GlycoShape is an OA database of glycans 3D structural data and information that can be downloaded and/or used with Re-Glyco to rebuild glycoproteins from the RCSB PDB or EMBL-EBI AlphaFold repositories or own. GlycoShape can also predict N-glycosylation occupancy with GlcNAc Scanning. Developed and curated by Elisa Fadda research group @Elisa
Our latest blog on interesting facts about glycans we dig deeper into the UDP-glucuronic acid and glucuronyltransferases in the endoplasmic reticulum - which can be critical in drug metabolism.
Read at: https://research.bidmc.org/ncfg/blog/facts-about-udp-glucuronic-acid-and-glucuronosyltransferases-er
*Note: pun intended π
A spoonful of sugar #18 π¬
Plant receptor kinases translate and pass on chemical messages as part of many key biological processes. A new fabulous cryo-EM structure of the active complex between the kinase MIK2, the immunomodulatory peptide SCOOP and the co-receptor BAK1 shows how its binding hinges on N-glycosylation (https://doi.org/10.1038/s41477-024-01841-6)
You can rebuilt the fully glycosylated structure of the complex with https://glycoshape.org with some fancy-plant N-glycans :awesome:
@MissGayle We are based in the UK, luckily! But we are always making plans :P
On this page we are focusing on #science, yet we are not immune to the political and social environment around all of us
We are a small research group interested in all about sugar biology π¬ structural biology π± (see above) and computational biophysics π»
We operate *exclusively* here on #mastodon #fediverse, where the scientific discourse needs to be better supported
We think we are doing our bit, please support (π+ReTooT) #science posts to amplify scientific content on free servers!
A spoonful of sugar #17 π¬
Everyone needs a bit of sugar today, here is a treat
The oligosaccharyltransferase, or OST (EC 2.4.1.119), is a key enzyme that functionalizes nascent proteins with sugars called N-glycans
The 3D structure of this magnificent molecular machine has been solved by cryo-EM by Ana Ramirez et al. (PDB 8AGC) https://doi.org/10.1038/s41467-022-35067-x
Be like OST and plant one of the 195 N-glycans π± online on your protein 3D structure with https://glycoshape.org :awesome:
A spoonful of sugar #16 π¬
How does glycosylation affect not only structure and function of proteins, but also binding specificity?
In a new paper fresh off the #bioRxiv press https://doi.org/10.1101/2024.10.24.620132 in collaboration with Nicki Packer, Len Harrison and Ethan Goddard-Borger, we explain how glycosylation of CD52 (reconstructed with https://glycoshape.org) determines:
1) the peptide's conformation,
2) binding to the HMGB1 Box B and only then
3) to SIGLEC-10 :awesome:
6/6 Last but not least GlycoShape was and continues to be developed for and with the #glycotime community :blobcheerbounce: BIG MASSIVE THANK YOU π to all the beta testers around the world. Happy glycosylating! :awesome:
5/6 GlycoShape was developed with the generous support of ORACLE for Research and funded by the Science Foundation of Ireland (SFI) Additional resources provided by ICHEC and amazing ongoing support from IRIDIS HPC at the University of Southampton
4/6 GlycoShape (https://glycoshape.org) is an OA database and toolbox that allows you to restore the 3D structure of glycoproteins with a fast and accurate algorithm named Re-Glyco.
The database counts > 550 glycans to date, largely from the human glycome with examples from all species. For an overview check out the figure below β¬οΈ
3/6 Analogously, glycoproteins carry beautifully complex sugars, with precise structures and functions, yet invisible due to their fast dynamics and heterogeneous nature
2/6 What you see through a camera lens depends on the shutter speed.
Yet we all know that hummingbirds do have wings, and that these are precisely shaped to allow the fast and complex dynamics crucial to their ability to hover and feed on nectar
Some exciting #glycotime to start the week!
GlycoShape is fresh off the press today on Nature Methods https://www.nature.com/articles/s41592-024-02464-7 :awesome:
Check out the short thread below 1/6
The Nobel Prize in Chemistry 2024 goes to David Baker (1/2) and Demis Hassabis and John Jumper (1/2) for protein structure design and prediction from sequence with AI
https://www.nobelprize.org/prizes/chemistry/2024/summary/
Congratulations to all very worthy winners from all of us! π π₯³
As a reminder, just add sugars with http://glycoshape.org :awesome:
A spoonful of sugar #15 π¬
Arabinose is an aldopentose (five-membered ring sugar terminating with a CHO group) commonly found in plants as part of chains O-linked to hydroxy-Pro (Hyp) residues in the protein
As an example, look below at the magnificent structure of an algal mastigoneme resolved by cryo-EM (Dai et al. doi: 10.1016/j.cell.2024.03.005)
For all your arabinose (and Galf) needs, go to https://glycoshape.org , we got you covered! :awesome:
π¨ Part 2/2
In view of the next update we are extending the database to contain examples of glycan structures from bacteria, plants and important model organisms
Look β¬οΈ at these super fancy fucosylated N-glycan forms from C. elegans from the brilliant work by K. Paschinger, @iainwilson and team (see DOIs https://doi.org/10.1016/j.mcpro.2023.100505 and https://doi.org/10.1016/j.jbc.2023.103053) brewing now on our HPCs :awesome:
A spoonful of sugar #14 π¬
π¨ Part 1/2
We have updated the GlycoShape database that now counts 453 3D glycan structures!
Check it out at https://glycoshape.org :awesome:
One of the main changes is that now all glycans are listed by their GlyTouCan IDs, a unique identifier that allows you to search all data related to your favourite glycan across the GlyCosmos (DOI 10.1093/glycob/cwx066) π
A few structures still do not have GlyTouCan IDs, we are currently registering them
A spoonful of sugar #13 π¬
Our team continuously updates the glycan structure database on https://glycoshape.org with new glycans, through a process we call glycan of the week (GOTW) :awesome:
Every week each one of us has (at least) one glycan of their choice to run and analyse through a strict MD protocol for high-quality standards. The results are progressively added to the database.
If you would like your fav glycan in the database, let us know via comment or by email π
This month's interesting fact about glycoscience is about #glycopeptides made by bacteria and the importance of #carbohydrates in antibiotics.
Read the full post at: https://research.bidmc.org/ncfg/blog/facts-about-glycopeptides-made-bacteria
For more interesting facts check: https://research.bidmc.org/ncfg/blog
A spoonful of sugar #12 π¬
Glycans are an integral part of a glycoproteins structure and function, as shown in our most recent paper https://doi.org/10.7554/eLife.95708.3 showing how N-glycosylation allosterically regulates the ability of the SARS-CoV-2 S RBD to bind co-receptors
This ability is regulated by mutations, which can in turn allow viral evolution to alter the shield and the virus' immune profile
All glycans added with https://glycoshape.org :awesome:
#glycotime
