Synthesis of galactofuranose-based acceptor substrates for the study of the carbohydrate polymerase GlfT2

Despite the prevalence and importance of carbohydrate polymers, the molecular details of their biosynthesis remain elusive. Many enzymes responsible for the synthesis of carbohydrate polymers require a ‘primer’ or ‘initiator’ carbohydrate sequence. One example of such an enzyme is the mycobacterial galactofuranosyltransferase GlfT2 (Rv3808c), which generates an essential cell wall building block. We recently demonstrated that recombinant GlfT2 is capable of producing a polymer composed of alternating β-(1,5) and β-(1,6)-linked galactofuranose (Galf) residues. Intriguingly, the length of the polymers produced from a synthetic glycosyl acceptor is consistent with those found in the cell wall. To probe the mechanism by which polymer length is controlled, a collection of initiator substrates has been assembled. The central feature of the synthetic route is a ruthenium-catalyzed cross-metathesis as the penultimate transformation. Access to synthetic substrates has led us to postulate a new mechanism for length control in this template-independent polymerization. Moreover, our investigations indicate that lipids possessing but a single galactofuranose residue can act as substrates for GlfT2.     

Synthetic tyrosine polymers as substrates and inhibitors of tyrosine-specific protein kinases

Several synthetic random polymers of tyrosine containing glutamic acid, alanine, and lysine in various proportion served as substrates for tyrosine-specific protein kinases. The Km values for these substrates were much lower than for small polypeptides such as angiotensin. For the protein kinase coded by Fujinami virus, the best substrates (with the lowest Km) were polymers containing glutamic acid, alanine, and 8 to 10% tyrosine; for the insulin receptor protein kinase, the best substrate was a polymer containing 80% glutamic acid and 20% tyrosine. These polymers serve as inexpensive and tyrosine-specific substrates that can be used even with crude extracts and analyzed by the convenient filter paper assay. Several synthetic polymers with ordered sequences were found to be potent inhibitors of these tyrosine-specific protein kinases.     

New substrates for reliable enzymes: enzymatic modification of polymers

Recent studies clearly indicate that the modification of synthetic and natural polymers with enzymes is an environmentally friendly alternative to chemical methods using harsh conditions. New processes using lipases, proteases, nitrilases and glycosidases have been developed for the specific non-destructive functionalization of polymer surfaces. The specificity of enzymes has also been exploited in polymer synthesis; for example, lipases have been used for the production of optically active polyesters. Oxidoreductases have been used for the cross-linking and grafting of lignaceous materials and for the production of polymers from phenolics. Recent successes in this area are mainly attributable to advances in the design of reaction systems (e.g. biphasic systems and micellar solutions), while the enzymes are mainly from commercial sources.     

Well-defined protein–polymer conjugates—synthesis and potential applications

During the last decades, numerous studies have focused on combining the unique catalytic/functional properties and structural characteristics of proteins and enzymes with those of synthetic molecules and macromolecules. The aim of such multidisciplinary studies is to improve the properties of the natural component, combine them with those of the synthetic, and create novel biomaterials in the nanometer scale. The specific coupling of polymers onto the protein structures has proved to be one of the most straightforward and applicable approaches in that sense. In this article, we focus on the synthetic pathways that have or can be utilized to specifically couple proteins to polymers. The different categories of well-defined protein–polymer conjugates and the effect of the polymer on the protein function are discussed. Studies have shown that the specific conjugation of a synthetic polymer to a protein conveys its physico-chemical properties and, therefore, modifies the biodistribution and solubility of the protein, making it in certain cases soluble and active in organic solvents. An overview of the applications derived from such bioconjugates in the pharmaceutical industry, biocatalysis, and supramolecular nanobiotechnology is presented at the final part of the article.     

Towards a polymeric binding mimic for cytochrome CYP2D6

A series of fluorescent molecularly imprinted polymers has been prepared with a view to generating material capable of mimicking the binding characteristics of the metabolically important cytochrome isoform CYP2D6. Such polymers would have the possibility to form the sensing element in a high-throughput assay for the prediction of CYP2D6 affinity. The imprinted polymers possessed binding-dependent fluorescence. They re-bound their templates and various cross-reactivities were encountered for test compound/drug recognition. One polymer in particular exhibited a rational discrimination amongst the related synthetic templates and was reasonably successful in recognising CYP2D6 substrates from a drug panel.     

Hydrophobic salt-modified Nafion for enzyme immobilization and stabilization

Over the last decade, there has been a wealth of application for immobilized and stabilized enzymes including biocatalysis, biosensors, and biofuel cells. In most bioelectrochemical applications, enzymes or organelles are immobilized onto an electrode surface with the use of some type of polymer matrix. This polymer scaffold should keep the enzymes stable and allow for the facile diffusion of molecules and ions in and out of the matrix. Most polymers used for this type of immobilization are based on polyamines or polyalcohols - polymers that mimic the natural environment of the enzymes that they encapsulate and stabilize the enzyme through hydrogen or ionic bonding. Another method for stabilizing enzymes involves the use of micelles, which contain hydrophobic regions that can encapsulate and stabilize enzymes. In particular, the Minteer group has developed a micellar polymer based on commercially available Nafion. Nafion itself is a micellar polymer that allows for the channel-assisted diffusion of protons and other small cations, but the micelles and channels are extremely small and the polymer is very acidic due to sulfonic acid side chains, which is unfavorable for enzyme immobilization. However, when Nafion is mixed with an excess of hydrophobic alkyl ammonium salts such as tetrabutylammonium bromide (TBAB), the quaternary ammonium cations replace the protons and become the counter ions to the sulfonate groups on the polymer side chains (Figure 1). This results in larger micelles and channels within the polymer that allow for the diffusion of large substrates and ions that are necessary for enzymatic function such as nicotinamide adenine dinucleotide (NAD). This modified Nafion polymer has been used to immobilize many different types of enzymes as well as mitochondria for use in biosensors and biofuel cells. This paper describes a novel procedure for making this micellar polymer enzyme immobilization membrane that can stabilize enzymes. The synthesis of the micellar enzyme immobilization membrane, the procedure for immobilizing enzymes within the membrane, and the assays for studying enzymatic specific activity of the immobilized enzyme are detailed below.     

Microbial degradation of natural and of new synthetic polymers.

In landfills, deposited waste material is usually faced with strictly anoxic conditions. This means that the design of new biodegradable polymers must take into consideration that degradation should be possible especially in the absence of molecular oxygen. Poly-beta-hydroxybutyrate is depolymerized by the anaerobic fermenting bacterium Ilyobacter delafieldii through an extracellular hydrolase. Monomers are degraded inside the cells through classical beta-oxidation. Polyalkanoates containing odd-numbered or branched-chain acid monomers should he degraded in an analogous manner; in most cases the final mineralization of these residues requires special pathways. A comparison of the chemistry of natural polymer biodegradation leads to the conclusion that synthetic biodegradable polymers should be designed in the future to contain linkages which can be cleaved by extracellular hydrolytic enzymes. Recent findings on aerobic and anaerobic bacterial degradation of synthetic polyethers suggest that natural evolution of new depolymerizing enzymes, perhaps from existing hydrolases, could be possible in a reasonable amount of time, provided that the monomers are likely energy sources for a broad variety of microbes.     

Large cosolutes,small cosolutes,and dihydrofolate reductase activity

Protein enzymes are the main catalysts in the crowded and complex cellular interior, but their activity is almost always studied in dilute buffered solutions. Studies that attempt to recreate the cellular interior in vitro often utilize synthetic polymers as crowding agents. Here, we report the effects of the synthetic polymer cosolutes Ficoll, dextran, and polyvinylpyrrolidone, and their respective monomers, sucrose, glucose, and 1‐ethyl‐2‐pyrrolidone, on the activity of the 18‐kDa monomeric enzyme, Escherichia coli dihydrofolate reductase. At low concentrations, reductase activity increases relative to buffer and monomers, suggesting a macromolecular effect. However, the effect decreases at higher concentrations, approaching, and, in some cases, falling below buffer values. We also assessed activity in terms of volume occupancy, viscosity, and the overlap concentration (where polymers form an interwoven mesh). The trends vary with polymer family, but changes in activity are within threefold of buffer values. We also compiled and analyzed results from previous studies and conclude that alterations of steady‐state enzyme kinetics in solutions crowded with synthetic polymers are idiosyncratic with respect to the crowding agent and enzyme.     

Effect of blending lignin biopolymer on the biodegradability of polyolefin plastics

The ability of the lignin-degrading microorganism Phanerochaete chrysosporium to attack polyethylene and polypropylene was investigated using a series of polymer blends containing 10, 20 and 30% lignin obtained from the waste product of pulp and paper industry. In the cultivation medium, lignin peroxidase and Mn(II)peroxidase activities were detected. Degradation was verified by quantitative u.v. spectrophotometric analysis of the cultivation medium and by liberation of CO₂ from the blends. Measurement of the tensile strength after 30-days cultivation showed that the mechanical properties of the polymer blends were decreased during the biodegradation process. The isolation of oligomer fractions by tetrahydrofuran (THF) extraction of biodegraded polymers and their characterization by gel permeation chromatography (GPC), u.v. and Fourier transmission infrared (FTIR) spectroscopy indicates that biotransformation of the lignin component during the cultivation process initiates partial biodegradation of the synthetic polymer matrix.     

Squaric acid mediated synthesis and biological activity of a library of linear and hyperbranched poly(glycerol)-protein conjugates

Polymer-protein conjugates generated from side chain functional synthetic polymers are attractive because they can be easily further modified with, for example, labeling groups or targeting ligands. The residue specific modification of proteins with side chain functional synthetic polymers using the traditional coupling strategies may be compromised due to the nonorthogonality of the side-chain and chain-end functional groups of the synthetic polymer, which may lead to side reactions. This study explores the feasibility of the squaric acid diethyl ester mediated coupling as an amine selective, hydroxyl tolerant, and hydrolysis insensitive route for the preparation of side-chain functional, hydroxyl-containing, polymer-protein conjugates. The hydroxyl side chain functional polymers selected for this study are a library of amine end-functional, linear, midfunctional, hyperbranched, and linear-block-hyperbranched polyglycerol (PG) copolymers. These synthetic polymers have been used to prepare a diverse library of BSA and lysozyme polymer conjugates. In addition to exploring the scope and limitations of the squaric acid diethylester-mediated coupling strategy, the use of the library of polyglycerol copolymers also allows to systematically study the influence of molecular weight and architecture of the synthetic polymer on the biological activity of the protein. Comparison of the activity of PG-lysozyme conjugates generated from relatively low molecular weight PG copolymers did not reveal any obvious structure-activity relationships. Evaluation of the activity of conjugates composed of PG copolymers with molecular weights of 10000 or 20000 g/mol, however, indicated significantly higher activities of conjugates prepared from midfunctional synthetic polymers as compared to linear polymers of similar molecular weight.     

Microbial degradation of natural and of new synthetic polymers

Abstract In landfills, deposited waste material is usually faced with strictly anoxic conditions. This means that the design of new biodegradable polymers must take into consideration that degradation should be possible especially in the absence of molecular oxygen. Poly-β-hydroxybutyrate is depolymerized by the anaerobic fermenting bacterium Ilyobacter delafieldii through an extracellular hydrolase. Monomers are degraded inside the cells through classical β-oxidation. Polyalkanoates containing odd-numbered or branched-chain acid monomers should he degraded in an analogous manner; in most cases the final mineralization of these residues requires special pathways. A comparison of the chemistry of natural polymer biodegration leads to the conclusion that synthetic biodegradable polymers should be designed in the future to contain linkages which can be cleaved by extracellular hydrolytic enzymes. Recent findings on aerobic and anaerobic bacterial degradation of synthetic polyethers suggest that natural evolution of new depolymerizing enzymes, perhaps from existing hydrolases, could be possible in a reasonable amount of time, provided that the monomers are likely energy sources for a broad variety of microbes.     

Hydrolysis of diethyl diferulates by a tannase from Aspergillus oryzae

Diferulic acid forms cross-links in naturally occurring plant cell wall polymers such as arabinoxylans and pectins. We have used model ethyl esterified substrates to find enzymes able to break these cross-links. A tannase from Aspergillus oryzae exhibited esterase activity on several synthetic ethyl esterified diferulates. The efficiency of this esterase activity on most diferulates is low compared to that of a cinnamoyl esterase, FAEA, from Aspergillus niger. Of the diferulate substrates assayed, tannase was most efficient at hydrolysing the first ester bond of the 5–5- type of dimer. Importantly and unlike the cinnamoyl esterase, tannase from A. oryzae is able to hydrolyse both ester bonds from the 8–5-benzofuran dimer, thus forming the corresponding free acid product. These results suggest that tannases may contribute to plant cell wall degradation by cleaving some of the cross-links existing between cell wall polymers.     

Biotransformation enzymes in fish as tools for biomonitoring aquatic environment

Biotransformation in fish--as in mammals--is catalyzed by several enzymes. These convert liposoluble endogenous and exogenous substrates to more water-soluble compounds prior to excretion. The biotransformation enzymes are induced by environmental pollutants. The induction can be expected to precede the onset of more serious changes at higher organization levels. We have studied the effect of petroleum from a ship spill and bleached kraft mill effluent on hepatic biotransformation enzyme activities of local fish species perch (Perca fluviatilis) and vedace (Coregonus albula) in Finland. Four months after the petroleum spill an elevated level of monoxygenase as well as glutathione S-transferase enzyme activities was seen in perch. Afterwards the difference between the control perch and the exposed ones disappeared. Bleached kraft mill effluent had effect on hepatic biotransformation in vendace. Increasing exposure time and effluent concentration elevated the activities.     

Bioproduction of benzaldehyde in a solid–liquid two-phase partitioning bioreactor using <Emphasis Type="Italic">Pichia pastoris</Emphasis>

The bioproduction of benzaldehyde from benzyl alcohol using Pichia pastoris was examined in a solid–liquid two-phase partitioning bioreactor (TPPB) to reduce substrate and product inhibition. Rational polymer selection identified Elvax 40W as an effective sequestering phase, possessing partition coefficients for benzyl alcohol and benzaldehyde of 3.5 and 35.4, respectively. The use of Elvax 40W increased the overall mass of benzaldehyde produced by approx. 300% in a 5 l bioreactor, relative to a single phase biotransformation. The two-phase system had a molar yield of 0.99, indicating that only minor losses occurred. These results provide a promising starting point for solid–liquid TPPBs to enhance benzaldehyde production, and suggest that multiple, targeted polymers may provide relief for transformations characterized by multiple inhibitory substrates/product/by-products.     

Hepatocytes: the powerhouse of biotransformation

Liver is the most important organ involved in biotransformation of xenobiotics. Within the main organisational unit, the hepatocyte, is an assembly of enzymes commonly classified as phase I and phase II enzymes. The phase I enzymes principally cytochrome P450 catalyse both oxidative and reductive reactions of a bewildering number of xenobiotics. Many of the products of phase I enzymes become substrates for the phase II enzymes, which catalyse conjugation reactions making use of endogenous cofactors. As xenobiotic metabolising enzymes are responsible for the toxicity of many chemicals and drugs, testing the role of the biotransformation enzymes and the transporters within the hepatocyte is critical. New methodologies may be able to provide information to allow for better in vitro to in vivo extrapolation of data.     

Characterization of biotransformation enzyme activities in primary rat proximal tubular cells

The proximal tubule is a frequent target for nephrotoxic compounds due to it's ability to transport and accumulate xenobiotics and their metabolites, as well as by the presence of an organ-selective set of biotransformation enzymes. The aim of the present study was to characterize the activities of different biotransformation enzymes during primary culturing of rat proximal tubular cells (PT cells). Specific marker substrates for determining cytochrome P450 (CYP450) activity of primary cultured PT cells include 7-ethoxyresorufin (CYP1A1), caffeine (CYP1A), testosterone (CY2B/C, CYP3A), tolbutamide (CYP2C) and dextromethorphan (CYP2D1). Activities of the CYP450 isoenzymes decreased considerably during culture with the greatest loss in activity within 24 h of culture. In addition, expression of CYP450 apoprotein, including CYP1A, CYP2C, CYP2D, CYP2E and CYP4A, was detected in microsomes from freshly isolated PT cells by immunoblotting using specific antibodies. CYP2B and CYP3A apoprotein could not be detected. Activity of the phase II biotransformation enzymes GST, GGT, beta-lyase and UGT was determined with 1-chloro-2,4-dinitrobenzene, L-glutamic acid gamma-(7-amido-4-methyl-coumarin), S-(1,1,2,2-tetrafluoroethyl)-L-cysteine and 1-naphthol, respectively, as marker substrates. Activity of the phase II enzymes remained more stable and, in contrast to CYP450 activity, significant activity was still expressed after 1 week of PT cell culture. Thus, despite the obvious advantages of PT cells as an in-vitro model for studies of biotransformation mediated toxicity, the strong time dependency of especially phase I and, to a lesser extent, phase II biotransformation activities confers limitations to their application.     

Polymers for enhanced oil recovery: fundamentals and selection criteria

With a rising population, the demand for energy has increased over the years. As per the projections, both fossil fuel and renewables will remain as major energy source (678 quadrillion BTU) till 2030 with fossil fuel contributing 78% of total energy consumption. Hence, attempts are continuously made to make fossil fuel production more sustainable and cheaper. From the past 40 years, polymer flooding has been carried out in marginal oil fields and have proved to be successful in many cases. The common expectation from polymer flooding is to obtain 50% ultimate recovery with 15 to 20% incremental recovery over secondary water flooding. Both naturally derived polymers like xanthan gum and synthetic polymers like partially hydrolyzed polyacrylamide (HPAM) have been used for this purpose. Earlier laboratory and field trials revealed that salinity and temperature are the major issues with the synthetic polymers that lead to polymer degradation and adsorption on the rock surface. Microbial degradation and concentration are major issues with naturally derived polymers leading to loss of viscosity and pore throat plugging. Earlier studies also revealed that polymer flooding is successful in the fields where oil viscosity is quite higher (up to 126 cp) than injection water due to improvement in mobility ratio during polymer flooding. The largest successful polymer flood was reported in China in 1990 where both synthetic and naturally derived polymers were used in nearly 20 projects. The implementation of these projects provides valuable suggestions for further improving the available processes in future. This paper examines the selection criteria of polymer, field characteristics that support polymer floods and recommendation to design a large producing polymer flooding.     

Polyoxazoline-peptide adducts that retain antibody avidity

Synthetic polymers have long been used to modify various properties of proteins such as activity and solubility. Polyethylene glycol (PEG) has been widely used to form adducts with enzymes and antibodies. In this study, the polyoxazoline family of water-soluble polymers was used to synthesize adducts containing a synthetic peptide recognized by a monoclonal antibody (MAb) directed against human protein C (hPC). This is the first application of direct conjugation of unterminated or "living" polymer to a peptide. The avidity of the antibody for the various adducts was characterized with respect to size and hydrophilicity of methyl- and ethyl-substituted polyoxazoline polymers (POX). Avidity of the adducts was not found to be dependent upon the hydrophilicity and was slightly decreased due to polymer modification. The methyl-POX-peptide adducts were found to be highly water soluble, while the ethyl-POX-peptide adducts showed sporadic problems with aqueous solubility. Because the polymer-peptide adducts retained avidity for the antibody, polyoxazoline polymers may have potential application to protein-adduct chemistry.     

Production of 11α-hydroxysteroids from sterols in a single fermentation step by Mycolicibacterium smegmatis

11α-hydroxylated steroid synthons are one of the most important commercially pharmaceutical intermediates used for the production of contraceptive drugs and glucocorticoids. These compounds are currently produced by biotransformation using fungal strains in two sequential fermentation steps. In this work, we have developed by a rational design new recombinant bacteria able to produce 11α-hydroxylated synthons in a single fermentation step using cholesterol (CHO) or phytosterols (PHYTO) as feedstock. We have designed a synthetic operon expressing the 11α-hydroxylating enzymes from the fungus Rhizopus oryzae that was cloned into engineered mutant strains of Mycolicibacterium smegmatis that were previously created to produce 4-androstene-3,17-dione (AD), 1,4-androstadiene-3,17-dione (ADD) from sterols. The introduction of the fungal synthetic operon in these modified bacterial chassis has allowed producing for the first time 11αOH-AD and 11αOH-ADD with high yields directly from sterols in a single fermentation step. Remarkably, the enzymes of sterol catabolic pathway from M. smegmatis recognized the 11α-hydroxylated intermediates as alternative substrates and were able to efficiently funnel sterols to the desired hydroxylated end-products.     

Reductive biotransformations of organic compounds by cells or enzymes of yeast.

Saccharomyces cerevisiae catalyses the asymmetric reductive biotransformation of a variety of compounds containing a carbonyl group or carbon-carbon double bond. Oxidoreductases participating in these reactions which have commercial potential in biotransformation processes are likely to have relatively broad substrate specificity. Important carbonyl reductases falling into this category include YADH- and yeast NADP-dependent beta-ketoester reductases. The enoyl reductase component of the FAS complex may have a role in asymmetric yeast reduction of carbon-carbon double bonds of unnatural substrates. Other nicotinamide-requiring oxidoreductases of yeast are also surveyed to rationalize observed biotransformations of whole yeast cells in terms of specific enzymes. Genetic and protein engineering may enable enzymes to be tailored to accept new substrates. A greater understanding of the enzymes and reactions involved will facilitate further optimization and exploitation of these catalytic systems in industrial processes.