Theoretical studies on peptidoglycans. II. Conformations of the disaccharide–peptide subunit and the three-dimensional structure of peptidoglycan

Possible conformations of the disaccharide–peptide subunit of peptidoglycan (of Staphylococcus aureus or Micrococcus luteus) have been studied by an energy-minimization procedure. The favored conformation of the disaccharide N-acetyl-glucosaminyl-β(1–4)-N-acetylmuramic acid (NAG-NAM) is different from that of cellulose or chitin; this disagrees with the assumption of earlier workers. The disaccharide–peptide subunit favors three types of conformations, among which two are compact and the third is extended. All these conformations are stabilized by intramolecular hydrogen bonds. Based on these conformations of the subunit, two different models are proposed for the three-dimensional arrangement of peptidoglycan in the bacterial cell wall.     

Conformational energy calculations of enzyme-substrate complexes of lysozyme. I. Energy minimization of monosaccharide and oligosaccharide inhibitors and substrates of lysozyme

Conformational energy calculations were performed on monosaccharide and oligosaccharide inhibitors and substrates of lysozyme to examine the preferred conformations of these molecules. A grid-search method was used to locate all of the low-energy conformational regions for N-acetyl-β-D -glycosamine (NAG), and energy minimization was then carried out in each of these regions. Three stable positions for the N-acetyl group have ben located, in two of which the plane of the amide unit is normal to the mean plane of the pyranosyl ring. Nine local energy minima were located for the —CH₂OH group. The positions of the two vicinal cis —OH groups are determined predominantly by interactions with either the —CH₂OH or the N-acetyl group. The most stable conformations of β-N-acetylmuramic acid (NAM) were determined from the study of the low-energy conformations of NAG. In the two stable orientations for the D -lactic acid side chain, the O—C—C′ plane (C′ being the carbon atom of the terminal carboxyl group) was found to be normal to the mean plane of the pyranosyl ring. The low-energy positions for the COOH group of NAM are determined mainly by interactions with neighboring groups. The conformational preferences of the α-anomers of NAG and NAM were also explored. The calculated conformation of the N-acetyl group for α-NAG was quite close to that determined by X-ray analysis. Two of the three lowest energy conformations of α-NAM are similar to the corresponding conformations of the β-anomer. A third low-energy structure, which has a hydrogen bond from the NH of the N-acetyl group to the C?O of the lactic acid group, corresponds very closely to the X-ray structure of this molecule. The preferred conformations of the disaccharides NAG–NAG, NAM–NAG and NAG–NAM were also investigated. Two preferred orientations of the reducing pyranosyl ring relative to the nonreducing ring were found for all of these disaccharides, both of which are close to the extended conformation. In one of these conformations, a hydrogen bond can form between the OH group attached to C₃ of the reducing sugar and the ring oxygen of the preceding residue. Each conformation can be stabilized further by a hydrogen bond between the CH₂OH (donor) of residue i + 1 and the C?O of residue i (acceptor). The interactions that determine conformations for all oligosaccharides containing both NAG and NAM are shown to be exclusively intraresidue and nearest neighbor interactions, so that it is possible to predict all stable conformations of oligosaccharides containing NAG and NAM in any sequence.     

Galectin-3 Interactions with Glycosphingolipids

Galectins have essential roles in pathological states including cancer, inflammation, angiogenesis and microbial infections. Endogenous receptors include members of the lacto- and neolacto-series glycosphingolipids present on mammalian cells and contain the tetrasaccharides lacto-N-tetraose (LNT) and lacto-N-neotetraose (LNnT) that form their core structural components and also ganglio-series glycosphingolipids. We present crystallographic structures of the carbohydrate recognition domain of human galectin-3, both wild type and a mutant (K176L) that influenced ligand affinity, in complex with LNT, LNnT and acetamido ganglioside a-G_M3 (α2,3-sialyllactose). Key structural features revealed include galectin-3's demonstration of a binding mode towards gangliosides distinct from that to the lacto/neolacto-glycosphingolipids, with its capacity for recognising the core β-galactoside region being challenged when the core oligosaccharide epitope of ganglio-series glycosphingolipids (G_M3) is embedded within particular higher-molecular-weight glycans. The lacto- and neolacto- glycosphingolipids revealed different orientations of their terminal galactose in the galectin-3-bound LNT and LNnT structures that has significant ramifications for the capacity of galectin-3 to interact with higher-order lacto/neolacto-series glycosphingolipids such as ABH blood group antigens and the HNK-1 antigen that is common on leukocytes. LNnT also presents an important model for poly-N-acetyllactosamine-containing glycans and provides insight into galectin-3's accommodation of extended oligosaccharides such as the poly-N-acetyllactosamine-modified N- and O-glycans that, via galectin-3 interaction, facilitate progression of lung and bladder cancers, respectively. These findings provide the first atomic detail of galectin-3's interactions with the core structures of mammalian glycosphingolipids, providing information important in understanding the capacity of galectin-3 to engage with receptors identified as facilitators of major disease.     

Preparation of Chitooligosaccharide-alditols by Hydrogenation with a Ruthenium Catalyst

The existence of glycosylated DNA-binding proteins was demonstrated in a whole cell extract from a filamentous fungus, Aspergillus oryzae. The proteins were specifically eluted from a DNA-cellulose column by the eluate containing shared double-stranded DNA and were detected by wheat germ agglutinin (WGA)-probing. The apparent molecular masses of these proteins on SDS-PAGE were 140 kDa, 115 kDa, 105kDa, 68 kDa, and 60 kDa. The labeling of the proteins by uridine 5′-diphosphate(UDP)-[¹⁴C]galactose using galactosyltransferase showed the same electrophoretic pattern with the WGA-probing. The [¹⁴C]- galactose-labeled saccharides were released from the proteins by mild-base treatment but not by N-glycopeptidase F digestion, indicating the O-glycosidic linkage of the saccharide chain attachment to proteins. The [¹⁴C]galactose-labeled saccharides co-migrated with galactose-(β1 → 4)-N-acetylglucosaminitoI on a silica gel plate. Thus, it was seen that several proteins which had the DNA-binding activity were modified by N-acetylglucosamine monosaccharide through an O-glycosidic linkage in A. oryzae.     

Activation of endo-β-N-acetylglucosaminidase from Arthrobacter protophormiae by various sugars

Endo-β-N-acetylglucosaminidase from Arthrobacter protophormiae was activated by the addition of glucose, mannose, N-acetylglucosamine, and β-allose. While the enzyme did not appear to be significantly affected by the addition of galactose or N-acetylgalactosamine. These results indicate that the C-4 and C-6 positions of the monosaccharide are the most important for enzyme activation. Moreover, the enzyme was activated by the addition of disaccharides such as cellobiose, gentiobiose, and di-N-acetylchitobiose, but not by polysaccharides such as starch and yeast mannan. In the presence of N-acetylglucosamine, the enzyme activation occurred well over pH 4.0 and the K_m value of the enzyme for (Man)₆(GlcNAc)₂-Asn-dansyl changes from 1.2 mM to 3.2 mM.     

Structures of the oligosaccharides isolated from milk of the platypus

Eight major oligosaccharides were isolated from platypus milk. By sequential exoglycosidase digestion and methylation study, their structures were elucidated as shown in Fig. 9 of this paper. The characteristics feature of the platypus milk oligosaccharides is that lacto-N-neotetraose and lacto-N-neohexaose are the major cores in contrast to human milk oligosaccharides in which lacto-N-tetraose and lacto-N-hexaose are found as the major core.     

Effects of enzymatic deglycosylation on the biological activities of human thrombin and antithrombin

Sequential digestion of human thrombin and antithrombin with neuraminidase, βgalactosidase, β-N-acetylglucosaminidase, and endo-β-N-acetylglucosaminidase D resulted in the successive removal of sialic acid, galactose, N-acetylglucosamine, and mannose and more N-acetylglucosamine residues. The products obtained after each stage of deglycosylation had electrophoretic mobilites that were consistent with the calculated change in mass expected from the cleavage of the sugar moieties. The modified thrombins did not lose fibrinogen-clotting activity, amidolytic activity, nor the ability to form complexes with antithrombin. In addition, asialothrombin and asialoagalactothrombin caused the same extent of platelet release as did control thrombin. The products obtained after removal of sugars from antithrombin retained thrombin-neutralizing activity. In the presence of heparin the inhibition of thrombin as well as factor Xa was enhanced. Thus, the sugar residues of thrombin and antithrombin are not required for the formation of enzyme-inhibitor complexes or for the other activities that were measured.     

Presence of two neutral disaccharides containing N-acetylhexosamine in bovine colostrum as free forms

Two neutral disaccharides which comprise 74.0% of the neutral oligosaccharides other than lactose were isolated from bovine colostrum taken 6 h after parturition. The chemical structures were revealed to be galactosyl-β-1,4-N-acetylglucosamine (N-acetyllactosamine, 70.3%) and N-acetylgalactosaminyl-β-1,4-glucose (3.7%). The two carbohydrates were the newly found oligosaccharides from mammalian milk in the free forms. 7 days after parturition, they had completely disappeared from bovine milk.     

New derivatization and separation procedures for reducing oligosaccharides

4-Trifluoroacetamidoaniline was reacted with reducing oligosaccharides in the presence of sodium cyanoborohydride to give aminoalditol derivatives, useful for linkage to proteins or solid matrices. A mixture of reducing oligosaccharides, difficult to separate by HPLC, was treated in the same way. The resulting derivatives were easily separated by HPLC.Abbreviations TFAN 4-trifluoroacetamidoaniline - LcOse₄ lacto-N-tetraose - IV²Fuc-LcOse₄ lacto-N-fucopentaose l - III⁴Fuc-LcOse₄ lacto-N-fucopentaose II - III³Fuc-nLcOse₄ lacto-N-fucopentaose III - IV²Fuc, III⁴Fuc-LcOse₄ lacto-N-difucohexaose I - II⁶Galß1-4GlcNAc-LcOse₄ lacto-N-hexaose - II³NeuAc-Lac 3-sialyllactose - GlcNAcß1-4GlcNAcß1-4GlcNAc chitotriose - GalNac1-3|Fuc1-2|Galß1-4Glc A-tetrasaccharide     

Nitrous acid deamination of amino-oligosaccharide alditols and their per-O-methylated derivatives

Per-O-methylated amino-oligosaccharide alditols prepared from lacto-N-tetraose, lacto-N-fucopentaose I, and the mixed populations of oligosaccharide chains from α₁-acid glycoprotein and hog gastric mucin have been used as model substrates to assess the scope of the reaction sequence, N-deacetylation-nitrous acid deamination followed by derivatization, in the fragmentation of complex amino-oligosaccharides. G.l.c.-mass spectrometry has been used as the major tool in the characterization of products.     

Chemical structures of oligosaccharides in milks of the American black bear (Ursus americanus americanus) and cheetah (Acinonyx jubatus)

The milk oligosaccharides were studied for two species of the Carnivora: the American black bear (Ursus americanus, family Ursidae, Caniformia), and the cheetah, (Acinonyx jubatus, family Felidae, Feliformia). Lactose was the most dominant saccharide in cheetah milk, while this was a minor saccharide and milk oligosaccharides predominated over lactose in American black bear milk. The structures of 8 neutral saccharides from American black bear milk were found to be Gal(β1–4)Glc (lactose), Fuc(α1–2)Gal(β1–4)Glc (2′-fucosyllactose), Gal(α1–3)Gal(β1–4)Glc (isoglobotriose), Gal(α1–3)[Fuc(α1–2)]Gal(β1–4)Glc (B-tetrasaccharide), Gal(α1–3)[Fuc(α1–2)]Gal(β1–4)[Fuc(α1–3)]Glc (B-pentasaccharide), Fuc(α1–2)Gal(β1–4)[Fuc(α1–3)]GlcNAc(β1–3)Gal(β1–4)Glc (difucosyl lacto-N-neotetraose), Gal(α1–3)Gal(β1–4)[Fuc(α1–3)]GlcNAc(β1–3)Gal(β1–4)Glc (monogalactosyl monofucosyl lacto-N-neotetraose) and Gal(α1–3)Gal(β1–4)GlcNAc(β1–3)Gal(β1–4)Glc (Galili pentasaccharide). Structures of 5 acidic saccharides were also identified in black bear milk: Neu5Ac(α2–3)Gal(β1–4)Glc (3′-sialyllactose), Neu5Ac(α2–6)Gal(β1–4)GlcNAc(β1–3)[Fuc(α1–2)Gal(β1–4)GlcNAc(β1–6)]Gal(β1–4)Glc (monosialyl monofucosyl lacto-N-neohexaose), Neu5Ac(α2–6)Gal(β1–4)GlcNAc(β1–3)[Gal(α1–3)Gal(β1–4)GlcNAc(β1–6)]Gal(β1–4)Glc (monosialyl monogalactosyl lacto-N-neohexaose), Neu5Ac(α2–6)Gal(β1–4)GlcNAc(β1–3){Gal(α1–3)Gal(β1–4)[Fuc(α1–3)]GlcNAc(β1–6)}Gal(β1–4)Glc (monosialyl monogalactosyl monofucosyl lacto-N-neohexaose), and Neu5Ac(α2–6)Gal(β1–4)GlcNAc(β1–3){Gal(α1–3)[Fuc(α1–2)]Gal(β1–4)[Fuc(α1–3)]GlcNAc(β1–6)}Gal(β1–4)Glc (monosialyl monogalactosyl difucosyl lacto-N-neohexaose). A notable feature of some of these milk oligosaccharides is the presence of B-antigen (Gal(α1–3)[Fuc(α1–2)]Gal), α-Gal epitope (Gal(α1–3)Gal(β1–4)Glc(NAc)) and Lewis x (Gal(β1–4)[Fuc(α1–3)]GlcNAc) structures within oligosaccharides. By comparison to American black bear milk, cheetah milk had a much smaller array of oligosaccharides. Two cheetah milks contained Gal(α1–3)Gal(β1–4)Glc (isoglobotriose), while another cheetah milk did not, but contained Gal(β1–6)Gal(β1–4)Glc (6′-galactosyllactose) and Gal(β1–3)Gal(β1–4)Glc (3′-galactosyllactose). Two cheetah milks contained Gal(β1–4)GlcNAc(β1–3)[Gal(β1–4)GlcNAc(β1–6)]Gal(β1–4)Glc (lacto-N-neohexaose), and one cheetah milk contained Gal(β1–4)Glc-3’-O-sulfate. Neu5Ac(α2–8)Neu5Ac(α2–3)Gal(β1–4)Glc (disialyllactose) was the only sialyl oligosaccharide identified in cheetah milk. The heterogeneity of milk oligosaccharides was found between both species with respect of the presence/absence of B-antigen and Lewis x. The variety of milk oligosaccharides was much greater in the American black bear than in the cheetah. The ratio of milk oligosaccharides-to-lactose was lower in cheetah (1:1–1:2) than American black bear (21:1) which is likely a reflection of the requirement for a dietary supply of N-acetyl neuraminic acid (sialic acid), in altricial ursids compared to more precocial felids, given the role of these oligosaccharides in the synthesis of brain gangliosides and the polysialic chains on neural cell adhesion.

     

Substrate specificity of mammalian endo-beta-N-acetylglucosaminidase: study with the enzyme of rat liver

The substrate specificity of mammalian endo-β-N-acetylglucosaminidase was studied in detail by using rat liver enzyme. The enzyme hydrolytically cleaves the N,N′-diacetylchitobiose moiety of Manα1 → 6 (Manα1 → 3)Manβ1 → 4GlcNacβ1 → 4R in which R represents either GlcNac → Asn or N-acetylglucosamine. The enzyme can hardly act on the sugar chains with Fucα1 → 3 or 6GlcNac → Asn or N-acetylglucosaminitol as their R residues. The sugar chains substituted at C-3 and C-6 positions of the Manα1 → 6 residue and at C-2 position of the Manα1 → 3 residue by other sugars are also cleaved by the enzyme. The sugar chains substituted at C-4 position of the β-mannosyl residue and at C-2 position of the Manα1 → 6 residue by other sugars are hydrolyzed at one place lower rate. The specificity of the mammalian endo-β-N-acetylglucosaminidase indicates that the enzyme is responsible for the formation of most of the oligosaccharides excreted in the urine of patients with congenital exoglycosidase deficiencies and also explains why large amount of glycopeptides are excreted in the urine of fucosidosis patients.     

The metabolism of d-galactosamine and N-acetyl-d-galactosamine in rat liver

d-[1-¹⁴C]Galactosamine appears to be utilized mainly by the pathway of galactose metabolism in rat liver, as evidenced by the products isolated from the acid-soluble fraction of perfused rat liver. These products were eluted in the following order from a Dowex 1 (formate form) column and were characterized as galactosamine 1-phosphate, sialic acid, UDP-glucosamine, UDP-galactosamine, N-acetylgalactosamine 1-phosphate, N-acetylglucosamine 6-phosphate, UDP-N-acetylglucosamine, UDP-N-acetylgalactosamine and an unidentified galactosamine-containing compound. In addition, [1-¹⁴C]glucosamine was found in the glycogen, an incorporation previously shown to result from the substitution of UDP-glucosamine for UDP-glucose in the glycogen synthetase reaction. Analysis of the [1-¹⁴C]glucosamine-containing disaccharides released from glycogen by β-amylase provided additional evidence that they consist of a mixture of glucose and glucosamine in a 1:1 ratio, but with glucose predominating on the reducing end. UDP-N-acetylgalactosamine was shown to result from the reaction of UTP with N-acetylgalactosamine 1-phosphate in the presence of a rat liver extract.     

Galactosyltransferase activities in pancreas, liver and gut of the developing rat

Two galactosyltransferase activities (1 and 2) were measured in the pancreas, liver and gut of the developing rat embryo. 1. N-Acetylglucosamine:Galactosyltransferase. UDP [¹⁴C]galactose + N-acetylglucosamine → [¹⁴C]galactosyl-β-(1 → 4)-N-acetylglucosamine + UDP. 2. N-Acetylgalactosamine-protein:Galactosyltransferase. UDP [¹⁴C]galactose + N-acetylgalactosamine-protein → [¹⁴C]galactosyl-β-(1 → 3)-N-acetylgalactosamine-protein + UDP. Galactosyltransferases 1 and 2 increased in the pancreas, about 10- and 40-fold in specific activity, respectively, from 11 to 12 days in utero to birth. During this period the activities of both transferases in the liver were somewhat variable, but showed no definite trend. A drop in the level of galactosyltransferase 1 in the pancreas occurred at birth or shortly thereafter. The “Golgimarker” enzyme for liver, galactosyltransferase 1, may be absent or present at low levels in adult rat pancreas.Zymogen granule membrane preparations apparently are devoid of these galactosyltransferase activities. Bromodeoxyuridine, which inhibits the development of the synthetic capability of the specific exocrine proteins, had essentially no effect on the normal accretion of the galactosyltransferase activities in organ cultures of pancreatic rudiments from 13-day rat embryos.     

LARGE SCALE BIOSYNTHESIS OF GANGLIOSIDE ANALOGUES BY RERF-LC-AI CELLS CULTURED IN HYPERFlask

The efficient production of ganglioside analogues was accomplished using RERF-LC-AI cells cultured in HYPERFlask (High Yield PERformance Flask). Eight kinds of ganglioside analogues (GM3, GM2, sialylparagloboside, GD3, di-sialylated lacto-N-tetraose, and another three kinds of analogues with intricate structures) were synthesized by the saccharide primer method using lung squamous-cell carcinoma line RERF-LC-AI and 12-azidododecyl β-lactoside primer. The yield for each analogue obtained using HYPERFlask was higher than yields obtained from 100-mm dishes.     

PURIFICATION AND PROPERTIES OF BRAIN N-ACETYL-β-HEXOSAMINIDASE A

—N-Acetyl-β-hexosaminidase A was purified to homogeneity from human and monkey brains by the conventional procedures followed by concanavalin A–Sepharose affinity chromatography. The optimal activity was observed at pH 4·5 for both enzyme preparations with both the aglycones N-acetylglucosamine and N-acetylgalactosamine derivatives. The K_m values for hexosaminidase A from monkey brain were 0·26 mm and 0·04 mm respectively for N-acetylglucosamine and N-acetylgalactosamine. K_m values obtained for glucosamine and galactosamine derivatives for the human brain hexosaminidase A were of the same order. The glycoprotein nature of the enzymes was established by the affinity towards concanavalin A as well as by the presence of sialic acid, galactose, glucose, mannose and hexosamines in the enzyme molecule from monkey brain.     

Fertilization studies in the hamster : The role of cell-surface carbohydrates

The nature of complementary binding sites on the surfaces of hamster gametes has been analysed using mono- and oligosaccharides, glycoproteins and glycosidases in an in vitro system. The binding of capacitated spermatozoa to the zona pellucida was inhibited by several mono- and oligosaccharides related to fucose, galactose, and acetylated amino sugars, but not by unrelated sugars. Several glycoproteins with prosthetic carbohydrate groups rich in or terminated by galactose or N-acetylglucosamine residues were also potent inhibitors of fertilization. Of all the glucoproteins tested, two plasma glycoproteins, α₁-acid glycoproteins (orosomucoid) and fetuin were most effective. In their native form they were non-inhibitory but their desialylated (galactoseterminated) forms completely prevented the sperm-zona binding. Agalacto-orosomucoid with N-acetylglucosamine terminals also inhibited fertilization. The treatment of capacitated spermatozoa with α- -fucosidase, α- -galactosidase and β-N-acetylhexosaminidase, but not with other glycosidases, trypsin and arylsulphatase, resulted in the complete inhibition of fertilization. Inhibitory saccharides and glycosidases did not interfere with sperm motility and had no effect on sperm-oolemma fusion. The pretreatment of cumulus-free oocytes with these agents did not inhibit sperm zona pellucida binding either. These results provide evidence that sperm-zona pellucida binding is mediated by ligands on the sperm surface containing fucose, galactose, N-acetylglucosamine and N-acetylgalactosamine residues.     

Specific detection of N-acetylglucosamine-containing oligosaccharide chains on ovine submaxillary asialomucin

Human milk β-N-acetylglucosaminide β1 → 4-galactosytransferase (EC 2.4.1.38) was used to galactosylate ovine submaxillary asialomucin to saturation. The major [¹⁴C]galactosylated product chain was obtained as a reduced oligosaccharide by β-elimination under reducing conditions. Analysis by Bio-Gel filtration and gas-liquid chromatography indicated that this compound was a tetrasaccharide composed of galactose, N-acetylglucosamine and reduced N-acetylgalactosamine in a molar ratio of 2:0.9:0.8. Periodate oxidation studies before and after mild acid hydrolysis in addition to thin-layer chromatography revealed that the most probable structure of the tetrasaccharide is $\text{Gal}\text{β1 → 3([}{}^{14}\text{C}\text{]}\text{Gal}\text{β1 → 4}\text{GlcNac}\text{β1 → 6)}\text{GalNAcol}$. Thus it appears that Galβ1 → 3(GlcNAcβ1 → 6)GalNAc units occur as minor chains on the asialomucin. The potential interference of these chains in the assay of α-N-acetylgalactosaminylprotein β1 → 3-galactosyltransferase activity using ovine submaxillary asialomucin as an receptor can be counteracted by the addition of N-acetylglucosamine.     

Influence of local interactions on protein structure. I. Conformational energy studies of N-acetyl-N′-methylamides of pro-X and X-pro dipeptides

Conformational energy calculations using an Empirical Conformational Energy Program for Peptides (ECEPP) were carried out on the N-acetyl-N′-methylamides of Pro-X, where X = Ala, Asn, Asp, Gly, Leu, Phe, Ser, and Val, and of X-Pro, where X = Ala, Asn, Gly, and Pro. The conformational energy was minimized from starting conformations which included all combinations of low-energy single-residue minima and several standard bend structures. It was found that almost all resulting minima are combinations of low-energy single-residue minima, suggesting that intra residue interactions predominate in determining conformation. The calculations also indicate, however, that inter residue interactions can be important. In addition, librational entropy was found to influence the relative stabilities of some minima. Because of the existence of 10–100 low-energy minima for each dipeptide, the normalized statistical weight of an individual minimum rarely exceeds 0.3, suggesting that these dipeptides have considerable conformational flexibility and exist as statistical ensembles of low-energy structures. The propensity of each dipeptide to form bend conformations was calculated, and the results were compared with available experimental data. It was found that bends are favored in Pro-X dipeptides because ?_Pro is fixed by the pyrrolidine ring in a conformation which is frequently found in bends, but that bends are not favored in X-Pro dipeptides because interactions between the X residue and the pyrrolidine ring restrict the X residue to conformations which are not usually found in bends.