Structural studies on the core and the O-polysaccharide repeating unit of Pseudomonas aeruginosa immunotype 1 lipopolysaccharide.

The structure of the lipopolysaccharide (LPS) of Pseudomonas aeruginosa immunotype 1 was studied after mild acid and strong alkaline degradations by MS and NMR spectroscopy. Three types of LPS molecules were found, including those with an unsubstituted glycoform 1 core (A) or an isomeric glycoform 2 core substituted with one O-polysaccharide repeating unit (B) or with a long-chain O-polysaccharide. Therefore, of two core glycoforms, only glycoform 2 accepts the O-polysaccharide. In the structures A and B, Kdo, Hep, Hep7Cm, GalNAcAN3Ac, GalNFoAN, QuiNAc, GalNAla represent 3-deoxy-d-manno-octulosonic acid, l-glycero-d-manno-heptose, 7-O-carbamoyl-l-glycero-d-manno-heptose, 2-acetamido-3-O-acetyl-2-deoxygalacturonamide, 2-formamido-2-deoxygalacturonamide, 2-acetamido-2,6-dideoxyglucose and 2-(l-alanylamino)-2-deoxygalactose, respectively; all sugars are in the pyranose form and have the d configuration unless otherwise stated. One or more phosphorylation sites may be occupied by diphosphate groups. In a minority of the LPS molecules, an O-acetyl group is present in the outer core region at unknown position. The site and the configuration of the linkage between the O-polysaccharide and the core and the structure of the O-polysaccharide repeating unit were defined in P. aeruginosa immunotype 1. The QuiNAc residue linked to the Rha residue of the core was found to have the beta configuration, whereas in the interior repeating units of the O-polysaccharide this residue is in the alpha-configuration. The data obtained are in accordance with the initiation of biosynthesis of the O-polysaccharide of P. aeruginosa O6, which is closely related to immunotype 1, by transfer of d-QuiNAc-1-P to undecaprenyl phosphate followed by synthesis of the repeating O-antigen tetrasaccharide.     

Structural studies of the exopolysaccharide consisting of a nonasaccharide repeating unit isolated from Lactobacillus rhamnosus KL37B

A novel structure of exopolysaccharide from the lactic acid bacteria (LAB) Lactobacillus rhamnosus KL37B, from the human intestinal flora, is described. During the structural investigation of the exopolysaccharide it was found that the repeating unit is a nonasaccharide, which is the largest repeating unit found in LAB exopolysaccharides to date. The polysaccharide material was prepared by TCA extraction of a bacterial cell mass, purified by anion-exchange and gel permeation chromatography and characterized using chemical and enzymatic methods. On the basis of monosaccharide and methylation analysis and also 1D and 2D ¹H and ¹³C NMR spectroscopy the exopolysaccharide was shown to be composed of the following nonasaccharide repeating unit:The physicochemical cell surface study and adhesive properties indicated distinct surface properties of Lactobacillus rhamnosus strain KL37B with high adhesive abilities to Caco-2 cells, hydrophobicity and slime production, in comparison to other Lactobacillus strains used as controls.     

Synthesis of a repeating unit and the dimer of the repeating unit of the major chain of Shigella flexneri O-antigen polysaccharide

Methyl glycoside of the tetrasaccharide GlcNAc(beta 1-2)Rha(alpha 1-2)Rha(alpha 1-3)Rha, which represents a repeating unit of the basic chain of Shigella flexneri O-antigenic polysaccharides, was synthesized using acylated monosaccharide synthons. A dimer of the repeating unit, octasaccharide [GlcNAc(beta 1-2)Rha(alpha 1-2) Rha(alpha 1-3)Rha(alpha 1-3)]2-OMe was obtained by TrClO4-catalyzed condensation of two tetrasaccharide blocks.     

Multigram syntheses of the disaccharide repeating units of chondroitin 4- and 6-sulfates.

The multigram syntheses of beta-D-glucopyranosyluronic acid-(1-->3)-2-acetamido-2-deoxy-4- and 6-O-sulfo-D-galactopyranose disodium salt, the disaccharide repeating units of chondroitin 4- and 6-sulfates, are described. The disaccharide benzyl methyl 2,3,4-tri-O-benzoyl-beta-D-glucopyranosyluronate- (1-->3)-2-acetamido-2-deoxy-alpha-D-galactopyranoside was used as a common intermediate. Selective benzoylation at O-6 followed by O-sulfonation at C-4 of the aminosugar moiety, saponification and catalytic hydrogenation afforded the 4-O-sulfo derivative, whereas selective O-sulfonation at C-6 followed by similar deprotection steps provided the 6-O-sulfo derivative in high yield.     

Mechanisms underlying dioxygen reduction in laccases. Structural and modelling studies focusing on proton transfer

Background  

Laccases are enzymes that couple the oxidation of substrates with the reduction of dioxygen to water. They are the simplest members of the multi-copper oxidases and contain at least two types of copper centres; a mononuclear T1 and a trinuclear that includes two T3 and one T2 copper ions. Substrate oxidation takes place at the mononuclear centre whereas reduction of oxygen to water occurs at the trinuclear centre.     

Structural elucidation of a novel exopolysaccharide produced by a mucoid clinical isolate of Burkholderia cepacia. Characterization of a trisubstituted glucuronic acid residue in a heptasaccharide repeating unit.

The structure of the exopolysaccharide (EPS) produced by a clinical isolate of Burkholderia cepacia isolated from a patient with fibrocystic lung disease has been investigated. By means of methylation analyses, carboxyl reduction, partial depolymerization by fuming HCl and chemical degradations such as Smith degradation, lithiumethylenediamine degradation and beta-elimination, supported by GC/MS and NMR spectroscopic analyses, the repeat unit of the EPS has been identified and was shown to correspond to the acidic branched heptasaccharide with the following structure: [formula: see text]. This partially acetylated acidic polymer, distinguished by the presence of the less usual D-isomer of rhamnose and of a trisubstituted glucuronic acid residue, could represent the main EPS produced by this bacterial species.     

Production of a glucoglucuronan by a rhizobia strain infecting alfalfa. Structure of the repeating unit

The Rhizobium sp. T1 strain. which induces nodule formation on alfalfa and clover roots, produces, during growth, an extracellular polysaccharide composed of D-glucose and D-glucuronic acid noted glucoglucuronan. During the bacterial growth, the pH of the medium decreases slightly. The control of pH in the growth medium slightly reduces the glucoglucuronan production. Under the conditions tested in the present work, the weight-average molecular weight of the polymers produced with or without pH control are similar: Mw approximately 2 x 10(6); the repeating unit determined by chemical and NMR analyses corresponds to the disaccharide: --> 3)-beta-D-GlcpA-(1-->4)-beta-D-Glcp-(1 -->.     

Organization and heterogeneity of sequences within a repeating unit of human Y chromosome deoxyribonucleic acid.

Fragments of 3.4 kilobases (kb) are released from DNA of human males, but not DNA of human females, by cleavage with restriction endonucleases HaeIII, EcoRI, or EcoRII. Most, if not all, reiterated DNA which is specific for the Y chromosome (it-Y DNA) is present within these male-specific 3.4-kb molecules. Although such 3.4-kb molecules are themselves localized to the Y chromosome, this is not true for all sequences within them. At least two distinguishable types of reiterated sequences are found within each 3.4-kb molecule. One type consists of at least two families which are highly reiterated and are not confined to the Y chromosome. The other type is composed of an estimated minimum of 39 families, each moderately reiterated and localized to the Y chromosome. Y-specific and non-Y-specific sequences are interspersed with one another in the same 3.4-kb molecule. In the average 3.4-kb molecule, three 800 nucleotide lengths of Y-specific sequences alternate with four 250 nucleotide lengths of non-Y-specific sequences. Since the total number of families of Y-specific sequences, calculated on the basis of reiteration frequency and total abundance in a male genome, greatly exceeds the number of Y -specific sequences present in a single 3.4-kb molecule, it necessarily follows that the population of these 3.4-kb molecules is heterogeneous.     

Location of the O-acetyl substituents on a nonasaccharide repeating unit of sycamore extracellular xyloglucan

The locations of the O-acetyl substituents on the major nonasaccharide repeating unit of the xyloglucan isolated from sycamore extracellular polysaccharides were determined by a combination of analytical methods, including f.a.b.-m.s. and 1H-n.m.r. spectroscopy. The O-2-linked-beta-D-galactosyl residue of the nonasaccharide was found to be the dominant site of O-acetyl substitution. Both mono-O-acetylated and di-O-acetylated beta-D-galactosyl residues were detected. The degree of O-acetylation of the beta-D-galactosyl residue, was estimated by 1H-n.m.r. spectroscopy to be 55-60% at O-6, 15-20% at O-4, and 20-25% at O-3. 1H-n.m.r. spectroscopy also indicated that approximately 50% of the beta-D-galactosyl residues are mono-O-acetylated, 25-30% are di-O-acetylated, and 20% are not acetylated.     

Different regions of a complex statellite DNA vary in size and sequence of the repeating unit.

The 1.688 g/cm³ satellite DNA of Drosophila melanogaster is composed primarily of 359 base-pair units repeated in tandem. Most of these units contain a single cleavage site for both HaeIII and HinfI restriction endonucleases; however, some units lack one or both sites. Previously we had shown that the distribution of HaeIII and HinfI endonuclease sites varies widely between different regions of 1.688 g/cm³ satellite DNA; for example, some regions contain HaeIII sites in every unit and other regions (>10,000 base-pairs) contain no HaeIII sites (Carlson &; Brutlag, 1977). We have now cloned molecules of 1.688 g/cm³ satellite DNA which lack HaeIII sites and have shown that the absence of sites is caused by sequence variation rather than base modification. This result indicates that regions of 1.688 g/cm³ satellite DNA with different distributions of restriction sites differ in the sequence of their repeating units. We also show that a large fraction of the satellite DNA which is not cleaved by HaeIII endonuclease still contains HinfI endonuclease sites (and AluI sites) spaced about 359 base-pairs apart. However, one cloned segment lacking HaeIII sites was found to contain 33 tandem copies of a novel 254 base-pair unit. Sequence analysis showed that this 254 base-pair unit is homologous to the 359 repeat except for a 98 base-pair deletion. These data suggest that both units have evolved from a common ancestor and that each has subsequently become amplified into separate tandem arrays.     

The polysaccharides from heterocyst and spore envelopes of a blue-green alga. Structure of the basic repeating unit.

The polysaccharides from the envelopes of heterocysts and spores of Anabaena cylindrica consist of repeating units containing 1 mannosyl and 3 glucosyl residues, all linked by beta(1 yields 3) glycosidic bonds, with glycosidic bonds, with glucose, xylose, galactose, and mannose present in side branches. Degradation of the polysaccharides with specific glycosidases has permitted identification of the linkages to almost all of the branches. When the polysaccharides, from which all but two types of side branches had been cleaved, were digested with a beta(1 yields 3) endoglucanase, glucose, a tri-, and a pentasaccharide were produced. The oligosaccharide products were identified as (see article of journal). The backbones of the polysaccharides were sequenced from the reducing terminus by a modified Smith degradation. Analysis with NaB3H4 at each stage of the degradation showed that the backbones terminate in the sequence Man-Glc-Glc-Glc and are therefore presumed to have the structure (Man-Glc-Glc-Glc)n, and that they contain an average of from 128 to 150 sugar residues. From the information obtained, the repeating sequences of the original polysaccharides from the two types of differentiated cells of A. cylindrica could be largely deduced and appeared to be identical.     

Photophysical and electrochemical properties of a fullerene-stoppered rotaxane.

The photophysical and electrochemical properties of a fumaramide rotaxane stoppered with C(60) are reported. The results evidenced the strong binding interactions between the template and the macrocycle, which are also supported by molecular modelling.     

Synthesis of a spacer-containing repeating unit of the capsular polysaccharide of Streptococcus pneumoniae type 23F.

The synthesis is reported of 3-aminopropyl 4-O-(4-O-beta-D-glucopyranosyl-2-O-alpha-L-rhamnopyranosyl-beta-D- galactopyranosyl)-beta-L-rhamnopyranoside 3'-(glycer-2-yl sodium phosphate) (25 beta), which represents the repeating unit of the capsular polysaccharide of Streptococcus pneumoniae type 23F (American type 23) [(----4)-beta-D-Glcp-(1----4)-[Glycerol-(2-P----3)] [alpha-L- Rhap-(1----2)]-beta-D-Galp-(1----4)-beta-L-Rhap-(1----)n). 2,4,6-Tri-O-acetyl-3-O-allyl-alpha-D-galactopyranosyl trichloroacetimidate (5) was coupled with ethyl 2,3-di-O-benzyl-1-thio-alpha-L-rhamnopyranoside (6). Deacetylation of the resulting disaccharide derivative, followed by benzylidenation, and condensation with 2,3,4-trio-O-acetyl-alpha-L-rhamnopyranosyl trichloroacetimidate (10) afforded ethyl 4-O-[3-O-allyl-4,6-O-benzylidene-2-O-(2,3,4-trio-O-acetyl- alpha-L-rhamnopyranosyl)-beta-D-galactopyranosyl]-2,3-di-O-benzyl-1-thio - alpha-L-rhamnopyranoside (11). Deacetylation of 11, followed by benzylation, selective benzylidene ring-opening, and coupling with 2,3,4,6-tetra-O-acetyl-alpha-D-glucopyranosyl trichloroacetimidate (15) gave ethyl 4-O-[3-O-allyl-6-O-benzyl-4-O-(2,3,4,6- tetra-O-acetyl-beta-D-glucopyranosyl)-2-O-(2,3,4-tri-O-benzyl-alpha-L- rhamnopyranosyl)-beta-D-galactopyranosyl]-2,3-di-O-benzyl-1-thio-alpha-L - rhamnopyranoside (16). Deacetylation of 16 followed by benzylation, deallylation, and acetylation yielded ethyl 4-O-[3-O-acetyl-6-O-benzyl-4-O-(2,3,4,6-tetra-O-benzyl-beta-D-glucopy ran osyl)- 2-O-(2,3,4-tri-O-benzyl-alpha-L-rhamnopyranosyl)-beta-D-galactopyranosyl ]-2,3- di-O-benzyl-1-thio-alpha-L-rhamnopyranoside (20). The glycosyl bromide derived from 20, when coupled with 3-benzyloxycarbonylamino-1-propanol, gave the beta-glycoside (21 beta) as the major product. Deacetylation of 21 beta followed by condensation with 1,3-di-O-benzylglycerol 2-(triethylammonium phosphonate) (27), oxidation, and deprotection, afforded 25 beta.     

Synthesis of a hexasaccharide,the repeating unit of O-deacetylated GXM of C. neoformans serotype A

beta-D-GlcpA-(1-->2)-alpha-D-Manp-(1-->3)-[beta-D-Xylp-(1-->2)]-alpha-D-Manp-(1-->3)[-beta-D-Xylp-(1-->2)]-alpha-D-Manp, the repeating unit of the exopolysaccharide from Cryptococcus neoformans serovar A, was synthesized as its allyl glycoside. Thus, 3-O-selective acetylation of allyl 4,6-O-benzylidene-alpha-D-mannopyranoside afforded 2, and subsequent glycosylation of 2 with 2,3,4-tri-O-benzoyl-D-xylopyranosyl trichloroacetimidate furnished the beta-(1-->2)-linked disaccharide 4. Debenzylidenation followed by benzoylation gave allyl 2,3,4-tri-O-benzoyl-beta-D-xylopyranosyl-(1-->2)-3-O-acetyl-4,6-di-O-benzoyl-alpha-D-mannopyranoside (5), and selective 3-O-deacetylation gave the disaccharide acceptor 6. Coupling of 6 with 2-O-acetyl-3,4,6-tri-O-benzoyl-alpha-D-mannopyranosyl trichloroacetimidate yielded the trisaccharide 8, and subsequent deallylation and trichloroacetimidation gave 2,3,4-tri-O-benzoyl-beta-D-xylopyranosyl-(1-->2)-[2-O-acetyl-3,4,6-tri-O-benzoyl-alpha-D-mannopyranosyl-(1-->3)]-4,6-di-O-benzoyl-alpha-D-mannopyranosyl trichloroacetimidate (9). Condensation of the trisaccharide donor 9 with the disaccharide acceptor 6 gave the pentasaccharide 10 whose 2-O-deacetylation gave the acceptor 11. Glycosylation of 11 with methyl 2,3,4-tri-O-acetyl-alpha-D-glucopyranosyluronate trichloroacetimidate and subsequent deprotection gave the target hexasaccharide.     

Insight into coordination of dilead unit by molecules of 4-thiazolidinone-2-thione: Structural and computational studies

The reaction of Pb²⁺ ions with 4-thiazolidinone-2-thione (Hrd) yields to coordination of the uncommon dilead unit (Pb₂²⁺) by the N-deprotonated molecule of the ligand. The powder structure determination of the complex reveals an almost planar dimeric structure with the {N,S} coordination mode. The intermolecular distance of the Pb-Pb moiety (3.51(4) Å) is lower than the van der Waals parameter suggesting the formation of a bond. The structure in the solid state and DFT calculations of molecular orbitals and the presence of a bond critical point between the lead atoms clearly demonstrate the existence of a single bond within the Pb-Pb unit formed by the 6p orbital electrons. The lone pairs of the 6s orbitals do not participate in bonding with the ligand atoms and are likely bisdirected. FT-IR and FT-Raman spectra confirm the molecular structure since all the modes of the NH group disappear in the spectra of the complex, while the stretching mode of the CS bond shifts to lower values, as would be expected for this coordination fashion.     

Conformational studies on beta-bend containing a cis peptide unit.

Conformational studies have been carried out on the X-cis-Pro tripeptide system (a system of three linked peptide units, in the trans-cis-trans configuration) using energy minimization techniques. For X, residues Gly, L-Ala, D-Ala and L-Pro have been used. The energy minima have been classified into different groups based upon the conformational similarity. There are 15, 20, 18 and 6 minima that are possible for the four cases respectively and these fall into 11 different groups. A study of these minima shows that, (i) some minima contain hydrogen bonds--either 4-->1 or 1-->2 type, (ii) the low energy minima qualify themselves as bend conformations, (iii) cis' and trans' conformations are possible for the prolyl residue as also the C gamma-endo and C gamma-exo puckerings, and (iv) for Pro-cis-Pro, cis' at the first prolyl residue is ruled out, due to the high energy. The available crystal structure data on proteins and peptides, containing cis-Pro segment have been examined with a view to find the minima that occur in solid state. The data from protein show that they fall under two groups. The conformation at X in X-cis-Pro is near extended when it is a non-glycyl residue. In both peptides and proteins there exists a preference for trans' conformation at prolyl residue over cis' when X is a non-glycyl residue. The minima obtained can be useful in modelling studies.     

Sequential oligopeptides. Conformational studies of the oligopeptides and a polypeptide with the repeating sequence L-norvalyl-glycyl-L-proline

Conformational studies of a series of oligopeptides (from the tripeptide to the octadecapeptide) with the repeating sequence L -norvalyl-glycyl-L -proline and a polytripeptide with this sequence are reported. By means of chiroptical techniques, unordered conformations are found for all oligopeptides in water, trifluoroethanol, and ethylene glycol and for the water-insoluble polymer in trifluoroethanol. In ethylene glycol the polymer assumes a collagen-like structure. Infrared studies indicate that all the oligomers, in contrast to the polymer, are unordered in the solid state.