Run an MD simulation of any protein in the AlphaFold Protein Structure Database using AF-CALVADOS

Thanks to @sobuelow.bsky.social AF-CALVADOS is now on Colab

colab.research.google.com/github/KULL-...

Epigenetic memory of colitis promotes tumour growth - Nature Colonic stem cells retain a memory of inflammation following disease resolution and there is a mechanistic link between chronic inflammation and malignancy, suggesting potential strategies to mitigate cancer risk in patients with chronic inflammatory conditions.

Nature research paper: Epigenetic memory of colitis promotes tumour growth

go.nature.com/4t3apvK

Essays in Biochemistry Have an idea for an upcoming themed issue? We want to hear from you!

Essays in Biochemistry publishes themed issues looking at interesting, timely and relevant subjects from across the molecular biosciences. Interested in leading a themed issue? Then fill out our proposal form.🧪 https://ow.ly/xrh050XNAvV

Antiviral reverse transcriptases reveal the evolutionary origin of telomerase Defense-associated reverse transcriptases (DRTs) employ diverse and distinctive mechanisms of cDNA synthesis to protect bacteria against viral infection. However, much of DRT family diversity remains ...

1/10 Genome maintenance by telomerase is a fundamental process in nearly all eukaryotes. But where does it come from?

Today, we report the discovery of telomerase homologs in a family of antiviral RTs, revealing an unexpected evolutionary origin in bacteria.
www.biorxiv.org/content/10.1...

A real triumph for #glycotime and basic research, thanks to the work of Steve Withers and others.🧪

An extracellular multidomain sulfatase contains a first in class mucin targeting binding module. Whilst its C-terminal domain encodes a CTD-like domain similar to type IX secretion systems from Bacteroidota suggesting a novel export mechanism.

We define the cellular location of the 8 characterised sulfatases. Desulfation of galactose occurs both extra and intracellularly, whilst desulfation of 6S-N-acetylglucosamine is exclusively periplasmic

A. muciniphila sulfatases have novel adaptations not previously observed in the characterised Bacteroidota homologues. Infact these features are rare evolutionary events within the subfamilies of the respective enzymes.

A. muciniphila requires processed glycopeptide/glycoprotein forms of colonic mucins for optimal growth, which cannot be recapitulated through trypsin or proteinase K treatment suggesting a microbiome dependent process is needed

The role of Akkermansia muciniphila sulfatases in colonic mucin utilisation Akkermansia muciniphila , an obligate mucin degrader, is a major member of the human colonic microbiota and has been associated positive health outcomes. Mucins are complex glycoproteins that contain ...

Happy to have this collaborative work out on Biorxiv on how Akkermansia muciniphila deploys it’s carbohydrate sulfatases to metabolise colonic mucin, and that processed glycopeptides/proteins of colonic mucin are a favoured carbon source #glycotime.

www.biorxiv.org/content/10.1...

Structural unification of diverse transmembrane acyltransferases reveals a conserved fold for the Transmembrane Acyl Transferase (TmAT) superfamily The movement of acyl groups across biological membranes is essential for many cellular processes. One major family of proteins catalysing this reaction are the acyl transferase family 3 (AT3) proteins...

A cool use of DALI/FoldSeek building on new human HG-SNAT protein enabled Bethan Kinniment-Williams & co., to structural unify the TmAT superfamily of membrane-bound acyltransferases first proposed by Milton Saier Jnr in TCDB. @jnb-lab.bsky.social
www.jbc.org/article/S002...

The GH139 family utilises a non-canonical Asn as a catalytic base, like GH95, but also appears to use the substrates methyl group to help position the catalytic acid; explaining the specificity for methyl fucose and not fucose.

Our latest work on rhamnogalacturonan ii degradation (RGII): Functional and structural characterisation of GH139 that removes O2 methylated fucose from RGII #glycotime

doi.org/10.1016/j.jb...

We also show that carbohydrate sulfatases are immune to the effects of arylsulfamate inhibition and that a carbohydrate sulfamate was also ineffective.

We demonstrate that a panel of arylsulfamate sulfatase inhibitors limit the growth of sulfatase containing Bacteroides, but this is through binding a lipid kinase and not S1 carbohydrate sulfatase inhibition. Some of the most severe effects could be reduced through carbon source selection.

Happy to have this work on the effectiveness of sulfamate based inhibitors on carbohydrate sulfatases out in @pnas.org www.pnas.org/doi/10.1073/pnas. #glycotime

The summary is: Current sulfatase inhibitor technology is not effective on S1 carbohydrate sulfatases of the human colonic microbiota.

By deep characterisation of 186 N-glycan standards, we @thencfg.bsky.social have made the most comprehensive targeted LC-MS glycomic assay to date.
Non-reduced native glycan analysis is key.
We hope this enables anyone with QqQ and interest in #glycotime to measure specific N-glycan structures.

New lysins for medically and environmentally important Mycobacteriales at Newcastle University on FindAPhD.com PhD Project - New lysins for medically and environmentally important Mycobacteriales at Newcastle University, listed on FindAPhD.com

PhD available with me & Paul James looking for exciting new enzymes - www.findaphd.com/phds/project...

Glycocalyx dysregulation impairs blood–brain barrier in ageing and disease - Nature Disruption of mucin-domain glycoprotein expression and function in the endothelial glycocalyx are associated with ageing and Alzheimer’s disease, leading to dysregulated blood–brain barrier function.

Happy to share this new #glycotime work with collaborator Tony Wyss-Coray, led by grad student Sophia Shi, mucin loss at the BBB is associated with aging and cognitive decline, can be reversed by restoration with with gene therapy. Aging is a mucinopathy!

www.nature.com/articles/s41...

Swift Universal Glycan Acquisition (SUGA) Enables Quantitative Glycan Profiling across Diverse Sample Types The ability to rapidly analyze complex mixtures of glycans derived from glycoproteins is important, but techniques are often laborious and require multiple glycan derivatization steps. Here, we descri...

Our new paper in print describes a new approach: release and analysis of N-glycans in less than 24 hours. A perfect approach for those that are glycan-curious as it does not require changing any of your proteomics buffers! 1/5
#glycotime #teammassspec
pubs.acs.org/doi/10.1021/...

The tunnel is assembled through domain closure and allows formation of the catalytic site. These features, and a processive mode of action, are found in several other polysaccharide lyases families and mammalian glycosaminoglycan epimerases.

We show that the length of the catalytic tunnel determines substrate specificity; longer tunnels restrict activity to beta linked substrates whilst shorter tunnels allow activity on mix linked alpha and beta substrates. Some enzymes with very open tunnels are promiscuous.

Bacterial polysaccharide lyase family 33: Specificity from an evolutionarily conserved binding tunnel | PNAS Acidic glycans are essential for the biology of multicellular eukaryotes. To utilize them, microbial life including symbionts and pathogens has evo...

Happy to have this deep dive into polysaccharide lyase family 33 out:

www.pnas.org/doi/suppl/10...

We define features driving substrate specificity, catalytic mechanism, and evolutionary links with multiple lyases and epimerises #glycotime @PNASNews

Oops, thanks for the working link!

ÅNGSTRÖM-RESOLUTION IMAGING OF CELL-SURFACE GLYCANS🍬🍬🍬

For the first time, we are able to image the molecular architecture of the glycocalyx at Ångström resolution. A dream come true!

Read the preprint: biorxiv.org/content/10.110…

And find our tweetorial below!
#glycotime

PhD Programmes, Research Projects & Studentships in the UK & Europe FindAPhD is a comprehensive guide to PhD studentships and postgraduate research degrees

I have a PhD on how human gut bacteria feed off host glycans and produce metabolites that alter host cell behaviour #glycotime
findaphd.com

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