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Reposted by Francis O'Reilly

Kevin Drew @ksdrew.bsky.social · Jul 29

We are excited to share our preprint describing DirectContacts2! Here we develop a machine learning model to discriminate between direct and indirect protein interactions. We use our model to construct a highly accurate wiring diagram of the human cell.

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

DirectContacts2: A network of direct physical protein interactions derived from high-throughput mass spectrometry experiments

Cellular function is driven by the activity proteins in stable complexes. Protein complex assembly depends on the direct physical association of component proteins. Advances in macromolecular structur...

www.biorxiv.org

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Francis O'Reilly @fjoreilly.bsky.social · Aug 5

This in situ strategy opens the door to mapping dynamic macromolecular machines directly in their cellular context, and hints that much has been missed by previous AP-MS studies of the interactome.

Francis O'Reilly @fjoreilly.bsky.social · Aug 5

Using PhIX-MS combined with cryo-EM and integrative modeling, we discovered how the ubiquitination enzyme UBE3C, the reductase TXNL1, and the assembly factor PSMD5 bind to the proteasome, providing important information on their functions.

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Francis O'Reilly @fjoreilly.bsky.social · Aug 5

Many proteasome binders are transient or low-affinity and are very difficult to visualize with conventional methods. To overcome this, we developed PhIX-MS (Photo-induced In situ Crosslinking Mass Spectrometry) to map native protein interactions directly inside cells.

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Francis O'Reilly @fjoreilly.bsky.social · Aug 5

‼️ Exciting new preprint from a close collaboration with Kylie Walters' group. Our study maps the binding sites of key regulators of the proteasome in situ.
www.biorxiv.org/content/10.1...

Structures of dynamic interactors at native proteasomes by PhIX-MS and cryoelectron microscopy

Proteasome function depends on a network of transient interactions that remain structurally and functionally unresolved. We developed PhIX-MS (Photo-induced In situ Crosslinking-Mass Spectrometry), a ...

www.biorxiv.org

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Marcel Dickmanns | 🌿❄️🔬 @madic.bsky.social · Jul 26

New preprint: In situ Architecture of #Plasmodesmata.

Using #cryoET, #AlphaFold & proteomics, we uncover the native organization of plant intercellular nanopores.

🔗 doi.org/10.1101/2025...

🧪🧵1/n
#teamtomo #PlantScience #Physcomitrium #Arabidopsis #cryoEM

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Francis O'Reilly @fjoreilly.bsky.social · Jul 22

A great lineup of speakers!

Symposium on Structural Proteomics 2025 @ssp2025.bsky.social · Jul 22

Time to get signed up for the Symposium on Structural Proteomics! This time at @humantechnopole.bsky.social in Milan 6th-8th October Full speaker lineup announced. Thanks to @thermofishersci.bsky.social @brukercorporation.bsky.social, Affipro and MSVision for support
Info
ssp2025.squarespace.com

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Francis O'Reilly @fjoreilly.bsky.social · Jul 21

Time to get signed up for the next Symposium on Structural Proteomics! This time in beautiful Milan 6th-8th October.
ssp2025.squarespace.com

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Savitski Lab @savitski-lab.bsky.social · Jul 1

Beautiful work from my friend @kiranrpatil.bsky.social . Gut bacteria can accumulate Forever chemicals and help us get rid of them! Happy we could contribute! www.nature.com/articles/s41...

Human gut bacteria bioaccumulate per- and polyfluoroalkyl substances - Nature Microbiology

Human gut bacteria bioaccumulate per- and polyfluoroalkyl substances (PFAS), commonly known as forever chemicals, in intracellular aggregates. Colonization of gnotobiotic mice with bioaccumulating bac...

www.nature.com

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Sjors Scheres @sjorsscheres.bsky.social · Jun 25

We have a 3-year funded postdoc position to work on structures of #amyloid filaments. If you are an expert in protein biochemistry, structural biology or #cryoEM / #cryoET, this could be for you! Feel free to email me with any questions. Come join us! 🤩

www.nature.com/naturecareer...

Postdoctoral Scientist - Structural Studies - Dr Sjors Scheres - LMB 2640 - Cambridgeshire job with MRC Laboratory of Molecular Biology (LMB) | 12840844

Postdoctoral Scientist Starting Salary: £41,344 Fixed term: 3 years MRC Laboratory of Molecular Biology, Cambridge, UK We are looking for a postdoc...

www.nature.com

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Chemjobber @chemjobber.bsky.social · Jun 2

Biblically accurate nitrogen

Dave Palmer @davepalmerusask.bsky.social · Jun 2

Fear not! For I bring you glad tidings of great hypervalency

A nitrogen atom with many bonds and one arrow extending it from it like heavenly rays from an angel.

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European Research Council (ERC) @erc.europa.eu · May 28

🎉 Congratulations to Wolfgang Baumeister @maxplanck.de, awarded the 2025 #ShawPrize in Life Science & Medicine for pioneering work in cryo-ET!

Learn more 👉 europa.eu/!JBXDBG
#FrontierResearch #ERCSyG #CryoET #StructuralBiology #shawprize2025

ERC grantee wins the Shaw Prize in Life Science and Medicine

2025 Shaw Prize honours ERC-funded research in molecular imaging

europa.eu

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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · May 15

We've updated our AFESM website to now include biome filtering, allowing exploration of protein structures adapted to specific environments.
🌐 afesm.foldseek.com
Read more about the work in the skeetorial
🦋 bsky.app/profile/mart...
or our preprint
📄 www.biorxiv.org/content/10.1...

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Kelly Nguyen @kellythd-nguyen.bsky.social · Apr 16

We are looking for a postdoctoral fellow to join us to explore telomerase regulation by histones. Please get in touch if this may interest you.

MRC Laboratory of Molecular Biology @mrclmb.bsky.social · Apr 16

Excellent opportunity available for a motivated #postdoc to join @kellythd-nguyen.bsky.social’s group investigating the roles of histones in regulating telomerase using a multi-disciplinary approach.
More details: www.nature.com/naturecareer...
Apply by 04 MAY
#PostdocJobs #ScienceJobs

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Felix Steinruecke @felixsteinruecke.bsky.social · Apr 6

I’m excited to share my first paper in the Farnung lab, in which we report four cryo-EM structures of the human DNA replication machinery engaging with and progressing into a nucleosome.

Lucas Farnung @lucas.farnunglab.com · Apr 6

🔬 New from the Farnung Lab: We established a fully in vitro reconstituted chromatin replication system and report the first cryo-EM snapshots of the human replisome engaging nucleosomes. Brilliant work by @felixsteinruecke.bsky.social with support from @jonmarkert.bsky.social! tinyurl.com/replisome

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BTO | British Trust for Ornithology @btobirds.bsky.social · Apr 1

One of our satellite-tagged Cuckoos has hitched a ride on a cruise ship and is now in the UK, the earliest one of our superstar Cuckoos has ever reached us! 😮🛥️🧵

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Gerry Wright @gdwantibiotics.bsky.social · Mar 26

The latest discovery from the lab and great colleagues at McMaster and U Illinois, Chicago. Lariocidin, a new lasso peptide antibiotic that inhibits the ribosome. rdcu.be/efdha

A broad-spectrum lasso peptide antibiotic targeting the bacterial ribosome

Nature - A new lasso peptide antibiotic exhibits broad-spectrum activity against Gram-negative and Gram-positive bacteria by interfering with bacterial protein synthesis, is unaffected by common...

rdcu.be

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Science Magazine @science.org · Mar 20

In a new Science study, cryo–electron tomography captures the in-cell architecture of the mitochondrial respiratory chain, illuminating how the coordinated action of molecular machines drives life’s fundamental energy conversion.

Learn more in this week's issue: scim.ag/3FA3Ygq

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Jason Goes to Hell @benedictsred.bsky.social · Mar 12

“You see, that was funny because no one could imagine one banana costing $10.”

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Francis O'Reilly @fjoreilly.bsky.social · Mar 12

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Francis O'Reilly @fjoreilly.bsky.social · Mar 1

Happy retirement to Francis Collins, a scientific and administrative hero. He was always a strong advocate for the importance of biological research and the results are obvious and impressive.

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IMP @impvienna.bsky.social · Feb 7

Out of the lab, into the wild: when @pauligroup.bsky.social's Andi Pauli puts on her @ox.ac.uk blue, you know it's business time! Austria's national broadcast ORF interviewed her on how #Vienna has become such an amazing place for life science research.

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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · Feb 6

Foldseek-Multimer—now published in @naturemethods.bsky.social—our fast multimer search tool, enables complex comparisons against the full PDB in seconds. It comes with BFMD, a collection of 300K+ predictions gathered from community projects.
📄 nature.com/articles/s41...
🌐 search.foldseek.com

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Suyang Zhang @suyangzhang.bsky.social · Feb 3

Ever wondered how Pol II speed is controlled during productive elongation?
Our study reveals that the helicase RECQL5 triggers transcription braking, while the transcription-coupled DNA repair complex restores the elongation rate. #cryoEM #transcription

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

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