New preprint out - Jenn’s hard work over the last few years collaborating with @jnb-lab.bsky.social, Overkleeft Lab in Leiden, Spencer Williams, Hannah Bridges at Cryosparc and @pmoyniha.bsky.social. Feat. her beautiful 1.5A cryo structure with a covalent inhibitor 😍. www.biorxiv.org/content/10.6...

Permanent academic position as a Lecturer in cryo-ET open at York. We are looking for someone to lead a research program making the most of the stunning advances occurring in cryo-ET. It's a research and teaching post but with a focus on research in the early years. jobs.york.ac.uk/vacancy/lect...

Delighted to have this collaborative work out in @natmicrobiol.nature.com on how A. muciniphila deploys its sulfatases, both their localisation and substrate specificity, to metabolise colonic mucin www.nature.com/articles/s41... #glycotime.

Unique adaptations in sulfatases underpin colonic mucin degradation by Akkermansia muciniphila - Nature Microbiology

Structural and biochemical follow-up of a serendipitous discovery reveals that Akkermansia muciniphila carbohydrate sulfatases are uniquely adapted to digest colonic mucins in collaboration with other...

nature.com

In our latest chat with #ListerPrize2025 Fellows, Chris Hill @chillzaa.bsky.social at @york.ac.uk shares insights into how enteroviruses use the 3D structure of RNA to hijack host ribosomes. 🔗 lister-institute.org.uk/news/in-conv... ♻️ Make Chris's day: A comment or repost is good for the soul 👇

I'm excited that this collaborative work with Alan @acartmell47.bsky.social is finally out. We have developed some powerful tools to study carbohydrate sulfatases (a tricky class of enzyme!) and shown how they can be used with enzymes from host-associated bacteria.

Alan Cartmell@acartmell47.bsky.social · 3mo ago

Happy to have this collaborative work with Zach Armstrong now out in Angewandte chemie doi.org/10.1002/anie... . We use a linked assay, coupled with fluorescent probes, to analyse mucin active carbohydrate sulfatase kinetics, cellular location, and inhibition.

Folddisco is now published @natbiotech.nature.com. It’s a fast motif search for similar 3D DISCOntinuous residues like catalytic sites or zinc fingers across the entire protein universe. 📄 www.nature.com/articles/s41... 💾 folddisco.foldseek.com​​​​​​​​​​​​​​​​ 🌐 https://search.foldseek.com/folddisco

Structural motif search across the protein universe with Folddisco - Nature Biotechnology

Folddisco enables protein structural motif search in million scale databases.

nature.com

Martin Steinegger 🇺🇦@martinsteinegger.bsky.social · last yr.

Folddisco finds similar (dis)continuous 3D motifs in large protein structure databases. Its efficient index enables fast uncharacterized active site annotation, protein conformational state analysis and PPI interface comparison. 1/9🧶🧬 📄 www.biorxiv.org/content/10.1... 🌐 search.foldseek.com/folddisco

Now published in Nature Communications: www.nature.com/articles/s41... The anomer collapsing advance is something we continue to use today, and we hope others may find it useful. Furthermore, this library is the largest representation to date of the human N-glycome (3x the next biggest) #glycotime

Chris Ashwood@cashwood.proteaglyco.com · last yr.

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.

SPLICECRAFT v1.0 IS LIVE!!!!!!!!!!!! Open your terminal and type in "pipx install splicecraft" if you want to try it out, then spam "splicecraft update" often as I push updates frequently. A labor of love for the community I adore. Enjoy! 💚

Happy to have this collaborative work with Zach Armstrong now out in Angewandte chemie doi.org/10.1002/anie... . We use a linked assay, coupled with fluorescent probes, to analyse mucin active carbohydrate sulfatase kinetics, cellular location, and inhibition.

Fluorogenic Coupled Assays Reveal Catalytic Properties, Inhibition Constants and Cellular Location of Mucin‐Active Carbohydrate Sulfatases

We report plate-based coupled assays to rapidly and quantitatively determine the activity and selectivity of mucin-active carbohydrate sulfatases. This fluorogenic assay further enables inhibitor ide...

doi.org

First paper for PhD student in the Bolam / Lowe labs Natalia Łoś on a the characterisation of a new CBM family that binds (beta) mannan! #glycotime @natalia-los.bsky.social 🥳🥳 link.springer.com/article/10.1...

Unusual molecular architecture of a human gut microbiota β-mannanase reveals a new CBM family - Cellular and Molecular Life Sciences

β-mannans are plant structural and storage polysaccharides prevalent in the human diet. Their degradation in the gastrointestinal tract is mediated by the human gut microbiota (HGM) through expression...

link.springer.com

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-...

Kresten Lindorff-Larsen@lindorfflarsen.bsky.social · 8mo ago

We (@sobuelow.bsky.social & @kejohansson.bsky.social) tested AF-CALVADOS using the recently described PeptoneBench SAXS benchmark that contains SAXS data for >400 proteins with different amounts of order and disorder. The results look pretty good 😇 so we are sharing here while updating the preprint📝

Nature research paper: Epigenetic memory of colitis promotes tumour growth go.nature.com/4t3apvK

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.

go.nature.com

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

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...

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 ...

biorxiv.org

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

Nature@nature.com · 11mo ago

This first of its kind procedure could improve access to donor organs because the donor blood type would no longer matter go.nature.com/3IToaM3

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...

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 ...

biorxiv.org

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...

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...

jbc.org

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...

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.

bioRxivpreprint@biorxivpreprint.bsky.social · last yr.

N-Glycopedia: Libraries for Native N-glycan Structural Analysis https://www.biorxiv.org/content/10.1101/2025.06.09.658590v1

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

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

findaphd.com

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...

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.

nature.com

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/...

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...

pubs.acs.org

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

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...

pnas.org

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

Luciano A. Masullo@lumasullo.bsky.social · 2y ago

ÅNGSTRÖM-RESOLUTION IMAGING OF CELL-SURFACE GLYCANS 🧬🎨🍬 The glycocalyx, our cells' sugar coat, holds secrets in immunology, cancer, viral infections, and more. Visualizing its molecular architecture was impossible… until now. #glycotime #microscopy www.biorxiv.org/content/10.1...

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

PhD Programmes, Research Projects & Studentships in the UK & Europe

FindAPhD is a comprehensive guide to PhD studentships and postgraduate research degrees

findaphd.com