Sugar specificity of anti-B hemagglutinin produced by Streptomyces sp

A hemagglutinin specific for blood group B antigen has been purified to 190-fold from the culture fluid of a strain of $\text{Streptomyces}$ sp. by conventional procedure involving ammonium sulfate fractionation and column chromatography. The molecular weight of the partially purified preparation was estimated to be approximately 5000±1000; this value is extremely small as compared with those of hemagglutinins which have been so far isolated from various sources.Hemagglutination-inhibition tests revealed that the $\text{Streptomyces}$ agglutinin has a specificity to combine with D-galactose and several saccharides having D-galactose residues at the non-reducing terminal, and that the special configuration of the hydroxyl groups at C-2 and C-4, particularly the hydroxyl group at C-2, is essential for binding of the sugars to the hemagglutinin.     

Some Properties and Characterization of Rice Seed Hemagglutinin

The phytohemagglutinin of rice seed has been purified by a sequence of steps involving fractionation with ammonium sulfate and successive chromatography on DEAE-and eMcellulose and finally gel filtration on Bio-Gel P-100. The purified rice seed hemagglutinin was shown to be homogeneous by electrophoresis on polyacrylamide gel and its molecular weight was 10,000, calculated from both the Ve/Vo value of gel filtration on Bio-Gel P-100 and the sum of the individual constituents (amino acids, sugars and metals). In addition to amino acid, the rice seed hemagglutinin contained 26.8% covalently bound carbohydrate which was identified and quantitated by gas chromatography of the acetylated alditols. Glucose was the predominant sugar with lesser amounts of glucosamine, xylose, and mannose also being present. And the rice seed hemagglutinin contained 1 g atom of calcium per molecule. The molecular weight of the rice seed hemagglutinin is smallest compared with some of phytohemagglutinins isolated from leguminous seeds and other plant sources. The rice seed hemagglutinin has the blastogenetic activity for human peripheral lymphocytes as well as Phaseolus vulgaris phytohemagglutinins or concanavalin A, jack bean hemagglutinin.     

Further Study on the Relation of Polyoxin Structure to Chitin Synthetase Inhibition

As a part of studies on the mechanism of action of antibiotics polyoxins, effects of various N-aminoacyl derivatives of polyoxin C and other polyoxins on chitin-UDP acetylglucosaminyl-transferase (EC 2.4.1.16, chitin synthetase) prepared from phytopathogenic fungus Piricularia oryzae were investigated. It was found that they inhibited the enzyme in competition with the substrate UDP-N-acetylglucosamine, Inhibitor constants, Ki, for these polyoxins were determined and the values of binding affinity, ?ΔG_bind of the inhibitors to the enzyme were calculated from the Ki values. In addition, by using these ?ΔG_bind values the values of partial binding affinity, ?Δg for the several atoms and atomic groups or the several moieties contained in the polyoxin J molecule were estimated. From the results obtained, it was concluded that the carbamoylpolyoxamic acid moiety of polyoxins helps to stabilize the polyoxin-enzyme complex through the contributions of its oxygen atom at C?1″, amino group at C?2″, hydroxyl groups at C?3″ and C?4″, aliphatic carbon chain and terminal carbamoyloxy group.

The results obtained by the kinetic investigation using various nucleotides and nucleotide sugars suggested that there was a specific binding site on the enzyme corresponding to the uridine moiety of UDP-N-acetylglucosamine, and that the pyrimidine nucleoside moiety of polyoxins was also bound to this site.     

Crystal structure of the reduced Schiff-base intermediate complex of transaldolase B from Escherichia coli: mechanistic implications for class I aldolases.

Transaldolase catalyzes transfer of a dihydroxyacetone moiety from a ketose donor to an aldose acceptor. During catalysis, a Schiff-base intermediate between dihydroxyacetone and the epsilon-amino group of a lysine residue at the active site of the enzyme is formed. This Schiff-base intermediate has been trapped by reduction with potassium borohydride, and the crystal structure of this complex has been determined at 2.2 A resolution. The overall structures of the complex and the native enzyme are very similar; formation of the intermediate induces no large conformational changes. The dihydroxyacetone moiety is covalently linked to the side chain of Lys 132 at the active site of the enzyme. The Cl hydroxyl group of the dihydroxyacetone moiety forms hydrogen bonds to the side chains of residues Asn 154 and Ser 176. The C3 hydroxyl group interacts with the side chain of Asp 17 and Asn 35. Based on the crystal structure of this complex a reaction mechanism for transaldolase is proposed.     

New N-substituted hydrazones,derivatives of uridyl aldehyde

N-substituted isomeric hydrazones of uridyl aldehyde have been synthesized. The occurrence of the dominant E isomers with respect to the azomethine group was confirmed by means of NMR spectroscopy. Synthesized hydrazones feature an acetonide moiety as a protection of two hydroxyl groups on the ribose part. The attempt to remove the protecting group resulted in an azo-hydrazone tautomeric mixture. The described compounds may be valuable chiral ligands for metal chelation. Assessment of manganese(II) ion affinity to one selected hydrazone was performed.     

Immunochemical studies on blood groups: The internal structure and immunological properties of water-soluble human blood group A substance studied by Smith degradation,liberation, and fractionation of oligosaccharides and reaction with lectins

Carbohydrate structures in the interior of a blood group A active substance (MSS) were exposed by one and by two Smith degradations. Reactivities of the original glycoprotein and its Smith degraded products with 13 different lectins and with anti-I Ma were studied by quantitative precipitin assay. MSS and its first Smith degraded product completely precipitated Ricinus communis hemagglutinin with five times less of the first Smith degraded glycoprotein being required for 50% precipitation. The second Smith degraded material precipitated only 90% of the lectin. MSS did not precipitate peanut lectin, whereas its first and second Smith degraded products completely precipitated the lectin. The first Smith degraded glycoprotein also reacted well with Wistaria floribunda, Maclura pomifera, Bauhinia purpurea alba, and Geodia lectins indicating that its carbohydrate moiety could contain dGalNAc, dGalβ1 → 3dGalNAc, dGalβ1 → 4dGlcNAc, dGalβ1 → 3dGlcNAcβ1 → 3dGal and/or dGalβ1 → 4dGlcNAcβ1 → 6dGal and/or dGalβ1 → 4dGlcNAcβ1 → 6dGalNAc determinants at nonreducing ends. The second Smith degraded material precipitated well with Ricinus communis hemagglutinin, Arachis hypogaea, Geodia cydonium, Maclura pomifera, and Helix pomatia lectins showing that dGalNAc, dGalβ1 → 3dGalNAc, dGalβ1 → 4dGlcNAc residues at terminal nonreducing ends could be involved. Monoclonal anti-I Ma (group 1) serum reacted strongly with the first Smith degraded product indicating large numbers of anti-I Ma determinants, dGalβ1 → 4dGlcNAcβ1 → d 6dGal and/or dGalβ1 → 4dGlcNAcβ1 → 6dGalNAc at nonreducing ends. The comparable activities of the native and Smith degraded products with wheat germ lectin indicate capacity to react with DGlcNAc residues at nonreducing ends and/or at positions in the interior of the chain. The totality of lectin reactivities indicates heterogeneity of the carbohydrate side chains. Oligosaccharides with ³H at their reducing ends released from the protein core of the first and second Smith degraded products were obtained by treatment with 0.05 m NaOH and 1 M NaB³H₄ at 50 °C for 16 h (Carlson degradation). The liberated reduced oligosaccharides were fractionated by dialysis, followed by retardion, Bio-Gel P-2, P-4, and P-6 columns. They were further purified on charcoal-celite columns, and by preparative paper chromatography and high-pressure liquid chromatography. Their distribution by size was estimated by the yields on dialysis, Bio-Gel P-2, and Bio-Gel P-6 chromatography, and from the radioactivity of the reduced sugars. Of the oligosaccharide fractions from the first Smith degraded product, about 77% of the carbohydrate side chain residues contained from 1 to 6 sugars, 13% from 7 to perhaps 12 sugars, and 10% was nondialyzable (polysaccharides and glycopeptide fragments). Of the second Smith degraded product, approximately 82% of carbohydrate residues had from 1 to 6 sugars, 14% from 7 to perhaps 20 sugars and 4% was nondialyzable. The biological activity profile of the two Smith degraded products together with the size distributions of the oligosaccharides indicated that their carbohydrate side chains, comprised a heterogeneous population ranging in size from 1 to about 12 sugars. When most of these chains that are shorter than hexasaccharides are fully characterized it may be possible to reconstruct the overall structure of the carbohydrate moiety of the blood group substances and account for their biological activities.     

Purification and characterization of a hemagglutinin from Arachis hypogeae.

A. hypogaea hemagglutinin was purified by ammonium sulfate fractionation and Sepharose 6 B column chromatography. The homogeneity of the purified hemagglutinin was ascertained by ultracentrifugal analysis and polyacrylamide gel electrophoresis. It has a molecular weight of 106.500 and is a tetramer of a subunit with a molecular weight of 27.000. The purified hemagglutinin agglutinated neuraminidase-treated human erythrocytes regardless of their ABO group type, but did not agglutinate intact erythrocytes. In hapten inhibition assays with simple sugars, the so-called M?kel?'s group 2 sugars, which bear the same configuration of hydroxy groups at C-3 and C-4 as D-galactopyranose, were inhibitors for this hemagglutinin. It does not contain any carbohydrate, in contrast to most phytohemagglutinins except concanavalin A and wheat germ agglutinin.     

Molecular modeling of the conformational and sodium ion binding properties of the oligosaccharide component of ganglioside GM1

The receptor-like recognition behavior of the GM1 ganglioside has been examined theoretically in terms of conformational and binding properties. Modeling was conducted at two limiting conditions of dielectric constant in order to determine sensitivity to scaling of coulombic interactions. A systematic conformational search of the GM1 oligosaccharide in the absence of explicit solvent molecules indicates that there are many inherently low energy conformational states. Up to 39 conformers were found with energies within 5 kcal/mole of the observed lowest energy conformer. Using a dielectric constant of 80, a systematic search of sodium binding sites on GM1 identified 37 sites where a positively charged group might bind, while at least 12 sites were identified using a dielectric constant of 1. Notably important binding sites include pockets formed by the proximity of glycosidic (O1), sugar ring (O5), and exocyclic methylene hydroxyl (OH6) oxygens on the sugars. The oxygens of acetyl groups attached to sugars also contribute to the binding. Direct coordination with the carboxylate of sialic acid is not a prerequisite for cationic binding. The large number of conformational states and binding sites for the GM1 oligosaccharide are paradoxical to the specific recognition behavior of the molecule. This paradox can be explained in terms of bridging ligands, which are found from molecular dynamics to be capable of stabilizing molecular conformation. © 1994 John Wiley & Sons, Inc.     

Biosynthesis of saponins in the genus Medicago

Saponins from Medicago species are glycosidic compounds with an aglycone moiety formed through the enzymatic cyclization of 2,3-oxidosqualene by the β-amyrin cyclase. All the saponins from Medicago genus possess the triterpenic pentacyclic nucleus belonging to the class of β-amyrin. The so formed β-amyrin skeleton can be further modified by oxidative reactions, mediated by cytochromes belonging to the class of cytochrome P450, to give different saponin compounds, characterized by the presence of hydroxyl or carboxyl groups located in specific positions of the triterpenic skeleton. Based on the position and the oxidation degree of the substituents, it is possible to distinguish two groups of saponins (sapogenins) in Medicago spp: (1) sapogenins possessing an OH group on C-24 (soyasapogenols A, B and E) without any substituent at the C-28 atom, and (2) sapogenins possessing the COOH group at C-28 that are associated with different oxidation degrees (zero, OH, CHO, COOH) at C-23. These results seem to indicate that the oxidation at C-24 and the presence of the COOH group at C-28 are mutually exclusive. The subdivision in the aglycone moiety is reflected also in the sugar moiety, operated by glycosyltranferases, as the saponins of the two groups differ for the position and the nature of the sugar chains. Based on these findings, new considerations on the biosynthesis of saponins in the genus Medicago can be drawn and a biosynthetic scheme is proposed.     

Structural and functional characterization of BaiA,an enzyme involved in secondary bile acid synthesis in human gut microbe

Despite significant influence of secondary bile acids on human health and disease, limited structural and biochemical information is available for the key gut microbial enzymes catalyzing its synthesis. Herein, we report apo‐ and cofactor bound crystal structures of BaiA2, a short chain dehydrogenase/reductase from Clostridium scindens VPI 12708 that represent the first protein structure of this pathway. The structures elucidated the basis of cofactor specificity and mechanism of proton relay. A conformational restriction involving Glu42 located in the cofactor binding site seems crucial in determining cofactor specificity. Limited flexibility of Glu42 results in imminent steric and electrostatic hindrance with 2′‐phosphate group of NADP(H). Consistent with crystal structures, steady state kinetic characterization performed with both BaiA2 and BaiA1, a close homolog with 92% sequence identity, revealed specificity constant (k_cat/K_M) of NADP⁺ at least an order of magnitude lower than NAD⁺. Substitution of Glu42 with Ala improved specificity toward NADP⁺ by 10‐fold compared to wild type. The cofactor bound structure uncovered a novel nicotinamide‐hydroxyl ion (NAD⁺‐OH^?) adduct contraposing previously reported adducts. The OH^? of the adduct in BaiA2 is distal to C4 atom of nicotinamide and proximal to 2′‐hydroxyl group of the ribose moiety. Moreover, it is located at intermediary distances between terminal functional groups of active site residues Tyr157 (2.7 Å) and Lys161 (4.5 Å). Based on these observations, we propose an involvement of NAD⁺‐OH^? adduct in proton relay instead of hydride transfer as noted for previous adducts. Proteins 2014; 82:216–229. © 2013 Wiley Periodicals, Inc.     

Conformations and time-resolved fluorescence of oligomers of (−)-epicatechin with 4β → 8 interflavan bonds

Oligomers of (?)-epicatechin with 4β → 8 interflavan bonds, and as many as five monomer units, have been studied by conformational analysis and time-resolved fluorescence. The conformational analysis yields 2^x?1 conformations for each oligomer with x monomer units. There are two conformations accessible at each interflavan bond. These conformations are denoted by + and ?. The dominant conformations for the trimer and higher oligomers have an interaction between the phenolic hydroxyl groups on monomers i and i+2. This interaction involves the hydroxyl group at C(5) on monomer i, and either C(13) or C(8) of monomer i+2, depending on whether the conformation of the two intervening interflavan bonds is + + or + ?, respectively. Minor contributions to the ensemble for the tetramer and pentamer are made by conformations that contain the sequence of successive interflavan bonds denoted by ?+ or ??. In ?+ the interaction between monomer units i and i + 2 involves an aliphatic hydroxyl with a phenolic hydroxyl, and there are no hydroxyl-hydroxyl interactions between units iand i + 2 in ??. The onset of a different decay law for the fluorescence when x increases from 3 to 4 may be associated with the appearance of the ?+ and ?? conformations as minor constituents in the ensemble.     

Existence of a Novel Hemagglutinin Having No Protease Activity in Vibrio mimicus

The protease elaborated by Vibrio mimicus is known to possess hemagglutinating ability to chicken erythrocytes, the well-known HA/protease. A non-protease hemagglutinin (HA) with strong agglutinating ability towards rabbit erythrocytes was obtained from 32 hr culture supernatant of a pathogenic environmental strain of V. mimicus. This HA (V. mimicus HA: VMHA) appeared stable at relatively higher temperature and agglutinated the erythrocytes from rabbit, guinea pig and mouse but not the erythrocytes from chicken, bovine, horse and sheep. Simple sugars, metal ions and chelating agents failed to inhibit the activity of VMHA. The activity of VMHA was found to be sensitive to digestion by proteolytic enzymes including HA/protease. These results provide evidence for the existence of novel HA other than HA/protease in V. mimicus.     

Ribo-, Xylo-, and Arabino-Configured Adenine-Based Nucleoside Phosphonates: Synthesis of Monomers for Solid-Phase Oligonucleotide Assembly

Abstract

Adenine-based, regioisomeric nucleoside phosphonates with ribo, xylo and arabino configuration were synthesized in the protected form suitable for the phosphotriester-like, solid-phase synthesis of oligonucleotides. Phosphonate moiety was protected by 4-methoxy-1-oxido-2-picolyl group and the furanose hydroxyl by the dimethoxytrityl group.     

Structure of inclusion complexes of cyclomaltoheptaose (cycloheptaamylose): crystal structure of the 1-adamantanemethanol adduct

Cyclomaltoheptaose (cycloheptaamylose) has been crystallized with 1-adamantanemethanol as the guest molecule. The complex crystallized in space group C222(1), with unit-cell dimensions a = 19.162 (13), b = 23.965 (17), and c = 32.597 (27) A. The structure was solved by rotation-translation search-methods. The cyclomaltoheptaose exists as a dimer in the crystal by means of extensive hydrogen-bonding across the secondary hydroxyl ends of two cyclomaltoheptaose molecules. The two halves of the dimer are related by a crystallographic two-fold axis. The primary hydroxyl ends of two adjacent cyclomaltoheptaose molecules are also related by a crystallographic two-fold axis, but do not directly hydrogen bond to one another. Instead, they are held in place by a strong hydrogen bond from the hydroxyl group of the 1-adamantanemethanol to a primary hydroxyl group on an adjacent cyclomaltoheptaose molecule. Other stabilizing hydrogen bonds are formed via three water molecules which are situated at the primary hydroxyl interface, and others that form parallel columns stabilizing the crystal structure. A unique feature of this complex is the presence of trapped water in the cavity at the secondary hydroxyl interface. This water is distributed over 3 disordered sites. Its presence blocks one possible site for the 1-adamantanemethanol, which, instead, binds near the primary hydroxyl end, with its hydroxyl group and part of the adamantane moiety protruding from the cyclomaltoheptaose.     

Properties of the sugar carrier in baker's yeast

A total of 16 hexoses and pentoses were investigated with respect to transport intoSaccharomyces cerevisiae cells. All monosaccharides were transported across the cytoplasmic membrane but only those with an equatorial hydroxyl group in positions 1 and 4 of theC1 chair conformation and those with an equatorial hydroxyl group in position 2 and an equatorial −CH₂OH group in position 5 of the1C chair conformation reached an equilibrium distribution in the entire cell water volume. Other monosaccharides reached a distribution in only 20–66% of the intracellular water. The two groups of sugars are apparently transported by different carriers (either in parallel or in series), each of them showing countertransport and an apparent activation energy of 6,700–7,800 cal/mol. The carrier transporting the perfectly distributing sugars (Group 1) is affected by uranyl nitrate but not by 2,4-dinitrophenol, the other carrier (Group 2) is apparently not susceptible to uranyl ions but is influenced by 2,4-dinitrophenol. The space of distribution of the Group 1 sugars is reduced in hypertonic media in accordance with changes of intracellular water, that of the Group 2 sugars is altered only very slightly. The carriers differ in their kinetic parametres (mobility of the loaded carriers, maximum rate of transport). There is only a very indistinct competition for transport between representatives of the two groups. Preincubation with d-galactose induces the formation or unmasking of a transport system whereafter even the Group 2 sugars reach equilibrium in the entire cell water. Part I. Fol. microbiol. 10: 30, 1965.     

Phialophora parasitica, Causal Agent of Cherry Dieback

Structure-activity relationships of the phytotoxins stemphyloxin I and II from Stemphylium botryosum f. sp. lycopersici were investigated by quantitative comparison of their biological activity with chemically related phytotoxins from Phoma betae, betaenones A, B and C. Phytotoxicity was estimated by inhibition of incorporation of¹⁴C-leucine into proteins of exponentially growing tomato cells. The values of 50 % inhibition for stemphyloxin I and II and for betaenones A, B and C were 0.075, 16, 55, 350 and 1 μM respectively. The β-ketoaldehyde moiety appeared to be essential in, conferring biological activity and its toxicity was influenced by its spatial orientation. The presence of an hydroxyl group in stemphyloxin I and II enhanced activity in comparison with the respective compounds betaenones C and A which lack this group.     

Structure-activity relationship of a neurite outgrowth-promoting substance purified from the brown alga,Sargassum macrocarpum, and its analogues on PC12D cells

The structure-activity relationship of a neurite outgrowth-promotingsubstance (designated as MC14) from the brown alga, Sargassummacrocarpum, was analysed. Eight synthetic carotenoids and1,4-benzoquinone were used to determine the moiety of the MC14molecule structurally responsible for the nerve growth factor(NGF)-mediated neurite outgrowth-promoting activity on PC12D cells.The bioassays showed that none of these carotenoids exhibitedNGF-potentiating activity. In contrast, 1,4-benzoquinone enhancedsignificantly NGF-mediated neurite outgrowth from PC12D cells, therebeing a 260% increase over the activity of negative control (10 ngmL^-1 NGF). The effect of quinone structure on NGF-potentiatingactivity, when examined using 12 naturally occurring quinones,demonstrated that lawsone, alizarin and lapachol significantly enhancedNGF-mediated neurite outgrowth by 329%, 325% and 265%,respectively, of that in the negative control. These results show thatquinone is the structural moiety of MC14 molecule responsible for theneurite outgrowth-promoting activity. In addition, the hydroxyl groupbonded to quinone had a significant effect on neuritogenic activity. Thebearing of a hydroxyl group at the 1'-position of benzoquinone, and thebearing of two hydroxyl groups at the 1' and 2'-positions of anthraquinone,played a crucial role in enhancing the neurite outgrowth-promoting actionof NGF.     

Phenolic esters with potential anticancer activity - the structural variable

The conformational preferences of several potential anticancer dihydroxycinnamic esters with a variable length alkyl chain were studied by quantum-mechanical (DFT) calculations (both for the isolated molecule and for aqueous solutions). The orientation of the hydroxyl ring substituents and of the alkyl ester moiety relative to the carbonyl group showed these to be the most determinant factors for the overall stability of this type of phenolic systems, strongly dependent on an effective π-electron delocalization. Compared to the parent caffeic acid (dihydroxycinnamic acid), esterification was found to lead to a higher conformational freedom, and to affect mainly the energy barrier corresponding to the (O=)C-OR internal rotation. No particular differences were verified to occur upon lengthening of the ester alkyl chain, except when this is branched instead of linear. The vibrational spectra of the whole series of compounds were simulated, based on their calculated harmonic vibrational frequencies, and a preliminary assignment was performed. Figure Schematic representation of the dihydroxycinnamic esters studied in the present work and of the main internal rotations affecting the overall stability of the molecules. (R=(CH₂)_n, n = 0,1,2,3,7,11 for MC, EC, PC, BC, OC and DC, respectively; R=(CHCH₃) for IPC. The atom numbering is included, with the exception of the alkyl ester group)     

Theoretical studies and vibrational spectra of <Emphasis Type="Italic">1H</Emphasis>-indole-3-acetic acid. Exploratory conformational analysis of dimeric species

Theoretical studies on 1H-indole-3-acetic acid (IAA) were performed to investigate the conformational properties of dimeric species and vibrational spectra. Experimental infrared spectra at 100 K and 297 K and Raman spectrum at 297 K were analyzed and compared against calculations performed at B3LYP/6-31G** level. A exploratory study of the conformational space of dimeric species was performed. Our analysis showed that dimeric forms predicted theoretically contribute distinctively to the assignments of experimental results. These structures are defined by the orientation of the acetyl moieties with respect to the plane of indole ring. The dimers are formed by two symmetrical IAA monomers (one of them with the acetyl moiety upward oriented, Re-face, and the other isomer having the acetyl moiety downward oriented, Si-face) in tail-to-tail way. The X-ray geometry and FTIR vibrational frequencies were compared with the results of DFT calculations. A conformational equilibrium involving the non-equivalent IAA dimers: CCT-CCT, A⁺A⁺T-A^-A^-T, A⁺A^-T-A^-A⁺T, and A⁺CT-A^-CT was found. The relation of the conformational properties of the IAA molecule with the features of the vibrational spectra was described in detail. The band assignments were discussed as related to the conformations properties. Our analysis shows the significance of the theoretical study of the conformational space of the monomeric molecule in the rationalization of experimental results.     

The Role of Metal Ions in the Hemagglutinating Activity of the Wax Bean Hemagglutinin

The phytohemagglutinin of the wax bean (Phaseolus vulgaris) could be resolved into an active and an inactive component when subjected to gel filtration on Sephadex G-100 in the presence of 8m urea and 0.001 m EDTA, pH 5.5. Subsequent chromatography of the active component on Sephadex G-100 at pH 7.5 in the absence of urea revealed the presence of an inactive fraction (F-1-A) and a fraction (F-1-B) which had 35% of the activity of the original hemagglutinin. The activity of fraction F-1-A could be restored to that of the native hemagglutinin by treatment with cupric ions, whereas the activity of fraction F-1-B could be fully restored by treatment with either cupric or calcium ions.