Characterisation of oligosaccharides released from human-blood-group O erythrocyte glycopeptides by the endo-beta-galactosidase of Bacteroides fragilis. A study of the enzyme susceptibility of branched poly(N-acetyllactosamine) structures

Desialylated human blood group O erythrocyte glycopeptides were digested with the endo-beta-galactosidase of Bacteroides fragilis and the enzyme-released products reduced with NaBH4 and purified by Bio-Gel P-4 chromatography. Three linear and six branched oligosaccharides of poly(N-acetylllactosamine) type, which together accounted for 90% of the oligosaccharide alditols, were characterised by fast-atom-bombardment mass spectrometry and gas-liquid chromatography/mass spectrometry. Linkage and composition data were obtained for the remaining material. The salient findings were (a) the branched oligosaccharide alditols each contained the sequence: (Formula: see text) and (b) there was no evidence for the terminal branch-point sequence: (Formula: see text). Together these observations indicate that, as with erythrocyte glycolipids described previously [Scudder, P., Hanfland, P., Uemura, K. & Feizi, T. (1984) J. Biol. Chem. 259, 6586-6592], the endo-beta-galactosidase of Bacteroides fragilis cannot hydrolyse branch-point beta-galactosidic linkages on erythrocyte membrane glycopeptides.     

Primary structure of the low-molecular-weight carbohydrate chains of Helix pomatia alpha-hemocyanin. Xylose as a constituent of N-linked oligosaccharides in an animal glycoprotein

alpha-Hemocyanin of Helix pomatia is a copper-containing glycoprotein which serves as an oxygen carrier in the hemolymph. Its carbohydrate moiety has as constituents fucose, xylose, 3-O-methylgalactose, mannose, galactose, N-acetylgalactosamine, and N-acetyl-glucosamine residues. Alkaline borhydride did not split off any carbohydrate material, suggesting the absence of O-glycosidic chains. The N-glycosidic carbohydrate chains of this glycoprotein were liberated by hydrazinolysis of a Pronase digest then fractionated as alditols on Bio-Gel P-4. The fractions containing the low-molecular-weight glycans were investigated by 500-MHz 1H NMR spectroscopy in conjunction with sugar and methylation analysis. The largest, and most abundant, compound was established to be: (Formula: see text). Another compound was characterized as the afuco analogue of this structure. H. pomatia alpha-hemocyanin is the first example of an animal glycoprotein having xylose as a constituent of N-glycosidic carbohydrate chains.     

Rat alveolar macrophages require NADPH for superoxide production in the respiratory burst. Effect of NADPH depletion by paraquat

Alveolar macrophages can be stimulated by concanavalin A to produce extracellular superoxide. Conflicting opinions exist, however, concerning the relative importance of the oxidation of either NADPH or NADH in the generation of (Formula: see text) by surface membrane-stimulated phagocytic cells. Alveolar macrophages were obtained from adult male rats by lavage with phosphate-buffered saline. Cells (approximately 10(6)/ml) were incubated in Krebs-Ringer phosphate 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid buffer and ferricytochrome c for 15 min at 37 degrees C before addition of concanavalin A. Release of (Formula: see text) was detected as the difference in cytochrome c reduction, followed at 550 nm, in the absence and presence of superoxide dismutase. Superoxide production by concanavalin A-stimulated alveolar macrophages was markedly increased in the presence of glucose but fructose, lactate, and pyruvate were without effect. Paraquat (methylviologen), an oxidation-reduction dye, significantly reduced concanavalin A-stimulated (Formula: see text) production when incubated at 1 mM with alveolar macrophages in the absence of glucose. The effect of paraquat was reversed by glucose, but fructose, lactate, and pyruvate could not reverse paraquat inhibition. Paraquat enhanced oxidation of NADPH (but not NADH) by cell supernatant and increased pentose phosphate shunt activity in resting macrophages, but did not affect mitochondrial respiration or ATP content of alveolar macrophages. These results suggest that paraquat is able to specifically deplete NADPH in alveolar macrophages while not affecting NADH or ATP. Our conclusion is that NADPH is essential for the production of (Formula: see text) by concanavalin A-stimulated alveolar macrophages.     

Structure of neutral oligosaccharides derived from mucus glycoproteins of human seminal plasma

The primary structures of nine major saccharide alditols in the fraction of neutral carbohydrates derived from human seminal plasma mucin have been established on the basis of fast atom bombardment and electron impact mass spectrometry combined with methylation analysis, exoglycosidase digestion, and CrO3 oxidation, as follows. Formula: see text.     

Fracture Faces in the Cell Envelope of Escherichia coli

Freeze-fracturing of Escherichia coli cells in the presence of 30% (v/v) glycerol resulted in a double cleavage of the cell envelope exposing two convex and two concave fracture faces ([Formula: see text], [Formula: see text] and [Formula: see text], [Formula: see text]) with characteristic patterns. Complementary replicas revealed the relationship of the fracture faces to their corresponding fracture planes. The inner fracture plane splits the plasma membrane at one particular level. Apparently the outer fracture plane was located in the outer part of the wall, as it was separated by a layer ([Formula: see text]) from the fractured profile (CW1) presumably corresponding to the murein layer. The outer fracture plane did alternate toward the cell periphery, exposing complementary smooth areas ([Formula: see text] and [Formula: see text]). When cells were freeze-fractured in the absence of glycerol, the outer cell surface appeared as an etching face rather than a fracture face. A schematic representation of the relative location of the different fracture faces in the E. coli cell envelope is given.     

Limits to the rate of adaptive substitution in sexual populations

In large populations, many beneficial mutations may be simultaneously available and may compete with one another, slowing adaptation. By finding the probability of fixation of a favorable allele in a simple model of a haploid sexual population, we find limits to the rate of adaptive substitution, [Formula: see text], that depend on simple parameter combinations. When variance in fitness is low and linkage is loose, the baseline rate of substitution is [Formula: see text], where [Formula: see text] is the population size, [Formula: see text] is the rate of beneficial mutations per genome, and [Formula: see text] is their mean selective advantage. Heritable variance [Formula: see text] in log fitness due to unlinked loci reduces [Formula: see text] by [Formula: see text] under polygamy and [Formula: see text] under monogamy. With a linear genetic map of length [Formula: see text] Morgans, interference is yet stronger. We use a scaling argument to show that the density of adaptive substitutions depends on [Formula: see text], [Formula: see text], [Formula: see text], and [Formula: see text] only through the baseline density: [Formula: see text]. Under the approximation that the interference due to different sweeps adds up, we show that [Formula: see text], implying that interference prevents the rate of adaptive substitution from exceeding one per centimorgan per 200 generations. Simulations and numerical calculations confirm the scaling argument and confirm the additive approximation for [Formula: see text]; for higher [Formula: see text], the rate of adaptation grows above [Formula: see text], but only very slowly. We also consider the effect of sweeps on neutral diversity and show that, while even occasional sweeps can greatly reduce neutral diversity, this effect saturates as sweeps become more common-diversity can be maintained even in populations experiencing very strong interference. Our results indicate that for some organisms the rate of adaptive substitution may be primarily recombination-limited, depending only weakly on the mutation supply and the strength of selection.     

Structure of oligosaccharides and the linkage region between keratan sulfate and the core protein on proteoglycans from monkey cornea

Structural analyses were performed on the intact glycopeptides and on the linkage region oligosaccharide-peptides derived from the keratan sulfate proteoglycan from monkey cornea (Nakazawa, K., Newsome, D.A., Nilsson, B., Hascall, V.C., and Hassell, J.R. (1983) J. Biol. Chem. 258, 6051-6055) using trifluoroacetolysis, Smith degradation, chromium trioxide oxidation, and gas-liquid chromatography-mass spectrometry. The following structure was found for the linkage region (formula; see text) The following structures were found for the intact oligosaccharide peptides (formula; see text) and (formula; see text) The structure of the linkage region for keratan sulfate on corneal proteoglycans is clearly derived from a complex type of N-linked glycoprotein oligosaccharide precursor, indicating that only the oligosaccharides that have been processed to the complex type are used as primers for synthesizing keratan sulfate chains. The high mannose oligosaccharide in Formula 3 is an intermediate in the normal pathway for biosynthesis of complex type oligosaccharides. The structure in Formula 2, in which a single Man alpha 1-2 is retained on the Man alpha 1-3 branch while the Man alpha 1-6 branch is unsubstituted, can be an intermediate for an alternate, presumably minor pathway for complex oligosaccharide formation (Kornfeld, S., Gregory, W., and Chapman, A. (1979) J. Biol. Chem. 254, 11649-11654) in certain cases. This structure has not previously been shown to be present on normal glycoproteins.     

Unifying Time to Contact Estimation and Collision Avoidance across Species

The [Formula: see text]-function and the [Formula: see text]-function are phenomenological models that are widely used in the context of timing interceptive actions and collision avoidance, respectively. Both models were previously considered to be unrelated to each other: [Formula: see text] is a decreasing function that provides an estimation of time-to-contact (ttc) in the early phase of an object approach; in contrast, [Formula: see text] has a maximum before ttc. Furthermore, it is not clear how both functions could be implemented at the neuronal level in a biophysically plausible fashion. Here we propose a new framework - the corrected modified Tau function - capable of predicting both [Formula: see text]-type ("[Formula: see text]") and [Formula: see text]-type ("[Formula: see text]") responses. The outstanding property of our new framework is its resilience to noise. We show that [Formula: see text] can be derived from a firing rate equation, and, as [Formula: see text], serves to describe the response curves of collision sensitive neurons. Furthermore, we show that [Formula: see text] predicts the psychophysical performance of subjects determining ttc. Our new framework is thus validated successfully against published and novel experimental data. Within the framework, links between [Formula: see text]-type and [Formula: see text]-type neurons are established. Therefore, it could possibly serve as a model for explaining the co-occurrence of such neurons in the brain.     

Structural studies on phosphorylated oligosaccharides derived from yeast mannan by 1H(31P) relayed spin-echo difference spectroscopy (RESED)

Phosphorylated and nonphosphorylated tri- and tetrasaccharides were isolated from yeast mannan and analyzed by 500-MHz 1H NMR spectroscopy. Relayed spin-echo difference spectroscopy (RESED) was used to reveal subspectra of the phosphorylated residues. In this way the attachment position of the phosphate group could be established. The structures of the phosphorylated compounds turned out to be (Formula: see text) and (Formula: see text) RESED spectroscopy has proved to be a suitable method in analyzing low amounts of phosphorylated oligosaccharides.     

Structures of oligomannoside chains of alpha-mannosidase from porcine kidney

Lysosomal acid alpha-mannosidase from porcine kidney was found to contain mannose (4.8%), galactose (0.9%), fucose (0.5%), N-acetylglucosamine (3.1%), and mannose 6-phosphate (0.1%). Approximately 50% of the total hexose of the oligosaccharide chains could be released by endo-beta-N-acetylglucosaminidase-H (endo-H). They were predominantly neutral, oligomannoside-type oligosaccharides containing 5, 6, and 9 mannose residues, respectively, in the centesimal ratio of 36:25:34. 500-MHz 1H-NMR spectroscopy in conjunction with sequential exoglycosidase digestion of the reduced compounds revealed that each of the three fractions consisted of a single isomer only; the Man9 compound has the following structure: (Formula: see tex). The Man6-compound lacks Man residues D1, D2, and D3, while the Man5-compound lacks Man-C as well. In addition to the neutral ones, some (5%) phosphorylated oligomannoside-type oligosaccharides were obtained. The endo-H resistant glycopeptides were subjected to hydrazinolysis. Approximately 60% of the oligosaccharides released by hydrazine were found to be of rather small size; their composition can be represented asMan2-3GlcNAc[Fuc]0-1GlcNAcol. The remaining 40% consist of larger-size galactose-containing, N-acetyllactosamine-type oligosaccharides. Studies involving sequential exoglycosidase digestion and 500-MHz 1H-NMR spectroscopy performed on the highly purified small-sized compounds revealed the following four structures for the endo-H-resistant oligosaccharides: (Formula: see text).     

Robustness and information propagation in attractors of random boolean networks

Attractors represent the long-term behaviors of Random Boolean Networks. We study how the amount of information propagated between the nodes when on an attractor, as quantified by the average pairwise mutual information ([Formula: see text]), relates to the robustness of the attractor to perturbations ([Formula: see text]). We find that the dynamical regime of the network affects the relationship between [Formula: see text] and [Formula: see text]. In the ordered and chaotic regimes, [Formula: see text] is anti-correlated with [Formula: see text], implying that attractors that are highly robust to perturbations have necessarily limited information propagation. Between order and chaos (for so-called "critical" networks) these quantities are uncorrelated. Finite size effects cause this behavior to be visible for a range of networks, from having a sensitivity of 1 to the point where [Formula: see text] is maximized. In this region, the two quantities are weakly correlated and attractors can be almost arbitrarily robust to perturbations without restricting the propagation of information in the network.     

Mapping of redox state of mitochondrial cytochromes in live cardiomyocytes using Raman microspectroscopy

This paper presents a nonivasive approach to study redox state of reduced cytochromes [Formula: see text], [Formula: see text] and [Formula: see text] of complexes II and III in mitochondria of live cardiomyocytes by means of Raman microspectroscopy. For the first time with the proposed approach we perform studies of rod- and round-shaped cardiomyocytes, representing different morphological and functional states. Raman mapping and cluster analysis reveal that these cardiomyocytes differ in the amounts of reduced cytochromes [Formula: see text], [Formula: see text] and [Formula: see text]. The rod-shaped cardiomyocytes possess uneven distribution of reduced cytochromes [Formula: see text], [Formula: see text] and [Formula: see text] in cell center and periphery. Moreover, by means of Raman spectroscopy we demonstrated the decrease in the relative amounts of reduced cytochromes [Formula: see text], [Formula: see text] and [Formula: see text] in the rod-shaped cardiomyocytes caused by H(2)O(2)-induced oxidative stress before any visible changes. Results of Raman mapping and time-dependent study of reduced cytochromes of complexes II and III and cytochrome [Formula: see text] in cardiomyocytes are in a good agreement with our fluorescence indicator studies and other published data.     

Critical motor number for fractional steps of cytoskeletal filaments in gliding assays

In gliding assays, filaments are pulled by molecular motors that are immobilized on a solid surface. By varying the motor density on the surface, one can control the number [Formula: see text] of motors that pull simultaneously on a single filament. Here, such gliding assays are studied theoretically using Brownian (or Langevin) dynamics simulations and taking the local force balance between motors and filaments as well as the force-dependent velocity of the motors into account. We focus on the filament stepping dynamics and investigate how single motor properties such as stalk elasticity and step size determine the presence or absence of fractional steps of the filaments. We show that each gliding assay can be characterized by a critical motor number, [Formula: see text]. Because of thermal fluctuations, fractional filament steps are only detectable as long as [Formula: see text]. The corresponding fractional filament step size is [Formula: see text] where [Formula: see text] is the step size of a single motor. We first apply our computational approach to microtubules pulled by kinesin-1 motors. For elastic motor stalks that behave as linear springs with a zero rest length, the critical motor number is found to be [Formula: see text], and the corresponding distributions of the filament step sizes are in good agreement with the available experimental data. In general, the critical motor number [Formula: see text] depends on the elastic stalk properties and is reduced to [Formula: see text] for linear springs with a nonzero rest length. Furthermore, [Formula: see text] is shown to depend quadratically on the motor step size [Formula: see text]. Therefore, gliding assays consisting of actin filaments and myosin-V are predicted to exhibit fractional filament steps up to motor number [Formula: see text]. Finally, we show that fractional filament steps are also detectable for a fixed average motor number [Formula: see text] as determined by the surface density (or coverage) of the motors on the substrate surface.     

Architecture of the Outer Membrane of Escherichia coli III. Protein-Lipopolysaccharide Complexes in Intramembraneous Particles

In a previous paper (A. Verkleij, L. van Alphen, J. Bijvelt, and B. Lugtenberg, Biochim. Biophys. Acta 466:269-282, 1977) we have hypothesized that particles on the outer fracture face of the outer membrane ([Formula: see text]), with corresponding pits on the inner fracture face of the outer membrane ([Formula: see text]), consist of lipopolysaccharide (LPS) aggregates stabilized by divalent cations and that they might contain protein and/or phospholipid. In the present paper the roles of LPS, cations, and proteins in these [Formula: see text] particles are described more extensively, using a strain that lacks the major outer membrane proteins, b, c, and d (b(-) c(-) d(-)), and has a reduction in the number of [Formula: see text] particles of 75%. To study the role of divalent cations in the formation of [Formula: see text] particles, these b(-) c(-) d(-) cells were grown or incubated with Ca(2+), Mg(2+), or putrescine. The presence of Ca(2+) resulted in the appearance of many [Formula: see text] particles and [Formula: see text] pits. Mg(2+) and putrescine were less effective than Ca(2+). Introduction of these particles was not accompanied by alterations in the relative amounts of LPS and cell envelope proteins. Ca(2+) treatment of a heptoseless derivative of a b(-) c(-) d(-) strain did not result in morphological changes. Incubation of Ca(2+)-treated cells with ethylenediaminetetraacetate caused the disappearance of the introduced particles as well as the release of more than 60% of the cellular LPS. These results strongly support the hypothesis that LPS is involved in the formation of [Formula: see text] particles and [Formula: see text] pits. The roles of various outer membrane proteins in the formation of [Formula: see text] particles were studied by comparing the freeze-fracture morphology of b(-) c(-) d(-) cells with that of cells which contain one of the outer membrane proteins b, c, d, and e or the receptor protein for bacteriophage lambda. The results showed that the presence of any of these five proteins in a b(-) c(-) d(-) background resulted in a large increase in the number of [Formula: see text] particles and [Formula: see text] pits, indicating that these proteins are, independent of each other, involved in the formation of [Formula: see text] particles and [Formula: see text] pits. The simplest explanation for the results is that in wild-type cells each particle consists of LPS complexed with some molecules of a single protein species, stabilized by either divalent cations or polyamines. It is hypothesized that the outer membrane of the wild-type cell contains a heterogeneous population of particles, of which 75% consists of protein b-LPS, protein c-LPS, and protein d-LPS particles. A function of these particles as aqueous pores is proposed.     

A contribution to the generalization of the Gompertz function

SCHARF (1976) discusses various growth models. For the Gompertz function the differential equation (Formula: see text) is used. In words: the difference between relative growth rate and relative growth acceleration is constant. On the other hand, according to WENK (1973), the differential equation (Formula: see text) applies to the Gompertz function. It can be shown mathematically that (Formula: see text) applies in general. From Eq. (2) one obtains without trouble (Formula: see text). Therefore, the property leading to the Gompertz function may be defined as follows; the logarithmic derivation of the relative growth rate is constant. Eq. (2) is applicable only in special cases. It can be extended by assuming that c is not constant, but a function of time. In this way, a great number of growth functions can be found, which have to be regarded as model-based extensions of the Gompertz function.     

Structure of a major oligosaccharide of Taka-amylase A.

The structures of a major oligosaccharide of Taka-amylase A, shown below, is proposed based on the results of chemical (methylation and acetolysis) and enzymatic (digestions with exo and endo-glycosidases) analyses. This structure is an amendment of that proposed by Yamaguchi et al. (1971) (J. Biochem. 70, 587-594), in which one more mannose residue is attached (Formula: see text) through an alpha 1,2 linkage to the mannose residue which is alpha 1,3-linked to the intermost mannose residue.     

Determination of the structure of the carbohydrate chains of prostaglandin endoperoxide synthase from sheep

Prostaglandin endoperoxide synthase was isolated from sheep seminal vesicles. Sugar analysis of the glycoprotein revealed the presence of mannose and N-acetylglucosamine only. The carbohydrate moiety was released from the polypeptide backbone by hydrazinolysis. After re-N-acetylation and reduction, the resulting mixture of oligosaccharide-alditols was fractionated on Bio-Gel P-4 and their structures were investigated by 500-MHz1H-NMR spectroscopy. The carbohydrate chains turned out to be of the oligomannoside type containing six to nine mannose residues. The largest and most abundant compound was established to be: (formula; see text) For the smaller structures heterogeneity occurs with respect to the outer alpha(1----2)-linked mannose residues. Furthermore, a small amount of Man6GlcNAc-ol (artefact of the hydrazinolysis procedure) was detected by 1H-NMR spectroscopy and fast atom bombardment mass spectrometry.     

Application of DFT methods to the study of the coordination environment of the VO2+ ion in V?proteins

Density functional theory (DFT) methods were used to simulate the environment of vanadium in several V proteins, such as vanadyl-substituted carboxypeptidase (sites A and B), vanadyl-substituted chloroplast F(1)-ATPase (CF(1); site 3), the reduced inactive form of vanadium bromoperoxidase (VBrPO; low- and high-pH sites), and vanadyl-substituted imidazole glycerol phosphate dehydratase (IGPD; sites α, β, and γ). Structural, electron paramagnetic resonance, and electron spin echo envelope modulation parameters were calculated and compared with the experimental values. All the simulations were performed in water within the framework of the polarizable continuum model. The angular dependence of [Formula: see text] and [Formula: see text] on the dihedral angle θ between the V=O and N-C bonds and on the angle φ between the V=O and V-N bonds, where N is the coordinated aromatic nitrogen atom, was also found. From the results it emerges that it is possible to model the active site of a vanadium protein through DFT methods and determine its structure through the comparison between the calculated and experimental spectroscopic parameters. The calculations confirm that the donor sets of sites B and A of vanadyl-substituted carboxypeptidase are [[Formula: see text], H(2)O, H(2)O, H(2)O] and [N(His)(||), N(His)(⊥), [Formula: see text], H(2)O], and that the donor set of site 3 of CF(1)-ATPase is [[Formula: see text], OH(Thr), H(2)O, H(2)O, [Formula: see text]]. For VBrPO, the coordination modes [N(His)(||), N(His)(∠), OH(Ser), H(2)O, H(2)O(ax)] for the low-pH site and [N(His)(||), N(His)(∠), OH(Ser), OH(-), H(2)O(ax)] or [N(His)(||), N(His)(∠), [Formula: see text], H(2)O] for the high-pH site, with an imidazole ring of histidine strongly displaced from the equatorial plane, can be proposed. Finally, for sites α, β, and γ of IGPD, the subsequent deprotonation of one, two, and three imidazole rings of histidine and the participation of a carboxylate group of a glutamate residue ([N(His)(||), [Formula: see text], H(2)O, H(2)O], [N(His)(||), N(His)(||), [Formula: see text], H(2)O], and [N(His)(||), N(His)(||), [Formula: see text], OH(-), [Formula: see text]], respectively) seems to be the most plausible hypothesis.     

The biosynthesis of 4-hydroxycoumarin and dicoumarol by Aspergillus fumigatus Fresenius

A strain of Aspergillus fumigatus Fresenius, isolated from spoiled hay, converts melilotic acid (o-hydroxyphenylpropionic acid) and o-coumaric acid into 4-hydroxycoumarin and dicoumarol. The sequence is shown to be melilotic acid (I) [Formula: see text] coumaric acid (IV) [Formula: see text] beta-hydroxymelilotic acid (II) [Formula: see text] beta-oxomelilotic acid (III) [Formula: see text] 4-hydroxycoumarin (VI), on the basis of (1) studies on the formation of postulated intermediates, (2) experiments with isotopically labelled materials and (3) sequential enzyme induction. In the presence of semicarbazide, o-coumaraldehyde is formed from o-coumaric acid: there is no evidence, however, that this lies on the normal metabolic pathway.