Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Mapping and quantification of the major oligosaccharide components of heparin.

ABSTRACT: A new method of determining the oligosaccharide composition of commercial glycosaminoglycan heparin is described in which heparin was first depolymerized using heparin lyase (EC 4.2.2.7), and then analysed by a single h.p.l.c. step. All 20 of the porcine and bovine heparins examined were found to contain a small number of major oligosaccharide components, which on average comprised 86% of their mass. The five most abundant oligosaccharides have defined chemical structures. Although the relative abundance of oligosaccharides varied, the heparins examined were surprisingly similar. Porcine, bovine, low-Mr, and high and low antithrombin III (ATIII)-affinity heparins, however, each had distinctly different proportions of these major oligosaccharide components. The concentrations of one of these five oligosaccharides, containing a portion of the ATIII binding site, correlated with the anticoagulant activity of the ATIII-affinity-fractionated porcine-mucosal heparins from which it was derived. An additional oligosaccharide of undetermined structure was found in significant quantities in both bovine heparin and high ATIII-affinity porcine-mucosal heparin. The correlation between oligosaccharide concentration and anticoagulant activity suggests that the oligosaccharide is derived from a structural variant of the ATIII-binding site. Finally, for the heparins examined chondroitin/dermatan sulphate formed 0.6-7.4% of their mass.

SUBMITTER: Linhardt RJ

PROVIDER: S-EPMC1135151 | biostudies-other | 1988 Sep

REPOSITORIES: biostudies-other

ACCESS DATA

Json Xml

Similar Datasets

Divergent heparin oligosaccharide synthesis with preinstalled sulfate esters.

Project description:Traditional chemical synthesis of heparin oligosaccharides first involves assembly of the full length oligosaccharide backbone followed by sulfation. Herein, we report an alternative strategy in which the O-sulfate was introduced onto glycosyl building blocks as a trichloroethyl ester prior to assembly of the full length oligosaccharide. This allowed divergent preparation of both sulfated and non-sulfated building blocks from common advanced intermediates. The O-sulfate esters were found to be stable during glycosylation as well as typical synthetic manipulations encountered during heparin oligosaccharide synthesis. Furthermore, the presence of sulfate esters in both glycosyl donors and acceptors did not adversely affect the glycosylation yields, which enabled us to assemble multiple heparin oligosaccharides with preinstalled 6-O-sulfates.

| S-EPMC3324038 | biostudies-literature

Fine-mapping sequence mutations with a major effect on oligosaccharide content in bovine milk.

Project description:Human milk contains abundant oligosaccharides (OS) which are believed to have strong health benefits for neonates. OS are a minor component of bovine milk and little is known about how the production of OS is regulated in the bovine mammary gland. We have measured the abundance of 12 major OS in milk of 360 cows, which had high density SNP marker genotypes. Most of the OS were found to be highly heritable (h2 between 50 and 84%). A genome-wide association study allowed us to fine-map several QTL and identify candidate genes with major effects on five OS. Among them, a putative causal mutation close to the ABO gene on Chromosome 11 accounted for approximately 80% of genetic variance for two OS, N-acetylgalactosaminyllactose and lacto-N-neotetraose. This mutation lies very close to a variant associated with the expression levels of ABO. A third QTL mapped close to ST3GAL6 on Chromosome 1 explaining 33% of genetic variation of an abundant OS, 3'-sialyllactose. The presence of major gene effects suggests that targeted marker-assisted selection would lead to a significant increase in the level of these OS in milk. This is the first attempt to map candidate genes and causal mutations for bovine milk OS.

| S-EPMC6376028 | biostudies-literature

Mapping and identification of the major cell wall-associated components of Mycobacterium leprae.

Project description:Mycobacterium leprae, an obligate intracellular pathogen, can be derived only from host tissue and thus affords the opportunity to study in vivo-expressed products responsible for the particular pathogenesis of leprosy. Despite considerable progress in the characterization of the proteins and secondary gene products of M. leprae, there is little information on the nature of the proteins associated with the cell envelope. M. leprae has been fractionated into its major subcellular components, cell wall, cytoplasmic membrane, and soluble cytosol. A number of biochemical markers, including diaminopimelic acid content, monosaccharide composition, mycolic acid, and glycolipid distribution, were applied to their characterization, and two-dimensional gel electrophoresis was used to map the component proteins. A total of 391 major proteins spots were resolved, and 8 proteins were identified based on their reactivity to a panel of monoclonal antibodies and/or relative pI size. Microsequencing of six protein spots present in the cell wall fraction allowed identification of new proteins, including the protein elongation factor EF-Tu and a homolog for the Mycobacterium tuberculosis MtrA response regulator. These results, together with previous studies, contribute to the progressive knowledge of the composition of the in vivo-expressed proteins of M. leprae.

| S-EPMC108248 | biostudies-literature

Heparin mapping using heparin lyases and the generation of a novel low molecular weight heparin.

Project description:Seven pharmaceutical heparins were investigated by oligosaccharide mapping by digestion with heparin lyase 1, 2, or 3, followed by high performance liquid chromatography analysis. The structure of one of the prepared mapping standards, ?UA-Gal-Gal-Xyl-O-CH(2)CONHCH(2)COOH (where ?UA is 4-deoxy-?-l-threo-hex-4-eno-pyranosyluronic acid, Gal is ?-d-galactpyranose, and Xyl is ?-d-xylopyranose) released from the linkage region using either heparin lyase 2 or heparin lyase 3 digestion, is reported for the first time. A size-dependent susceptibility of site cleaved by heparin lyase 3 was also observed. Heparin lyase 3 acts on the undersulfated domains of the heparin chain and does not cleave the linkages within heparin's antithrombin III binding site. Thus, a novel low molecular weight heparin (LMWH) is afforded on heparin lyase 3 digestion of heparin due to this unique substrate specificity, which has anticoagulant activity comparable to that of currently available LMWH.

| S-EPMC3024469 | biostudies-literature

Molecular principles for heparin oligosaccharide-based inhibition of neutrophil elastase in cystic fibrosis.

Project description:Cystic fibrosis (CF) is a multifactorial disease in which dysfunction of protease-antiprotease balance plays a key role. The current CF therapy relies on dornase ?, hypertonic saline, and antibiotics and does not address the high neutrophil elastase (NE) activity observed in the lung and sputum of CF patients. Our hypothesis is that variants of heparin, which potently inhibit NE but are not anticoagulant, would help restore the protease-antiprotease balance in CF. To realize this concept, we studied molecular principles governing the effectiveness of different heparins, especially 2-O,3-O-desulfated heparin (ODSH), in the presence of sputum components and therapeutic agents. Using sputa from CF patients and an NE activity assay, we found that heparins are ineffective if used in the absence of dornase. This is true even when mucolytics, such as DTT or N-acetylcysteine, were used. Computational modeling suggested that ODSH and DNA compete for binding to an overlapping allosteric site on NE, which reduces the anti-NE potential of ODSH. NE inhibition of both DNA and ODSH is chain length-dependent, but ODSH chains exhibit higher potency per unit residue length. Likewise, ODSH chains exhibit higher NE inhibition potential compared with DNA chains in the presence of saline. These studies suggest fundamental differences in DNA and ODSH recognition and inhibition of NE despite engaging overlapping sites and offer unique insights into molecular principles that could be used in developing antiprotease agents in the presence of current treatments, such as dornase and hypertonic saline.

| S-EPMC6093248 | biostudies-literature

Mapping periplasmic binding protein oligosaccharide recognition with neutron crystallography.

Project description:Numerous studies have shown how periplasmic binding proteins (PBPs) bind substrates with exquisite specificity, even distinguishing between sugar epimers and anomers, or structurally similar ions. Yet, marked substrate promiscuity is also a feature encoded in some PBPs. Except for three sub-Ångström crystal structures, there are no reports of hydrogen atom positions in the remaining (> 1000) PBP structures. The previous X-ray crystal structure of the maltodextrin periplasmic-binding protein from Thermotoga maritima (tmMBP) complexed with oligosaccharide showed a large network of interconnected water molecules stretching from one end of the substrate binding pocket to the other. These water molecules are positioned to form multiple hydrogen bonds, as well as forming interactions between the protein and substrate. Here we present the neutron crystal structure of tmMBP to a resolution of 2.1 Å. This is the first neutron crystal structure from the PBP superfamily and here we unambiguously identify the nature and orientation of the hydrogen bonding and water-mediated interactions involved in stabilizing a tetrasaccharide in the binding site. More broadly, these results demonstrate the conserved intricate mechanisms that underlie substrate-specificity and affinity in PBPs.

| S-EPMC9587032 | biostudies-literature

Chemoproteomic mapping of human milk oligosaccharide (HMO) interactions in cells.

Project description:Human milk oligosaccharides (HMOs) are a family of unconjugated soluble glycans found in human breast milk that exhibit a myriad of biological activity. While recent studies have uncovered numerous biological functions for HMOs (antimicrobial, anti-inflammatory & probiotic properties), the receptors and protein binding partners involved in these processes are not well characterized. This can be attributed largely in part to the low affinity and transient nature of soluble glycan-protein interactions, precluding the use of traditional characterization techniques to survey binding partners in live cells. Here, we present the use of synthetic photoactivatable HMO probes to capture, enrich and identify HMO protein targets in live cells using mass spectrometry-based chemoproteomics. Following initial validation studies using purified lectins, we profiled the targets of HMO probes in live mouse macrophages. Using this strategy, we mapped hundreds of HMO binding partners across multiple cellular compartments, including many known glycan-binding proteins as well as numerous proteins previously not known to bind glycans. We expect our findings to inform future investigations of the diverse roles of how HMOs may regulate protein function.

| S-EPMC9709932 | biostudies-literature

Quantification and mapping of DNA modifications.

Project description:Apart from the four canonical nucleobases, DNA molecules carry a number of natural modifications. Substantial evidence shows that DNA modifications can regulate diverse biological processes. Dynamic and reversible modifications of DNA are critical for cell differentiation and development. Dysregulation of DNA modifications is closely related to many human diseases. The research of DNA modifications is a rapidly expanding area and has been significantly stimulated by the innovations of analytical methods. With the recent advances in methods and techniques, a series of new DNA modifications have been discovered in the genomes of prokaryotes and eukaryotes. Deciphering the biological roles of DNA modifications depends on the sensitive detection, accurate quantification, and genome-wide mapping of modifications in genomic DNA. This review provides an overview of the recent advances in analytical methods and techniques for both the quantification and genome-wide mapping of natural DNA modifications. We discuss the principles, advantages, and limitations of these developed methods. It is anticipated that new methods and techniques will resolve the current challenges in this burgeoning research field and expedite the elucidation of the functions of DNA modifications.

| S-EPMC8341653 | biostudies-literature

Epitope mapping of a monoclonal antibody directed against Neisserial Heparin Binding Antigen

Project description:This SuperSeries is composed of the SubSeries listed below.

2016-05-27 | GSE81379 | GEO

The risk of major bleeding in patients with suspected heparin-induced thrombocytopenia.

Project description:BackgroundThe presence of a hypercoagulable disorder such as heparin-induced thrombocytopenia (HIT) may protect against anticoagulant-associated bleeding.ObjectivesTo determine the incidence of major bleeding in patients with suspected HIT.MethodsWe performed a retrospective analysis of 310 patients suspected of having HIT from the Hospital of the University of Pennsylvania and an affiliated community hospital. We compared the cumulative incidence of major bleeding following suspicion for HIT by ultimate HIT status (HIT+ or HIT-) and exposure to an alternative anticoagulant (Tx+ or Tx-). Secondary outcomes included the incidence of new/progressive thrombosis and 30-day mortality.ResultsThe incidence of major bleeding was high in the HIT+Tx+, HIT- Tx+, and HIT-Tx- groups (35.7%, 44.0%, and 37.3%, respectively). The time to first major bleeding event did not differ between groups (P = .24). Factors associated with increased risk of major bleeding included intensive care unit admission (HR 2.24, 95% CI 1.44-3.47), platelet count < 25 × 109 /L (HR 2.13, 1.10-4.12), and renal dysfunction (HR 1.56, 1.06-2.27); 35.7% of HIT+Tx+, 13.8% HIT-Tx+, and 9.3% of HIT-Tx- patients experienced new or progressive thrombosis. Mortality was similar among the three groups (26.2% HIT+Tx+, 34.5% HIT-Tx+, and 26.7% of HIT-Tx- [P = .34]).ConclusionsAmong patients with suspected HIT, major bleeding was common regardless of HIT status. Contrary to our hypothesis, HIT+ patients were not protected from major bleeding. A better understanding of bleeding risk is needed to inform management decisions in patients with suspected HIT.

| S-EPMC6913895 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data