Recent advances on the synthesis of N-linked glycoprotein for the elucidation of glycan functions

Glycoproteins play roles in many biological events, while, the glycan structure-function relationship has remained to be studied. In order to understand glycan function, homogeneous glycoproteins have been synthesized. This review introduced recent progress of their synthetic approaches.     

Synthesis of an octamannosyled glycan chain, the key oligosaccharide structure in ER-associated degradation

The high-mannose type decasaccharide (Man(8)GlcNAc(2)), the proposed ligand of ER residing mannosidase-like proteins (MLP), and its monoglycosylated homologue (alpha-Glc(1)Man(8)GlcNAc(2)) were synthesized. The oligosaccharide assembly was performed in a convergent and stereoselective manner, using three oligosaccharide components, a core trisaccharide having a beta-mannoside bond, a liner mannotriose, and a branched mannotetraose.     

Petunia hybrida S-proteins: ribonuclease activity and the role of their glycan side chains in self-incompatibility

Summary Self-incompatibility in flowering plants is controlled by the S-gene, encoding stylar S (allele-specific) glycoproteins. In addition to three previously characterized Petunia hybrida S-proteins, we identified by N-terminal sequence analysis another stylar S-protein, co-segregating with the S _b-allele. Purified S-proteins reveal biological activity, as is demonstrated for two of them by the allele-specific inhibition of pollen tube growth in vitro. Moreover, the four isolated S-proteins are ribonucleases (S-RNases). Specific activities vary from 30 (S₁) to 1000 (S₂) units per min per mg protein. We attempted to investigate the functionality of the carbohydrate portion of the S-RNases. Deglycosylation studies with the enzyme peptide-N-glycosidase F (PNGase F) reveals differences in the number of N-linked glycan chains present on the four S-RNases. Variability in the extent of glycosylation accounts for most of the molecular weight differences observed among these proteins. By amino acid sequencing, the positions of two of the three N-glycosylation sites on the S₂-RNase could be located near the N-terminus. Enzymic removal of the glycan side chains has no effect on the RNase activity of native S-RNases. This suggests another role of the glycan moiety in the self-incompatibility mechanism.     

Crystal structure of a fully glycosylated HIV‐1 gp120 core reveals a stabilizing role for the glycan at Asn262

The crystal structure of a fully glycosylated HIV‐1 gp120 core in complex with CD4 receptor and Fab 17b at 4.5‐Å resolution reveals 9 of the 15 N‐linked glycans of core gp120 to be partially ordered. The glycan at position Asn262 had the most extensive and well‐ordered electron density, and a GlcNAc₂Man₇ was modeled. The GlcNAc stem of this glycan is largely buried in a cleft in gp120, suggesting a role in gp120 folding and stability. Its arms interact with the stems of neighboring glycans from the oligomannose patch, which is a major target for broadly neutralizing antibodies. Proteins 2015; 83:590–596. © 2014 Wiley Periodicals, Inc.     

Structure of an acidic microcapsular glycan from the reference strain (C.D.C. 866-57) for Serratia marcescens serogroup 01

The structure of the acidic polysaccharide from Serratia marcescens serogroup O1 has been investigated. NMR spectroscopy together with sugar and methylation analysis have been used as well as a uronic acid degradation. The polysaccharide consists of pentasaccharide repeating units having the following structure.

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The polysaccharide also contains one equivalent of O-acetyl groups per repeating unit present on, inter alia, a hydroxymethyl group.     

Differential representation of human skeletal remains in eroded and redeposited coastal deposits: A case study from the Marshall Islands

A historical cemetery on Majuro Atoll, Republic of the Marshall Islands, was partially washed away during an exceptional seasonal high tide. The osteological analysis of the human remains washed out by the tides showed that the anatomical representation of the bones found on the shoreline is distinctly skewed, caused by the erosion of the graves by wave action and the differential transport of bones by waves and currents. The two major factors involved in the observed differential preservation of skeletal elements appear to be (i) the overall weight of the bone and (ii) its ability to float. Light-weighted bones, such as the phalanges, or heavily spongiotic bones, such as vertebrae and patellae, float easily and — by wave and tidal action — can be carried out to sea, leaving the heavier bones, such as femora, tibiae, or non-floating bones, such as the crania and mandibles, behind.     

基于CGR的DNA序列的时间序列模型(英文)

利用DNA序列的混沌游戏表示(chaos game representation,CGR),提出了将2维DNA图谱转化成相应的类谱格式的方法。该方法不仅提供了一个较好的视觉表示,而且可将DNA序列转化成一个时间序列。利用CGR坐标将DNA序列转化成CGR弧度序列,并引入长记忆ARFIMA(p,d,q)模型去拟合此类序列,发现此类序列中有显著的长相关性且拟合度很好。     

Driving forces for data exchange

The subgroup ‘Driving Forces for Data Exchange’ as part of the SETAC LCA Workgroup on Data Availability and Quality is finishing its final report with recommendations and guidelines to stimulate availability and exchange of LCI data. Activities in the past three years involved a literature review, interviews with LCI data publishers and stakeholder discussions. The final report will be part of a SETAC ‘Code of Life Cycle Inventory Practice’, dealing with LCI data availability and quality aspects in a broader sense.     

Array-assisted Characterization of a Fucosyltransferase Required for the Biosynthesis of Complex Core Modifications of Nematode N-Glycans

Fucose is a common monosaccharide component of cell surfaces and is involved in many biological recognition events. Therefore, definition and exploitation of the specificity of the enzymes (fucosyltransferases) involved in fucosylation is a recurrent theme in modern glycosciences. Despite various studies, the specificities of many fucosyltransferases are still unknown, so new approaches are required to study these. The model nematode Caenorhabditis elegans expresses a wide range of fucosylated glycans, including N-linked oligosaccharides with unusual complex core modifications. Up to three fucose residues can be present on the standard N,N′-diacetylchitobiose unit of these N-glycans, but only the fucosyltransferases responsible for transfer of two of these (the core α1,3-fucosyltransferase FUT-1 and the core α1,6-fucosyltransferase FUT-8) were previously characterized. By use of a glycan library in both array and solution formats, we were able to reveal that FUT-6, another C. elegans α1,3-fucosyltransferase, modifies nematode glycan cores, specifically the distal N-acetylglucosamine residue; this result is in accordance with glycomic analysis of fut-6 mutant worms. This core-modifying activity of FUT-6 in vitro and in vivo is in addition to its previously determined ability to synthesize Lewis X epitopes in vitro. A larger scale synthesis of a nematode N-glycan core in vitro using all three fucosyltransferases was performed, and the nature of the glycosidic linkages was determined by NMR. FUT-6 is probably the first eukaryotic glycosyltransferase whose specificity has been redefined with the aid of glycan microarrays and so is a paradigm for the study of other unusual glycosidic linkages in model and parasitic organisms.     

Glycan microarray profiling of parasite infection sera identifies the LDNF glycan as a potential antigen for serodiagnosis of trichinellosis

Diagnostic methods for parasite infections still highly depend on the identification of the parasites by direct methods such as microscopic examination of blood, stool and tissue biopsies. Serodiagnosis is often carried out to complement the direct methods; however, few synthetic antigens with sufficient sensitivity and specificity are available. Here we evaluated a glycan microarray approach to select for synthetic glycan antigens that could be used for serodiagnosis of parasitic infections. Using a glycan array containing over 250 different glycan antigens, we identified GalNAcβ1–4(Fucα1–3)GlcNAc-R (LDNF) as a glycan antigen that is recognized by antibodies from Trichinella-infected individuals. We synthesized a neoglycoconjugate, consisting of five LDNF molecules covalently coupled to bovine serum albumin (BSA), and used this neoglycoconjugate as an antigen to develop a highly sensitive total-Ig ELISA for serological screening of trichinellosis. The results indicate that glycan microarrays constitute a promising technology for fast and specific identification of parasite glycan antigens to improve serodiagnosis of different parasitic infections, either using an ELISA format, or parasite-specific glycan arrays.     

A proposal for the representation of the stereochemistry of quadrivalent centers

The broken wedge, broken line, solid bar, and broken bar are either not reasonable or can be replaced by only one type of solid wedge in the stereochemical formulation. A convention based on a one-wedge symbolization is proposed, where a or b is used instead of c, d, e, f, g , or h . © 1992 Wiley-Liss, Inc.     

Closed loops of nearly standard size: common basic element of protein structure

Here, we report the identification of Ulip6, a novel unc-33 and dihydropyrimidinase related protein that belongs to the Ulip/CRMP protein family. Ulip6 was found in a yeast two-hybrid screen using the neuronal glycine transporter GlyT2 as bait. The rat and human Ulip6 sequences are highly homologous and most closely related to the liver enzyme dihydropyrimidinase (Ulip5). Northern and Western analysis of rat tissues revealed that the distribution of the Ulip6 mRNA and protein resembles those of brain-type Ulip proteins. Like Ulip1–4, Ulip6 is highly expressed in embryonic and early postnatal brain and spinal cord. These findings are consistent with Ulip6 having a function in neuronal differentiation and/or axon growth.     

Retention of maize auxin-binding protein in the endoplasmic reticulum: quantifying escape and the role of auxin

The localisation of maize (Zea mays L.) auxin-binding protein (ABP1) has been studied using a variety of techniques. At the whole-tissue level, tissue printing indicated that ABP1 is expressed to similar levels in all cells of the maize coleoptile and in the enclosed leaf roll. Within cells, the signals from immunofluorescence and immunogold labelling of ultrathin sections both indicated that ABP1 is confined to the endoplasmic reticulum (ER), none being detected in either Golgi apparatus or cell wall. This distribution is consistent with targeting motifs in its sequence. These observations are discussed with reference to the various reports which place a population of ABP1 on the outer face of the plasma membrane, including those suggesting that it is necessary on the cell surface for rapid, auxin-mediated protoplast hyperpolarisation. We have tested one proposed model to account for release of ABP1 from the ER, namely that auxin binding induces a conformational change in ABP1 leading to concealment of the KDEL retention motif. Using double-label immunofluorescence the characteristic auxin-induced rise in Golgi-apparatus signal was found, yet no change in the distribution of the ABP1 signal was detected. Maize suspension cultures were used to assay for auxin-promoted secretion of ABP1 into the medium, but secretion was below the limit of detection. This can be ascribed at least partly to the very active acidification of the medium by these cells and the instability of ABP1 in solution below pH 5.0. In the insect-baculovirus expression system, in which cell cultures maintain pH 6.2, a small amount of ABP1 secretion, less than 1% of the total, was detected under all conditions. Insect cells were shown to take up auxin and no inactivation of added auxin was detected, but auxin did not affect the level of ABP1 in the medium. Consequently, no evidence was found to support the model for auxin promotion of ABP1 secretion. Finally, quantitative glycan analysis was used to determine what proportion of ABP1 might reach the plasma membrane in maize coleoptile tissue. The results suggest that less than 15% of ABP1 ever escapes from the ER as far as the cis-Golgi and less than 2% passes further through the secretory pathway. Such leakage rates probably do not require a specialised mechanism allowing ABP1 past the KDEL retrieval pathway, but we are not able to rule out the possibility that some ABP1 is carried through associated with other proteins. The data are consistent with the presence of ABP1 both on the plasma membrane and in the ER. The relative sizes of the two pools explain the results obtained with immunofluorescence and immunogold labelling and illustrate the high efficiency of ER retention in plants. Received: 31 October 1996 / Accepted: 16 December 1996     

Hemocytes and Plasma of the Eastern Oyster (Crassostrea virginica) Display a Diverse Repertoire of Sulfated and Blood Group A-modified N-Glycans

The eastern oyster (Crassostrea virginica) has become a useful model system for glycan-dependent host-parasite interactions due to the hijacking of the oyster galectin CvGal1 for host entry by the protozoan parasite Perkinsus marinus, the causative agent of Dermo disease. In this study, we examined the N-glycans of both the hemocytes, which via CvGal1 are the target of the parasite, and the plasma of the oyster. In combination with HPLC fractionation, exoglycosidase digestion, and fragmentation of the glycans, mass spectrometry revealed that the major N-glycans of plasma are simple hybrid structures, sometimes methylated and core α1,6-fucosylated, with terminal β1,3-linked galactose; a remarkable high degree of sulfation of such glycans was observed. Hemocytes express a larger range of glycans, including core-difucosylated paucimannosidic forms, whereas bi- and triantennary glycans were found in both sources, including structures carrying sulfated and methylated variants of the histo-blood group A epitope. The primary features of the oyster whole hemocyte N-glycome were also found in dominin, the major plasma glycoprotein, which had also been identified as a CvGal1 glycoprotein ligand associated with hemocytes. The occurrence of terminal blood group moieties on oyster dominin and on hemocyte surfaces can account in part for their affinity for the endogenous CvGal1.     

A sensitive mapping strategy for monitoring the reproducibility of glycan processing in an HIV vaccine, RGP-160, expressed in a mammalian cell line

The external envelope glycoprotein (gp 160) of HIV-1 is a candidate for vaccines against AIDS. Most of the surface of the molecule is shielded by carbohydrate and the structures and locations of these glycans may be important in defining the immunogenicity of the viral coat. Here we report a sensitive mapping strategy for profiling and analysing the N-glycosylation of gp160, based on chemical release of glycans, fluorescent labelling and HPLC analysis. This approach has been validated in terms of establishing the reproducibility of all steps in the analytical procedure and on overall reproducibility on a run-to-run and day-to-day basis. The validated analysis technique was used to monitor the consistency of N-glycosylation of one rgp 160 vaccine candidate produced in bovine hamster kidney (BHK) cell culture. It was demonstrated that the variation in the glycan profiles of 6 different lots was not statistically significant.     

One-step immobilization and purification of genetic engineering CBD fusion EndoS on cellulose for antibodies Fc-glycan remodeling

The endoglycosidase (EndoS and its glycosynthase mutants D233A, D233Q) gene was fused with cellulose binding domain (CBD) using pET-35b vector and the fusion enzymes were successfully expressed in Escherichia coli. Then a simplified approach for one-step immobilization and purification of EndoS enzymes using cellulose as matrices were developed and excellent loading efficiency (81–90%) was achieved in optimal condition. The cellulose immobilized CBD-EndoS and the glycosynthase mutants presented high catalytic activity and were successfully applied in a two-step antibody Fc N-glycan remodeling, generating a therapeutic antibody with homogeneous glycoform in high efficiency. The cellulose immobilized CBD-EndoS and its mutants (D233A and D233Q) displayed excellent storage stability when stored at 4 degrees for one month. Reusability studies demonstrated that the cellulose immobilized CBD-EndoS and its mutants could be recycled for five times without obvious activity loss.     

Motion representation of the long fingers: A proposal for the definitions of new anatomical frames

Despite the availability of the International Society of Biomechanics (ISB) recommendations for the orientation of anatomical frames, no consensus exists about motion representations related to finger kinematics. This paper proposes novel anatomical frames for motion representation of the phalangeal segments of the long fingers. A three-dimensional model of a human forefinger was acquired from a non-pathological fresh-frozen hand. Medical imaging was used to collect phalangeal discrete positions. Data processing was performed using a customized software interface (“lhpFusionBox”) to create a specimen-specific model and to reconstruct the discrete motion path. Five examiners virtually palpated two sets of landmarks. These markers were then used to build anatomical frames following two methods: a reference method following ISB recommendations and a newly-developed method based on the mean helical axis (HA). Motion representations were obtained and compared between examiners. Virtual palpation precision was around 1 mm, which is comparable to results from the literature. The comparison of the two methods showed that the helical axis method seemed more reproducible between examiners especially for secondary, or accessory, motions. Computed Root Mean Square distances comparing methods showed that the ISB method displayed a variability 10 times higher than the HA method. The HA method seems to be suitable for finger motion representation using discrete positions from medical imaging. Further investigations are required before being able to use the methodology with continuous tracking of markers set on the subject?s hand.     

Investigation of the solution behavior of tri-n-butylphosphine copper(I) and silver(I) acetates using P{H} NMR spectroscopy

³¹P{¹H} NMR spectra of metal-organic [(ⁿBu₃P)_mMO₂CMe] (M = Cu, Ag; m = 1, 1.5, 2, 2.5, 3, 3.5, 4) have been studied in the temperature range of 308-178 K. Exchange parameters were determined for the appropriate silver(I) complexes. Possible ligand exchange mechanisms based on dissociative and associative processes are discussed.