Glycoscience
Glycoscience
Program Resources
GlyGen
GlyGen is a data integration and dissemination project that retrieves information from multiple international data sources. Click below to access tutorials on using GlyGen and other online GlyGen resources.
- Glycan searching tutorial
- Protein searching tutorial
- Glycoprotein searching tutorial
- GlyGen media and online resources
GLYCAM 
GLYCAM is a tool that facilitates computer modeling of carbohydrates.
CVLS4GAGs Beta
CVLS4GAGs Beta is a tool for modeling glycosaminoglycan interactions with proteins. The tool is available for use for investigators with an edu/org/gov affiliation.
Generated from the Glycoscience Program
- Accessible Resources (see Table 1 below)
Learn more about the resources being developed by the NIH Common Fund Glycoscience program:- Methods and technologies for synthesis of biomedically relevant carbohydrates (for biologists)
- Methods and technologies for synthesis of biomedically relevant carbohydrates (for chemists)
- Accessible tools for probing and analyzing carbohydrates and their interaction partners
- Polysaccharides resource guide
- Summary of available tools
Developed through the Glycoscience Program
- More Resources (see Table 2 below)
- Websites
- The GECKO Project: CRISPR/Cas9-based molecular biology for validated human glycosyltransferase knock out cell lines
- Haab Lab: Software for analyzing glycan-array data, More information here and here
- Kohler Lab: Photocrosslinking sugar technology that can be used to identify glycan-dependent interactions
- Zaia Research Group: GAG synthetic saccharides
- National Center for Functional Glycomics: Lectin Reference Data
- Wells and West Labs: Synthetic O-Glycan Standards
- Bertozzi Group: IsoTag Kit for Profiling Intact Glycopeptides and Isostamp v2.0 to analyze IsoTag data
- Li Lab: Info on synthetic useful glyco-enzymes and standard protocols for chemoenzymatic synthesis of O-glycans, glycosphingolipids, and bacterial polysaccharides
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Table 1. Accessible Resources Generated from the Glycoscience Program
| PI Name | Resource | Description | Publication(s) | Availability through Website or Company | Contact |
|---|---|---|---|---|---|
| Geert-Jan Boons | Automation of chemoenzymatic synthesis | Methods for automation of chemoenzymatic synthesis; Methods to prepare building blocks for use on his automated platform for chemoenzymatic synthesis of glycans; Commercialized a library of enzymes suitable for these purposes; Several glycans and glycan libraries have been synthesized and some have been used to prepare glycan arrays |
Glyco Expression Technology (www.glycoexpresstech.com); Zymtronix Catalytic Systems, Inc (https://zymtronix.com); VIAMUNE, Inc (ViaMune.html) |
[email protected] | |
| Lei Li | Automation of chemoenzymatic synthesis of O-glycans | Glyco-enzymes (for synthetic purposes) developed and standard protocols for chemoenzymatic synthesis of O-glycans; Machine driven approach for the automatic synthesis of glycans and glycopeptides (using a peptide synthesizer) | [email protected] | ||
| Marshall Wayne Bern | Byonic search | Enhancement of the Byonic proteomics search engine for glycopeptide analysis (Integrated analysis of complementary fragmentation modes, integrated analysis of MS1 and MS2 (that is, intact and fragmented peptides), and finally topology (“cartoon”) assignment for glycopeptide spectra). | proteinmetrics.com | N/A | |
| Brian Haab | CarboGrove | CarboGrove is a resource of glycan-binding specificities created through analyzed glycan-array data from all platforms. | PMID: 35352123 | carbogrove.org | [email protected] |
| Xi Chen | Chemoenzymatic synthesis of glycosphingolipids | Chemoenzymatic methods for the total synthesis of Glycosphingolipids; Necessary enzymes and substrates for assembly of easy-to-use reagent kits; Kits to prepare various glycosphingolipids via chemoenzymatic synthesis |
Integrated Micro-Chromatography Systems (IMCS) Inc. |
[email protected] | |
| Hai Yu | Chemoenzymatic synthesis of polysaccharides | Methods for the chemoenzymatic synthesis of several different bacterial oligosaccharides; Prepared and optimized enzymes for these purposes |
Integrated Micro-Chromatography Systems (IMCS) Inc. |
[email protected] | |
| Umesh Desai | CVLS For GAGs | A computational tool for understanding GAG recognition of proteins. | https://cvls4gags.vcu.edu /wmol/ |
[email protected] | |
| Robert J. Woods | GLYCAM-Web | An on-line platform for modeling glycan/glycoprotein 3D structures, searching and retrieving them from the protein database, and facilitating their simulation | https://www.glycam.org | [email protected] | |
| Lara Mahal | GlycoMiR | Integrated within GlycoEnzDB providing data on miRNA regulation of mRNA translation | Integrated within www.virtualglycome.org /GlycoEnzDB |
N/A | |
| Lori Yang | GlycoSense: Glycoprotein analysis via lectin suspension arrays | A simple flow cytometry assay using glycan-specific reagents conjugated to microspheres (beads) for multiplex detection of key glycofeatures | www.lectenz.com | [email protected] | |
| Natasha Zachara | Glycotuners (98 constructs), 7 Destination vectors encoding tuning; and 37 Gateway compatible constructs encoding OGT, OGA, GFAT1, and UAP, as well as mutants | A suite of tools that enable small molecular regulation (Trimethoprim/Shield) of the expression of the O-GlcNAc transferase (OGT), O-GlcNAcase (OGT), Glutamine Fructose-6phophate aminotransferase 1, 2 (GFAT1,2), and UDP-N-Acetylglucosamine Pyrophosphorylase (UAP1/2). | PMID: 34004049 | [email protected] | |
| Carolyn Bertozzi & Sharon Pitteri | IsoTag & IsoStamp | Reagent for orthogonal metabolic labeling of glycans | https://clickchemistrytools.com /isotag-kit/ |
N/A | |
| Jennifer Kohler | Photocrosslinking GlcNAc analog | Method and reagents that can be used to identify cellular binding partners of glycosylated molecules | https://www.utsouthwestern.edu /labs/kohler |
jennifer.kohler@ utsouthwestern.edu |
|
| Catherine Leimkuhler-Grimes | Probes | N-acetyl muramic acid orthogonal metabolic probes | https://www.tocris.com/products /click-n-acetylmuramic-acid-azide_7506 |
[email protected] |
Table 2. More Resources Generated from the Glycoscience Program
| PI Name | Resource | Description | Publication(s) | Availability through Website or Company |
|---|---|---|---|---|
| Stefan Ruhl | Affinity reagents | Harnesses sialic acid binding proteins found in human oral microflora as additional glycan binding affinity probes | PMID: 32820052 | |
| Alexei Demchenko | Automation of chemical synthesis | An HPLC based automated synthesis platform, and development of synthetic methods and polymer supports for solid-phase glycan synthesis | PMID: 27575052; PMID: 27808325; PMID: 29227649; PMID: 29693690; PMID: 29861508; PMID: 30147293; PMID: 30407673; PMID: 31066275; PMID: 31930269; PMID: 32785304 |
glyco-world.com |
| Adam Linstedt | Biosensors of GalNAc transferase activity | Protein-based fluorescence sensors that traffic in the secretory pathway to monitor GalNAc-transferase activity in living cells. The sensors can either be “pan” or isozyme specific. | PMID: 27632006; PMID: 25225288 |
|
| Weiping Tang | Catalytic methods development | Site-selective alkylation and acylation methods for carbohydrates; Mild way to prepare glycosyl chlorides, bromides, and esters for cross-coupling glycosylation. | PMID: 32026682; PMID: 31739665; PMID: 31066162; PMID: 34911160; PMID: 32691596 |
|
| Clay Bennett | Catalytic methods development | Stereoselective glycosylation reactions for the direct construction of beta-linked glycans using appropriately selected sulfonyl chloride promoters in the absence of directing groups; Construction of rare deoxy-sugar monosaccharides including a novel gold-catalyzed process for the cyclization of homopropargyl orthoformates; Automation of these new methods | PMID: 29572995; PMID: 31021647; PMID: 31305082; PMID: 32281384; PMID: 32293636; PMID: 34463017; PMID: 31880395; PMID: 31550879; PMID: 31755271; PMID: 29953219; PMID: 31534883 |
|
| Hien Nguyen | Catalytic methods development | New catalytic methods utilizing a phenathroline catalyst or a visible-light-mediated copper catalyst for the synthesis of glycans. | PMID: 30920099; PMID: 34168901; PMID: 29520326 |
|
| Matthew Brichacek | Catalytic methods development | A novel fluorescent multifunctional neoglycoside auxiliary (N-(2-ThioEthyl)-2-AminoBenzamide, (TEAB) synthesized as a versatile reagent for preparing thiol-functionalized glycans in high yield | PMID: 33761407; PMID: 34264248 |
|
| Liming Zhang | Catalytic methods development | New catalytic methods for the synthesis of glycans | PMID: 30439547; PMID: 31396001; PMID: 32431565; PMID: 34319729 |
|
| Jonathan Amster | GAG sequencing | Automated capillary electrophoresis-tandem mass spectrometry platform for the structural analysis of mixtures of glycosaminoglycan oligomers that are isolated in protein binding assays | PMID: 29501428; PMID: 30773923; PMID: 32718661; PMID: 31616929; PMID: 32641905 |
|
| Hannes Buelow | GAGs HTP assay for cell surface HS; DNA clones for scFvs encoding HIS-tagged anti-HS and Fc-fusion antibodies; protein preparations of scFvs | A high- throughput, multiplexed fluorescence-based platform to define the HS surface characteristics of a cell using a set of HS-specific single chain variable fragment (scFvs) antibodies. DNA clones for scFvs encoding HIS-tagged anti-HS and Fc-fusion antibodies will distributed upon request on a fee for service basis. Similarly, protein preparations of scFvs will be distributed on a fee for service basis. | In Press | (Scroll to More Resources section) |
| Lianchun Wang | Heparan Sulfate (HS) mutant mouse lung endothelial cells library | Heparan Sulfate (HS) mutant mouse lung endothelial cells library with all major HS-biosynthesizing and remodeling enzymes targeted, to enable systematic interrogation of HS structure-function relationship in a cellular context | PMID: 30377379 | https://www.kerafast.com/ |
| Yong Zeng | Microfluidic actuator-based targeted glycomic profiling method | Provides a “sample-in-answer-out” microfluidic lectin-antibody barcode array platform for sensitive, quantitative targeted glycomic profiling in a high-throughput manner. | PMID: 29306434 | |
| Ajit Varki | Sialoglycan Recognizing Probes (SGRPs) | A selection of biotin-labeled sialic acid binding proteins with distinct specificities and matched non-binding mutants | In Press | EMD Millipore |
| David Crich & Peter Andreana | Synthetic methods development for carbohydrate synthesis | New methods for the chemical synthesis of glycans | PMID: 34343001; PMID: 33350830; PMID: 32320231 |
|
| Chris West | T cruzi O-glycan standards & tools | T cruzi O-glycan standards & tools to identify novel glycosylation-associated drug targets for treating protozoan parasites | PMID: 30649355 | https://ast.uga.edu/t-cruzi-o-glycans |
| Adam Linstedt | T3Inh-1 | Membrane-permeant, isozyme-selective, small molecule inhibitor of GalNAc-T3. Effective in cells and mice. Mechanism is direct and mixed-mode. | PMID: 28362263 | |
| Huiwang Ai | UGAcS, UXPS, bapaUGAc, ecpApple, and UGlcS | UGAcS is a genetically encoded fluorescent indicator for UDP-GlcNAc, and UXPS serves as the control indicator with responses to UTP and UDP; bapaUGAc is a genetically encoded fluorescent indicator for UDP-GlcNAc in the ER and Golgi, and ecpApple serves as the control indicator with responses to pH changes; UGlcS is genetically encoded fluorescent indicator for UDP-Glucose. | PMID: 34729420 | www.addgene.org/Huiwang_Ai (plasmids are available from Addgene or by contacting [email protected]) |
| Christina Woo | Writing and erasing O-GlcNAc from target proteins in cells | Fused nanobodies to O-GlcNAc transferase (OGT) or O-GlcNAcase (OGA) as proximity-directing agents to selectively “write” and “erase” O-GlcNAc from a target protein in cells | PMID: 33686291; PMID: 32119511; PMID: 34783346; PMID: 33950562 |
www.addgene.org/Christina_Woo |
| Xu Wang | Nanopore sequencer for GAGs (pending) | This platform will enable single chain sequencing of glycosaminoglycans | PMID: 31121093; PMID: 28000682 |
