Lipase catalyzed polytransesterification in an organic solvent

Summary Lipase-catalyzed polytransesterification ofbis(2,2,2-trifluoroethyl) dodecanedioate with aliphatic diols (from 1,2-ethanediol to 1,6-hexanediol) was studied with 4 enzymes and a number of solvents. The effects of experimental parameters were investigated with the purpose of obtaining a polyester of as high as possible average molar mass. The highest mass average molar mass (M _w) of 34,750 g mol^-1 (DP = 122) was obtained under vacuum with 1,4-butanediol,Mucor miehei lipase, and diphenyl ether as solvent.     

Incorporating efficient radial basis function networks and significant amino acid pairs for predicting GTP binding sites in transport proteins

Background

Guanonine-protein (G-protein) is known as molecular switches inside cells, and is very important in signals transmission from outside to inside cell. Especially in transport protein, most of G-proteins play an important role in membrane trafficking; necessary for transferring proteins and other molecules to a variety of destinations outside and inside of the cell. The function of membrane trafficking is controlled by G-proteins via Guanosine triphosphate (GTP) binding sites. The GTP binding sites active G-proteins initiated to membrane vesicles by interacting with specific effector proteins. Without the interaction from GTP binding sites, G-proteins could not be active in membrane trafficking and consequently cause many diseases, i.e., cancer, Parkinson… Thus it is very important to identify GTP binding sites in membrane trafficking, in particular, and in transport protein, in general.

Results

We developed the proposed model with a cross-validation and examined with an independent dataset. We achieved an accuracy of 95.6% for evaluating with cross-validation and 98.7% for examining the performance with the independent data set. For newly discovered transport protein sequences, our approach performed remarkably better than similar methods such as GTPBinder, NsitePred and TargetSOS. Moreover, a friendly web server was developed for identifying GTP binding sites in transport proteins available for all users.

Conclusions

We approached a computational technique using PSSM profiles and SAAPs for identifying GTP binding residues in transport proteins. When we included SAAPs into PSSM profiles, the predictive performance achieved a significant improvement in all measurement metrics. Furthermore, the proposed method could be a power tool for determining new proteins that belongs into GTP binding sites in transport proteins and can provide useful information for biologists.

     

Xylanases in bleaching: From an idea to the industry

Abstract: The utilization of hemicellulases in bleaching of kraft (sulphate) pulp is considered as one of the most important new large-scale industrial applications of enzymes. This is partly due to the great potential of an environmentally safe method. This method has in a short period also proven to be economically realistic. The main enzymes needed in the enzyme-aided bleaching have been shown to belong to the group of endo-/gb-xylanases. Xylanases act mainly on the relocated, reprecipitated xylan on the surface of the pulp fibres. Enzymatic hydrolysis of this specific type of xylan renders the structure of the fibres more permeable. The hydrolysis of xylan or mannan in the inner fibre layers may also enhance the bleachability. In practical process conditions, properties of the enzymes such as substrate specificity and the pH and temperature optima are of utmost importance. The benefits obtained by enzymes are dependent on the chemical bleaching sequence used as well as on the residual lignin content of pulp. The main goals in the enzyme-aided bleaching of kraft pulps have been the reduction of consumption of chlorine chemicals in the bleaching process and consequently lowering the AOX of the effluents. Enzymes have been applied as a pretreatment both in conventional (C/D)EDED and in ECF (elementary chlorine-free) bleaching sequences. In the production of TCF (totally chlorine-free) pulps, enzymes have also been successfully used for increasing the brightness of pulp.     

Lipase-Catalyzed Synthesis of Poly(1,4-Butanediol Succinate) in Organic Solvent

During the last decade, lipase has gained interest as a biocatalyst for synthesis in organic solvent systems. The paper describes the lipase catalyzed oligocondensation of bis(2-chloroethyl) succinate and 1,4-butanediol to obtain poly (1,4-butanediol succinate). The reaction was carried out at 37°C in organic solvents without any addition of water. Various lipases and solvents were screened to obtain a maximum degree of polymerization. Based on gel permeation chromatography, the highest average molecular weight of the oligomer obtained was 1570 g/mol with a polydispersity of 1.2 when a mixture of 70% diisopropyl ether and 30% chloroform was used as a solvent. The degree of polymerization was 8 in this case. According to thin-layer chromatography, a trimer (HO(CH₂)₄OCO(CH₂)₂COO(CH₂)₄OH) was formed at an early stage, with a subsequent condensation with bis(2-chloroethyl) succinate to give higher oligomers. The structure of the oligomers was confirmed by ¹³C NMR and IR spectra.     

Determination of the solubilizing activity of a cellulase complex with dyed substrates

When the solubilizing activity of a microbial cellulase complex (e.g.,Trichoderma viride) is determined with conventional methods based on formation of reducing sugars, the results depend on the concentration ratio of cellobiose and glucose in the reaction mixture and thus on the β-glucosidase present and on the type of measurement of reducing sugars. The use of dyed substrates is one way to avoid this problem. The release of coloured compounds from a dyed substrate is proportional to the solubilization.     

Production of Phanerochaete chrysosporium lignin peroxidase under various culture conditions

Lignin peroxidase production by the white-rot fungus Phanerochaete chrysosporium is markedly influenced by the buffer system employed. In immobilized P. chrysosporium cultures with carbon-limited glucose medium, the use of acetate buffer resulted in higher lignin peroxidase activities than tartrate. With acetate as the buffer in shake-flask cultures a 20% to over 100% improvement in lignin peroxidase production was obtained as compared to tartrate-buffered systems. Of trace elements, Cu²⁺, Mn²⁺ and Zn²⁺ seemed to have the greatest influence on lignin peroxidase production. Furthermore, an increase in the Cu²⁺ and Zn²⁺ concentrations resulted in considerably higher ligninase activities. Although it has been shown previously that high manganese levels repress ligninase production, for maximum ligninase production the presence of some Mn²⁺ appeared to be necessary. The concentration of phosphorus had surprisingly little effect on ligninase production. Highest lignin peroxidase activities were obtained with lower phosphorus concentrations, but reasonably high activities were obtained within the whole studied phosphorus range of 0.12–4.60 g l^–1. Diammonium tartrate alone was a better nitrogen source than a mixture of diammonium tartrate, proteose peptone and yeast extract. The addition of solid manganese (IV) oxide to 3-day-old immobilized biocatalyst cultures increased the maximum ligninase activity obtained by about one-third. Correspondence to: S. Linko     

Prediction of transporter targets using efficient RBF networks with PSSM profiles and biochemical properties

SUMMARY: Transporters are proteins that are involved in the movement of ions or molecules across biological membranes. Currently, our knowledge about the functions of transporters is limited due to the paucity of their 3D structures. Hence, computational techniques are necessary to annotate the functions of transporters. In this work, we focused on an important functional aspect of transporters, namely annotation of targets for transport proteins. We have systematically analyzed four major classes of transporters with different transporter targets: (i) electron, (ii) protein/mRNA, (iii) ion and (iv) others, using amino acid properties. We have developed a radial basis function network-based method for predicting transport targets with amino acid properties and position specific scoring matrix profiles. Our method showed a 10-fold cross-validation accuracy of 90.1, 80.1, 70.3 and 82.3% for electron transporters, protein/mRNA transporters, ion transporters and others, respectively, in a dataset of 543 transporters. We have also evaluated the performance of the method with an independent dataset of 108 proteins and we obtained similar accuracy. We suggest that our method could be an effective tool for functional annotation of transport proteins. AVAILABILITY: http://rbf.bioinfo.tw/~sachen/ttrbf.html     

Fuels and industrial chemicals through biotechnology. 2

An overview of research on the biotechnical production of fuels and industrial chemicals during the two-year period of 1983-1984 is presented. Ethanol fermentation has continued to be the subject of major interest. A considerable amount of work has been directed to alternative feedstocks such as pentose sugars and lactose, and to bacterial fermentations. Reports on extrusion cooking as a continuous pretreatment method for subsequent ethanol fermentation, and on novel alternative downstream processing techniques have been published. In addition to ethanol fermentation, much attention has been paid to the biotechnical production of 2,3-butanediol, and of a number of organic and amino acids. In general, there appears to be a growing interest in the application of biocatalysis for the production of specialty chemicals, although only a few examples will be discussed in this paper. The construction of a demonstration plant to produce ethanol from molasses by a two 10 kL bed-volume immobilized yeast bioreactors at the Kyowa Hakko Kogyo Company Hofu plant, the announcement by Nitto Chemical Industries Company to begin the biotechnical production of acrylamide, and the French decision to construct pilot plants for the biotechnical production of acetone-butanol-ethanol cosolvent and of ethanol from renewable resources represent major scale-up developments.     

Ethanol production from whey with immobilized living yeast

Summary Living Kluyveromyces fragilis yeast cells were succesfully entrapped in calcium alginate gel beads at cell loadings of 4 to 16 g yeast (0.8 to 3.2 g d.m.) per 1 g of sodium alginate. In batch systems, about 90 % conversion in 48 h was obtained both with free and immobilized yeast using demineralized whey of 5 to 10 % lactose content as substrate. In continuous packed-bed column operation nearly a constant 2 % product ethanol concentration could be maintained at 5 % substrate lactose level for at least one month.