. Constituting this library required four key steps: (1) preparing unprotected building blocks by chemical synthesis or enzymatic degradation of xyloglucan polymers; (2) generating the donor synthon in the enzymatic coupling by temporarily introducing a lactosyl motif on the 4-OH of the terminal glucosyl units of the xylogluco-oligosaccharides; (3) synthesizing the corresponding alpha-fluorides, followed by their de-O-acetylation and the glycosynthase-catalyzed condensation of these donors onto various acceptors; and (4) enzymatically releasing lactose or galactose from the reaction product, affording the target molecules in good overall yields. These complex oligosaccharides proved useful for mapping the active site of a key enzyme in plant cell wall biosynthesis and modification: the xyloglucan endo-transglycosylase (XET). We also report some preliminary enzymatic results regarding the efficiency of these compounds.     

Orientation of grafted polymer chains at the air-water interface studied by PM-IRRAS

Monolayers of polystyrene-polyethylene oxide (PS-PEO) copolymers at the air-water interface have been studied with the Modulation Polarization Infra Red Spectroscopy technique (PM-IRRAS) to measure the orientation of the PEO chains with respect to the normal to the interface. At surface densities intermediate between the dilute regime and the brush regime, the average tilt angle has been determined: it decreases continuously with the surface density in the monolayer, in good agreement with previous results (M.C. Fauréet al., Macromolecules 32, 8538 (1999)). The further stretching of the molecules in the brush regime has also been measured. No substantial volume fraction of PEO crystal domains has been detected in the very dense regime Received 16 April 1999 and Received in final form 26 August 1999     

Negative tension induced by lipid uptake

Membrane fusion is an important process in cell biology. While the molecular mechanisms of fusion are actively studied at a very local scale, the consequences of fusion at a larger scale on the shape and stability of the membrane are still not explored. In this Letter, the evolution of the membrane tension during the fusion of positive small unilamellar vesicles with a negative giant unilamellar vesicle has been experimentally investigated and compared to an existing theoretical model. The tension has been deduced using videomicroscopy from the measurement of the fluctuation spectrum and of the time correlation function of the fluctuations. We show that fusion induces a strong decrease in the effective tension of the membrane which eventually reaches negative values. Under these conditions, we show that localized instabilities appear on the vesicle. The membrane finally collapses, forming dense lipid structures.     

Unexpected stability of phospholipid langmuir monolayers deposited on Triton X-100 aqueous solutions

We studied at the molecular level the interaction between neutral detergent Triton X-100 aqueous solution and a phospholipid Langmuir monolayer deposited on top using surface pressure measurement and grazing incidence X-ray diffraction (GIXD). Macroscopically, the detergent-phospholipid system follows the Gibbs law. However, GIXD shows that the detergent and the phospholipid segregate at the interface. The molecular organization of pure phospholipid domains is imposed by the detergent through surface pressure. Compression and expansion of the surface monolayer system in its final state reveal the stability of the phospholipids domains against dissolution by the detergent in the subphase, even above the detergent cmc. This resistance to dissolution is suppressed by an expansion of the monolayer.     

Chemical Composition,Antioxidant and Antiproliferative Activities of Taraxacum officinale Essential Oil

Taraxacum officinale (TO) has been historically used for medicinal purposes due to its biological activity against specific disorders. To investigate the antioxidant and the antiproliferativepotential of TO essential oil in vitro and in vivo, the chemical composition of the essential oil was analyzed by GC-MS. The in vivo antioxidant capacity was assessed on liver and kidney homogenate samples from mice subjected to acetaminophen-induced oxidative stress and treated with TO essential oil (600 and 12,000 mg/kg BW) for 14 days. The in vitro scavenging activity was assayed using the 1,1-diphenyl-2-picrylhydrazyl (DPPH) and the reducing power methods. The cytotoxic effects against the HeLa cancer cell line were analyzed. The GC-MS analysis showed the presence of 34 compounds, 8 of which were identified as major constituents. The TO essential oil protected mice’s liver and kidneys from acetaminophen-induced oxidative stress by enhancing antioxidant enzymes (catalase, superoxide dismutase, and glutathione) and lowering malondialdehyde levels. In vitro, the TO essential oil demonstrated low scavenging activity against DPPH (IC₅₀ = 2.00 ± 0.05 mg/mL) and modest reducing power (EC₅₀ = 0.963 ± 0.006 mg/mL). The growth of the HeLa cells was also reduced by the TO essential oil with an inhibition rate of 83.58% at 95 µg/mL. Current results reveal significant antioxidant and antiproliferative effects in a dose-dependent manner and suggest that Taraxacum officinale essential oil could be useful in formulations for cancer therapy.     

Domain structure in a superconducting ferromagnet

The domain structure is inherent to all ferromagnets and the recent discovery of the superconducting ferromagnets raises the question of the modification of this domain structure by superconductivity. In the framework of the general London theory, applicable to both singlet and triplet superconductors, we demonstrate that superconductivity leads to a dramatic shrinkage of the domain width. The presence of this dense domain structure has to be taken into account for all magnetic measurements on superconducting ferromagnets, and the study of the domain structure evolution could provide important information on the mechanisms of superconductivity and magnetism interplay.