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Ben Cooper

@bfcoop.bsky.social
43 followers 62 following 10 posts
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Ben Cooper @bfcoop.bsky.social · 18/09/2026
Together, our results reveal striking divergence within an otherwise deeply conserved protein family. Same fundamental Amt/Mep/Rh scaffold — but distinct lipid interactions, substrate affinity and transport behaviour shaped by physiological context. Lots more to explore!
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Ben Cooper @bfcoop.bsky.social · 18/09/2026
But what does NeRh50 actually transport? ⚡ SSME revealed selective, electrogenic ammonium transport — but with ~70-fold lower apparent affinity than E. coli AmtB. Transport increased at alkaline pH, but was not stimulated by a proton gradient.
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Ben Cooper @bfcoop.bsky.social · 18/09/2026
Native MS confirmed that phospholipids remain tightly associated with purified NeRh50, while MD simulations revealed long-lived lipid interactions at the same monomer interfaces. Three complementary approaches, one intriguing lipid-binding site. 🧪💻
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Ben Cooper @bfcoop.bsky.social · 18/09/2026
First, the structure 🔬 Our 3.1 Å cryo-EM reconstruction revealed striking lipid-like densities surrounding NeRh50, particularly at the interfaces between monomers. Could lipids be an integral part of the NeRh50 architecture? 👀
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Ben Cooper @bfcoop.bsky.social · 18/09/2026
Really pleased to share our latest preprint, the result of a fantastic Anglo-Scots collaboration www.biorxiv.org/content/10.6... We uncover how the bacterial Rhesus protein NeRh50 diverges from canonical ammonium transporters 👇🧵 #CryoEM #MembraneProteins #MassSpectrometry #AmmoniumTransport
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Ben Cooper @bfcoop.bsky.social · 02/06/2026
It's a small project, but hopefully useful for others running RELION jobs. GitHub: github.com/bfcoop/relio... Feedback and feature suggestions are very welcome! #CryoEM #RELION #StructuralBiology #OpenSource
github.com
GitHub - bfcoop/relion_tracker: Track metrics from RELION optimiser STAR files directly in the terminal.
Track metrics from RELION optimiser STAR files directly in the terminal. - bfcoop/relion_tracker
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Ben Cooper @bfcoop.bsky.social · 02/06/2026
Features: • Automatic iteration detection and iteration subsetting • Terminal-based plotting • Multiple variable support • Overlay mode for comparing variables • No dependencies beyond the Python standard library
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Ben Cooper @bfcoop.bsky.social · 02/06/2026
Turning: grep _rlnChangesOptimalClasses run_it*_optimiser.star into: relion_tracker Class2D/job183 --var _rlnChangesOptimalClasses --iters 1 25
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Ben Cooper @bfcoop.bsky.social · 02/06/2026
relion_tracker provides a lightweight way to extract and visualise optimiser STAR variables directly in the terminal, with support for multiple variables and overlay plots.
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Ben Cooper @bfcoop.bsky.social · 02/06/2026
I've just released a small open-source utility for RELION users: relion_tracker. RELION stores a lot of useful information in the *_optimiser.star files, but I often found myself repeatedly grepping STAR files to see how metrics were changing across iterations.
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Reposted by Ben Cooper
Sonja-Verena Albers @archaellum.bsky.social · 03/02/2025
Would you expect that Bacteria use an archaellum for swimming? We didn't, but we found that some Chloroflexota do! Find the story here: www.biorxiv.org/content/10.1... A little thread below 1/n
biorxiv.org
Horizontal gene transfer of the functional archaellum machinery to Bacteria
Motility in Archaea is driven by a nanomachinery called the archaellum. So far, archaella have been exclusively described for the archaeal domain; however, a recent study reported the presence of arch...
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Reposted by Ben Cooper
Augustinas Silale @augustsilale.bsky.social · 03/02/2025
New preprint 🚨: with @madejmar.bsky.social we found that the Bacteroidetes beta-barrel assembly machinery is quite different to E. coli. www.biorxiv.org/content/10.1... #cryo-EM
Comparison of B. theta and E. coli BAM machineries. Only BamAD components are shared, and B. theta BAM has five novel components, BamF-I.
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Reposted by Ben Cooper
Nature Microbiology @natmicrobiol.nature.com · 23/01/2025
OUT NOW: KorB is a DNA clamp which slides along DNA to mediate long-range gene silencing upon interaction with the clamp-locking KorA protein by Tung Le & co @johninnescentre.bsky.social www.nature.com/articles/s41...
nature.com
KorB switching from DNA-sliding clamp to repressor mediates long-range gene silencing in a multi-drug resistance plasmid - Nature Microbiology
Structural and single-molecule analyses show the CTPase, KorB, is a sliding DNA clamp that interacts with a clamp-locking protein KorA to inhibit gene expression over distances of more than 1 kb in th...
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