Uronic acid sequence in alginate from different sources

Alginate may be considered as a block co-polymer of D-mannuronic and L-guluronic acids, and consists of three types of blocks: homopolymeric blocks of mannuronic acid (MM) and of guluronic acid (GG), and blocks with an alternating sequence (MG). The block composition of alginates has been characterized by a simple chemical method involving partial hydrolysis with acid, followed by fractional precipitation of the acid-resistant part of the alginate. Alginates from eleven different species of brown algae have been examined and, for five species, alginates from different tissues have been compared. The results indicate that young tissue is rich in MM blocks, and that the difference between the alginates from different species is mainly due to the alginates from the older parts of the plants. Extracellular alginates from two types of bacteria have been examined.     

Multiblock copolymers of L-lactide and trimethylene carbonate

Sequential copolymerizations of trimethylene carbonate (TMC) and l-lactide (LLA) were performed with 2,2-dibutyl-2-stanna-1,3-oxepane as a bifunctional cyclic initiator. The block lengths were varied via the monomer/initiator and via the TMC/l-lactide ratio. The cyclic triblock copolymers were transformed in situ into multiblock copolymers by ring-opening polycondensation with sebacoyl chloride. The chemical compositions of the block copolymers were determined from (1)H NMR spectra. The formation of multiblock structures and the absence of transesterification were proven by (13)C NMR spectroscopy. Differential scanning calorimetry (DSC), wide-angle X-ray scattering (WAXS), and dynamic mechanical analysis (DMA) measurements confirmed the existence of a microphase-separated structure in the multiblock copolymers consisting of a crystalline phase of poly(LLA) blocks and an amorphous phase formed by the poly(TMC) blocks. Stress-strain measurements showed the elastomeric character of these biodegradable multiblock copolymers, particularly in copolymers having epsilon-caprolactone as comonomer in the poly(TMC) blocks.     

Chemical modification of the bifunctional regulatory protein of maize leaf pyruvate,orthophosphate dikinase. Evidence for two distinct active sites

The active site(s) of the bifunctional regulatory protein of pyruvate,orthophosphate dikinase catalyze(s) the Pi-dependent activation (dephosphorylation) and ADP-dependent inactivation (phosphorylation) of maize leaf dikinase. The chemical modification studies of the regulatory protein active sites presented in this paper are interpreted as showing the two sites to be physically distinct. Pyridoxal 5'-phosphate and 2-nitro-5-thiocyanatobenzoate (NTCB) selectively inhibit the dikinase activating site, which is protected by the nonprotein substrate, Pi. Phenylglyoxal blocks both the activation and inactivation sites; the former is protected selectively by Pi and the latter by both the nonprotein substrate, ADP, and Pi. The Pi that protects the inactivation site is distinct from the activation substrate. Inhibition studies show Pi to be a parabolic competitive inhibitor of the ADP-dependent inactivation of dikinase, implying that besides substrate Pi, a second phosphate also binds to the regulatory protein. The above chemical modifications are not mutually exclusive; neither NTCB, 5,5'-dithiobis-(2-nitrobenzoate), nor pyridoxal 5'-phosphate blocks subsequent modification of the activation site by phenylglyoxal. Similarly, prior modification with NTCB does not affect modification by pyridoxal 5'-phosphate.     

White biotechnology for green chemistry: fermentative 2-oxocarboxylic acids as novel building blocks for subsequent chemical syntheses

Functionalized compounds, which are difficult to produce by classical chemical synthesis, are of special interest as biotechnologically available targets. They represent useful building blocks for subsequent organic syntheses, wherein they can undergo stereoselective or regioselective reactions. "White Biotechnology" (as defined by the European Chemical Industry [ http://www.europabio.org/white_biotech.htm ], as part of a sustainable "Green Chemistry,") supports new applications of chemicals produced via biotechnology. Environmental aspects of this interdisciplinary combination include: Use of renewable feedstock Optimization of biotechnological processes by means of: New "high performance" microorganisms On-line measurement of substrates and products in bioreactors Alternative product isolation, resulting in higher yields, and lower energy demand In this overview we describe biotechnologically produced pyruvic, 2-oxopentaric and 2-oxohexaric acids as promising new building blocks for synthetic chemistry. In the first part, the microbial formation of 2-oxocarboxylic acids (2-OCAs) in general, and optimization of the fermentation steps required to form pyruvic acid, 2-oxoglutaric acid, and 2-oxo-D-gluconic acid are described, highlighting the fundamental advantages in comparison to chemical syntheses. In the second part, a set of chemical formula schemes demonstrate that 2-OCAs are applicable as building blocks in the chemical synthesis of, e.g., hydrophilic triazines, spiro-connected heterocycles, benzotriazines, and pyranoic amino acids. Finally, some perspectives are discussed.     

Effects of Adult Dreissena polymorpha on Settling Juveniles and Associated Macroinvertebrates

The impact of Dreissena polymorpha settlement on recruitment of juvenile mussels and density of other macroinvertebrates was studied in field experiments using blank concrete blocks and tiles (control), blocks and tiles with attached empty zebra mussel shells, and blocks and tiles with attached living mussels. On blocks, dominant invertebrate taxa showed colonization patterns coinciding with increased habitat complexity owing to zebra mussel settlement or the biodeposition of faeces and pseudofaeces. Adult and especially juvenile zebra mussels preferred blocks with empty shells to blank blocks and blocks with living mussels; this might possibly be caused by a chemical cue that induces gregarious settlement. Lower recruitment on blocks with attached living mussels compared to blocks with only shells could be the consequence of ingestion of larvae by adult mussels and of competition for food. On tiles, the sediments deposited and the organic content of the sediment were investigated. Sedimentation was significantly higher on shell‐only and live‐mussel tiles compared to blank tiles. Organic matter differed significantly between blank and live‐mussel tiles.     

Direct determination of the π-helix structure and helix transition behavior of poly(β-phenethyl l-aspartate) via synchrotron X-ray diffraction

The helix-sense inversions of poly(β-phenethyl l -aspartate) (2P) and diblock copolymers (2P-3P), with 2P and poly(β-phenylpropyl l -aspartate) (3P) blocks, were studied in their solid states using synchrotron wide-angle X-ray diffraction and small-angle X-ray scattering. The characteristic parameters of the π-helix structure of 2P were directly determined in situ after the helix transition at a high temperature. In the 2P-3P block copolymers, the main chains of the 3P blocks initially convert from right- to left-handed α-helices, and then the 2P blocks convert irreversibly from right-handed α-helices to left-handed π-helices. The chemical structures of the side chains of poly(l -aspartic acid ester)s significantly affect their helix transition behaviors.     

Synthesis of the C-terminal region of opioid receptor like 1 in an SDS micelle by the native chemical ligation: effect of thiol additive and SDS concentration on ligation efficiency.

In the process of developing a method for the synthesis of membrane proteins, the conditions for native chemical ligation, namely, detergent concentration and the chemical characteristics of the thiol additive were investigated in detail. The C-terminal region of the opioid receptor like 1, ORL1(288-370), which contains C-terminal intracellular and transmembrane domains, was chosen as a model. The building blocks, ORL1(329-370) and ORL1(288-328)-SR-Gly-Arg(5)-Leu (-SR- : -SCH(2)CH(2)CO-) were most effectively condensed slightly below the critical micelle concentration of SDS and in the presence of mercaptoethanesulfonic acid as a thiol additive. The results showed that the concentration of SDS and the charge on the thiol additive are crucial factors for the effective synthesis of a membrane protein by native chemical ligation.     

A new chemical tool for exploring the role of the PDE4D isozyme in leukocyte function

Nicotinamide (2) is a potent and selective inhibitor of the PDE4D isozyme and as a chemical tool selectively blocks eosinophil mediator release and chemotaxis thus linking the role of PDE4D to eosinophil function.     

ChemDB update--full-text search and virtual chemical space

ChemDB is a chemical database containing nearly 5M commercially available small molecules, important for use as synthetic building blocks, probes in systems biology and as leads for the discovery of drugs and other useful compounds. The data is publicly available over the web for download and for targeted searches using a variety of powerful methods. The chemical data includes predicted or experimentally determined physicochemical properties, such as 3D structure, melting temperature and solubility. Recent developments include optimization of chemical structure (and substructure) retrieval algorithms, enabling full database searches in less than a second. A text-based search engine allows efficient searching of compounds based on over 65M annotations from over 150 vendors. When searching for chemicals by name, fuzzy text matching capabilities yield productive results even when the correct spelling of a chemical name is unknown, taking advantage of both systematic and common names. Finally, built in reaction models enable searches through virtual chemical space, consisting of hypothetical products readily synthesizable from the building blocks in ChemDB. AVAILABILITY: ChemDB and Supplementary Materials are available at http://cdb.ics.uci.edu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.     

Attenuated total reflection infrared spectroscopy of white-rot decayed beech wood

Small blocks of beech wood were exposed to the white-rot fungus Trametes versicolor for a period of 84 days to investigate chemical alteration in decayed wood by infrared spectroscopy. Decayed samples were analyzed at 2 week intervals by using attenuated total teflection (ATR) infrared spectroscopy as a rapid method. Analyses showed that chemical alteration in wood began after the second week of exposure. The appearance of new peaks indicated chemical modification of cell walls between days 28 and 70 of exposure to the fungus, and the disappearance of the peaks at day 84 indicates removal of the cell wall constituents. This investigation showed that ATR spectroscopy is a very applicable and rapid method for studying wood biodegradation.     

Fractional isolation and study of the structure of galactomannan from sophora (Styphnolobium japonicum) seeds

Two fractions (1 and 2) of the galactomannan from seeds of sophora (Styphnolobium japonicum) were isolated using cold and hot aqueous extraction with a total yield of 12.88%. The two fractions differed by the ratio between mannose (Man) and galactose (Gal) residues (4.8:1 and 5.3:1, respectively) and molecular weight (1190 and 1400 kDa, respectively). Aqueous solutions of these fractions were optically active ([alpha]D +4.80 degrees and -3.36 degrees, respectively) and highly viscous ([eta] 1028.8 and 1211.2 ml/g). 13C NMR spectra of both fractions were identical with respect to the number and positions of signals, which indicates that their primary structures were identical. Using chemical and spectroscopic (IR and NMR) methods, it was shown that the galactomannan has a main chain consisting of 1,4-beta-D-mannopyranose, some residues of which (16 and 17% in fractions 1 and 2, respectively) are alpha-galactosylated at the C-6 position. Frequencies of differently substituted mannobiose blocks in the chain, calculated for fraction 1 using NMR spectroscopic data, were 0.13 for the disubstitited blocks Gal(Man-Man)Gal, 0.37 for the sum of monosubstituted blocks Gal(Man-Man) and (Man-Man)Gal, and 0.50 for the unsubstituted block Man-Man.     

Evaluation of aluminum phosphide against wood-destroying insects

Aluminum phosphide, a well-known stored grain fumigant, available in solid formulation, has shown promise as wood fumigant. This chemical decomposes to phosphine when exposed to moisture. The feasibility of fumigant treatment to extend the service life of wood was evaluated in a small block test of two wood species. Hard wood (Mangifera indica L.) and conifer blocks (Pinus roxburghii Sargent) were fumigated with different concentrations (0.05, 0.1, 0.2, 0.4, 0.8, and 1.6%) of aluminum phosphide. Fumigated blocks were exposed to Lyctus africanus Lesne (Coleoptera; Lyctidae) larvae. Results revealed that aluminum phosphide showed complete mortality of Lyctus larvae at 0.2% concentration, that is, 0.93 g/m3 retention level. Mean mortality of 74% of Lyctus larvae was observed in soft wood blocks fumigated with lowest concentration, that is, 0.05% of aluminum phosphide, whereas in hard wood blocks > 85% mortality was observed at this concentration.     

Complex structural behavior of oligopurine-oligopyrimidine sequence cloned within the supercoiled plasmid.

Synthetic sequence GATCC(AG)7ATCG(AT)4CG(AG)7 was cloned into plasmid and its structural behavior under the influence of supercoiling was analysed by chemical modification at variety of experimental conditions. It was found that this sequence adopts at least two different non-B conformations depending on -delta and pH values. Moreover, 12 nucleotide long non-pur.pyr spacer region separating two identical (AG)7 blocks does not provide a significant energy barrier protecting against unusual structures formation.     

New hypothesis on the role of alternating sequences in calcium-alginate gels

The availability of mannuronan and mannuronan C-5 epimerases allows the production of a strictly alternating mannuronate-guluronate (MG) polymer and the MG-enrichment of natural alginates, providing a powerful tool for the analysis of the role of such sequences in the calcium-alginate gel network. In view of the calcium binding properties of long alternating sequences revealed by circular dichroism studies which leads eventually to the formation of stable hydrogels, their direct involvement in the gel network is here suggested. In particular, 1H NMR results obtained from a mixed alginate sample containing three polymeric species, G blocks, M blocks, and MG blocks, without chemical linkages between the block structures, indicate for the first time the formation of mixed junctions between G and MG blocks. This is supported by the analysis of the Young's modulus of hydrogels from natural and epimerized samples obtained at low calcium concentrations. Furthermore, the "zipping" of long alternating sequences in secondary MG/MG junctions is suggested to account for the shrinking (syneresis) of alginate gels in view of its dependence on the length of the MG blocks. As a consequence, a partial network collapse, macroscopically revealed by a decrease in the Young's modulus, occurred as the calcium concentration in the gel was increased. The effect of such "secondary" junctions on the viscoelastic properties of alginate gels was evaluated measuring their creep compliance under uniaxial compression. The experimental curves, fitted by a model composed of a Maxwell and a Voigt element in series, revealed an increase in the frictional forces between network chains with increasing length of the alternating sequences. This suggests the presence of an ion mediated mechanism preventing the shear of the gel.     

Principles of nanostructure design with protein building blocks

Currently there is increasing interest in nanostructures and their design. Nanostructure design involves the ability to predictably manipulate the properties of the self-assembly of autonomous units. Autonomous units have preferred conformational states. The units can be synthetic material science-based or derived from functional biological macromolecules. Autonomous biological building blocks with available structures provide an extremely rich and useful resource for design. For proteins, the structural databases contain large libraries of protein molecules and their building blocks with a range of shapes, surfaces, and chemical properties. The introduction of engineered synthetic residues or short peptides into these can expand the available chemical space and enhance the desired properties. Here we focus on the principles of nanostructure design with protein building blocks.     

Comparative analysis of human and bovine papillomaviruses

A method is presented for the analysis and comparison of nucleic acid and protein sequences utilizing all identity blocks (the term "identity block" refers to a set of consecutive matches between two sequences) above a prescribed length. Moreover, such identity blocks are determined for various groupings of amino acids according to chemical, functional, charge, and hydrophobic classifications. Alignment maps based on these classifications and containing all statistically significant identity blocks between two or more sequences are constructed. New theoretical results for determining the expected length of the longest identity block between sequences are also presented and are used, along with permutation procedures, to ascertain the significance of sequence identity blocks. As an example of the type of information that can be obtained, comparison has been made of the complete DNA sequences and the E1, E2, L1, and L2 genes of human and bovine papillomaviruses based on the classification schemes described above.     

Polysaccharide composition of mycelium and cell walls of the fungus Penicillium roqueforti

Preliminary data on the polysaccharide composition of mycelium and cell walls of the submergedly grown fungus Penicillium roqueforti were obtained. Mild acid hydrolysis of mycelium and cell walls led to formation of glucose, mannose and galactose, whereas acid treatment under drastic conditions afforded glucosamine as the hydrolysis product of chitin, which content in the cell walls was estimated as 19%. Sequential treatment of the mycelium with hot water and 1 M NaOH at room temperature gave rise to several polysaccharide fractions, which were characterized by their monosaccharide composition. The main fraction obtained by the action of alkali, according to NMR spectroscopy, mass spectrometry and chemical methods of structural analysis data, is a linear alpha-D-glucopyranan containing blocks of (1 --> 3)-linked glucose residues interconnected by (1 --> 4)-linkages. Water-soluble polysaccharides contained linear blocks of (1 --> 5)-linked beta-galactofuranose residues, probably connected with a mannan core. The data obtained may be important for chemotaxonomy of the genus Penicillium.     

HPMA as a scaffold for the modular assembly of functional peptide polymers by native chemical ligation

Synthetic peptides are valuable tools in fundamental and applied biomedical research. On one hand, these molecules provide highly efficient access to competitive inhibitors of molecular interactions and enzyme substrates by rational design. On the other hand, peptides may serve as powerful vectors to mediate cellular uptake of molecules that otherwise enter cells only poorly. The coupling of both such functionalities provides access to molecules interfering with molecular processes inside the cell. However, the combination of several functionalities on one synthetic peptide may be compromised by problems associated with the synthesis of long peptides. Native chemical ligation enables the chemoselective coupling of fully deprotected functional building blocks. However, peptide thioesters are still not accessible by standard solid-phase peptide synthesis. Here, we demonstrate the cofunctionalization of a thioester-activated N-hydroxypropyl methacrylamide (HPMA) copolymer (28,500 Da) with the cell-penetrating peptide (CPP) nonaarginine and a bioactive peptide as independent building blocks by native chemical ligation. Nonaarginine was employed as a cell-penetrating peptide (CPP), a fluorescein-labeled analogue of a pro-apoptotic peptide as a biofunctional cargo. Incorporation of the fluorescein label enabled the highly sensitive quantification of the coupling stoichiometry by fluorescence correlation spectroscopy (FCS) using 0.4 pmol/12 ng of labeled construct. A construct only bearing the functional cargo peptide required cellular import by electroporation in order to show activity. In contrast, a construct combining all functionalities was active upon incubation of cells, validating the modular nature of the approach.     

Semi‐synthesis of murine prion protein by native chemical ligation and chemical activation for preparation of polypeptide‐α‐thioester

Prions are suspected as pathogen of the fatal transmissible spongiform encephalopathies. Strategies to access homogenous prion protein (PrP) are required to fully comprehend the molecular mechanism of prion diseases. However, the polypeptide fragments from PrP show a high tendency to form aggregates, which is a gigantic obstacle of protein synthesis and purification. In this study, murine prion sequence 90 to 230 that is the core three‐dimensional structure domain was constructed from three segments murine PrP (mPrP)(90–177), mPrP(178–212), and mPrP(213–230) by combining protein expression, chemical synthesis and chemical ligation. The protein sequence 90 to 177 was obtained from expression and finally converted into the polypeptide hydrazide by chemical activation of a cysteine in the tail. The other two polypeptide fragments of the C‐terminal were obtained by chemical synthesis, which utilized the strategies of isopeptide and pseudoproline building blocks to complete the synthesis of such difficult sequences. The three segments were finally assembled by sequentially using native chemical ligation. This strategy will allow more straightforward access to homogeneously modified PrP variants. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.     

Syntheses and physical characterization of new aliphatic triblock poly(L-lactide-b-butylene succinate-b-L-lactide)s bearing soft and hard biodegradable building blocks

This study presents chemical syntheses and physical characterization of a new aliphatic poly(L-lactide-b-butylene succinate-b-L-lactide) triblock copolyester with soft and hard biodegradable building blocks. First, poly(butylene succinate) (PBS) prepolymers terminated with hydroxyl functional groups were synthesized through melt polycondensation from succinic acid and 1,4-butanediol. Further, a series of new PLLA-b-PBS-b-PLLA triblock copolyesters bearing various average PLLA block lengths were prepared via ring opening polymerization of L-lactide with the synthesized hydroxyl capped PBS prepolymer (Mn = 4.9 KDa) and stannous octanoate as the macroinitiator and catalyst, respectively. By means of GPC, NMR, FTIR, DSC, TGA, and wide-angle X-ray diffractometer (WAXD), the macromolecular structures and physical properties were intensively studied for these synthesized PBS prepolymer and PLLA-b-PBS-b-PLLA triblock copolyesters. 13C NMR and GPC experimental results confirmed the formation of sequential block structures without any detectable transesterification under the present experimental conditions, and the molecular weights of triblock copolyesters could be readily regulated by adjusting the feeding molar ratio of L-lactide monomer to the PBS macroinitiator. DSC measurements showed all single glass transitions, and their glass transition temperatures were found to be between those of PLLA and PBS, depending on the lengths of PLLA blocks. It was noteworthy that the segmental flexibilities of the hard PLLA blocks were found to be remarkably enhanced by the more flexible PBS block partner, and the PBS and PLLA building blocks were well mixed in the amorphous regions. Results of TGA analyses indicated that thermal degradation and stabilities of the PLLA blocks strongly depended on the average PLLA block lengths of triblock copolyesters. In addition, FTIR and WAXD results showed the coexistence of the assembled PLLA and PBS crystal structures when the average PLLA block length became larger than 7.8. These results may be beneficial for this new biodegradable aliphatic triblock copolyester to be applied as a potential biomaterial.