Webinar series at EMBL-EBI. Accessing structural data programmatically with PDBe. 6 May - 17 June 2026.

Starting on 6 May, our next webinar series will focus on different levels of programmatic access at @pdbeurope.bsky.social and the #AlphaFold DB.

Registration for each webinar is free but essential: www.ebi.ac.uk/training/eve...

🧬🖥️📊

We’ve refreshed the AlphaFold Database Entry Pages!

Explore the cleaner design, improved 3D viewer, and easier access from any device 👇
www.alphafold.ebi.ac.uk/entry/P04637

Or read more👇
www.ebi.ac.uk/about/news/u...

#AlphaFold #Bioinformatics #UXForScience
@pdbeurope.bsky.social

PANCS-Binders (phage-assisted noncontinuous selection of protein binders) screens multiple high-diversity protein libraries against a panel of dozens of targets for high-throughput binder discovery. @chembiobryan.bsky.social @mstyles-chembiol.bsky.social

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

The role of plasmid copy number and mutation rate in evolutionary outcomes - Nature Ecology & Evolution In an experimental multicopy plasmid evolution system that allows manipulation of mutation rate and copy number, low copy number promoted enrichment of beneficial alleles whereas high copy number main...

Happy to share this work, led by Olek Pisera, on dialing in a wide range of copy numbers for the orthogonal plasmid of OrthoRep. We used this ability to study how plasmid copy number influences evolutionary outcomes. www.nature.com/articles/s41...

📄 🌟 Preprint research from @juliankompa.bsky.social (@kjohnsson.bsky.social lab) and colleagues introduces Rho-tag and SiR-tag – engineered protein tags that bind unsubstituted rhodamine and silicon rhodamine dyes, respectively, with nanomolar affinity: bit.ly/40dXc7t

#Microscopy #Imaging

Engineering yeast multicellular behaviors via synthetic adhesion and contact signaling By designing synthetic toolkits for contact-based signaling (MARS) and cell-cell adhesion (SATURN), we program yeast to form multicellular structures and perform complex tasks, like building logic cir...

Online now @ Cell is the yeast multicellular engineering paper from Fankang Meng - the fruits of his productive PhD in our group. He developed modular synthetic biology tools to bring multicellular behaviours to yeast - specific adhesion, juxtacrine signalling and more. www.cell.com/cell/fulltex...

Fast, Bright and Reversible Rhodamine Tags for Live-Cell Imaging We present Rho-tag and SiR-tag, engineered protein tags derived from bacterial multidrug-resistance proteins that bind unsubstituted (silicon-) rhodamines with nanomolar affinity, enabling fast, rever...

Teaching an old bacterial protein new tricks: Fast, bright and reversible rhodamine tags for live-cell imaging:

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

Congratulations to Julian Kompa and the entire team.

SNAP-tag2 for faster and brighter protein labeling - Nature Chemical Biology SNAP-tag is a widespread tool for labeling protein for bioimaging. Now, Kühn et al. report SNAP-tag2 with increased labeling kinetics and brightness, which translates into a better performance in live...

Finally out in Nature Chem Bio:
SNAP-tag2 for faster and brighter protein labeling
www.nature.com/articles/s41...
Thank you Steffi and Veselin.

We're hiring for 2 postdocs to work in our lab in London on the newly announced Wellcome Trust SynHG project. If you know people looking to work on big-scale ambitious science like this, please RT and share this with them. Apply by 7/20, interviews in Aug. imperial.ac.uk/jobs/search-...

Fig. 4 Super-resolution microscopy in live and fixed cells with Rhobin. (A) Rhobin transiently binds rhodamine molecules and thereby constantly replenishes signal lost through photobleaching of dyes. (B-D) No-wash STED microscopy of live U2OS cells transiently expressing LifeAct-Rhobin2 labeled with 100 nM JFX650. (C, D) Zoom-ins of regions highlighted in (B) imaged either with confocal or STED microscopy. Scale bar: 20 μm (B) and 10 μm (C, D). (E-H) Rhobin enables timelapse STED microscopy of fast ER dynamics with minimal signal loss. U2OS stably expressing N-terminal tag fusions of SEC61B were stained with 1 μM Halo-JFX650 (HaloTag7, reHaloF) or 2 μM SiRhP (Rhobin2) and imaged at a frame rate of 0.387 fps for at least 100 time points. (F, G) Selected frames from timelapse acquisitions of Rhobin2:SEC61B labeled with SiRhP (F) or HaloTag7:SEC61B labeled with Halo-JFX650 (G). Scale bar: 2 μm. (H) Signal .CC-BY-NC 4.0 International licenseavailable under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprintthis version posted June 25, 2025.;https://doi.org/10.1101/2025.06.24.661379doi:bioRxiv preprint 22 loss during timelapse imaging. Mean ± SD signal inside cells over time for indicated constructs. (I-K) PAINT-type super-resolution microscopy with Rhobin. Rhobin2-SEC61B was transiently expressed in U2OS cells and labeled with 5 nM SiRhP after chemical fixation. Imaging under no- wash conditions and near-TIRF illumination. (I) Repeated, but transient binding of SiRhP molecules to Rhobin2 at low nanomolar concentrations can be observed as intensity bursts in intensity time traces extracted from a diffraction-limited area. See movie S3 for raw data of binding-induced blinking. (J) Sum image across 10,000 frames of an image stack, simulating a diffraction-limited image. (K). Reconstructed image from localized molecules in the full stack.

De novo designed bright, hyperstable rhodamine binders for fluorescence microscopy by Bo Huang and team: www.biorxiv.org/content/10.1...

Accurate de novo design of high-affinity protein-binding macrocycles using deep learning - Nature Chemical Biology A method for de novo design of peptide macrocyles called RFpeptides has been developed. RFpeptides is an extension of RoseTTAFold2 and RFdiffusion and combines structure prediction and protein backbon...

A new paper from the Institute for Protein Design at UW presents RFpeptides, an extension of RoseTTAFold2 and RFdiffusion for de novo design of macrocyclic peptide binders

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

This is wild!
Engineering E. coli bacteria to turn plastic waste into paracetamol (Tylenol)
www.nature.com/articles/s41...
www.nature.com/articles/s41...

Figure 1 Emission of SAH peptides

Huh?
Non-aromatic fluorescence from single α-helical peptides: Cell Reports Physical Science www.cell.com/cell-reports...

Please check out our new high-affinity split-HaloTag for live-cell protein labeling www.biorxiv.org/content/10.1...
Congratulations to Yin-Hsi Lin!

PhD Position in Peptide-Based Drug Discovery (Industry Collaboration, w/m/d)

We are hiring! Check out our open PhD position for an exciting industry collaboration with Novo Nordisk:
jobs.ethz.ch/job/view/JOP...

I had to recreate a FACS plot in R, for *reasons*. It was not obvious (to me) how to make a line and fill histogram, so here's a quick post showing how to do it.

quantixed.org/2025/06/05/l...

Applications are now open for the 4th edition of the “Ecole de Physique des Houches” on Fluorescence Markers for Advanced Microscopies, a WE-Heraeus seminar.
March 15th-20th 2026
Join us to learn everything you wanted to know about Fluorescent Markers for advanced microscopies.

Overview of ADD-tagging including ADP-ribosyl cyclase (ADPRC)-catalysed dinucleotide substrate generation and two step chemoenzymatic labelling of target proteins with the flavin transferase ApbE, followed by click chemistry-based functional group attachment.

🚨 preprint 2️⃣ this month: our (purely experimental🧪) venture into #ChemBio
We prouldy present: ADD-tagging of proteins (or "ADDing") —a super convenient enzymatic technique to install click chemistry handles on proteins.
Led by superstar @wahyuwidodo.bsky.social
www.biorxiv.org/content/10.1...
A 🧵👇🏽

We’re hiring. Postdoctoral and PhD positions available in Medicinal Radiochemistry.

Must have high level of skills and experience in synthetic chemistry, with knowledge of radiochemistry, cellular studies, in vivo imaging desirable.

@erc.europa.eu
@snsf-ch.bsky.social
@chemuzhch.bsky.social

Rapid continuous evolution of gene libraries towards arbitrary functions The emergence and evolution of new gene functions is central to biology, yet experimental tools that allow us to prospectively probe and understand this process are lacking. While systems for continuo...

We’re excited to share new work on the continuous in vivo evolution of gene libraries towards arbitrary functions. Led by superstar Olek Pisera, our experiments show that gene evolution is highly versatile...
www.biorxiv.org/content/10.1...

New molecular label could lead to simpler, faster tuberculosis tests MIT chemists found a way to identify a complex sugar molecule in the cell walls of Mycobacterium tuberculosis, the world’s deadliest pathogen. This labeling could lead to simpler, faster TB tests.

Lead author @ssmelyansky.bsky.social spearheaded a strategy to label a single sulfur-containing glycan called ManLAM on the cell envelope of the bacteria that cause #TB. news.mit.edu/2025/new-mol... or here: www.pnas.org/doi/10.1073/... 🧪 #glycotime @mitchemistry.bsky.social

Facile generation of drug-like conformational antibodies specific for amyloid fibrils - Nature Chemical Biology A quantitative fluorescence-activated cell sorting method for generating fully human conformational antibodies against amyloid aggregates associated with neurodegenerative disorders—without the need f...

A quantitative yeast-surface display and FACS approach generates fully human conformational antibodies against amyloid aggregates without the need for immunization

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

Excited to see this out in @science.org today!! www.science.org/doi/10.1126/...

📣 #Call for #Postdoc.Mobility. Expand your #research experience with a stay abroad. If you would like to find out more about this call, take part in our online information event on 12 May 2025.
➡️ buff.ly/Q2KkBWd
📆 Submission deadline: 5 August 2025

Fishing for covalent peptides Nature Chemical Biology - Electrophilic phage display has emerged as a powerful platform for discovering high-affinity or covalent peptide ligands. A new study reveals that this platform enables...

Check out the nice News and Views article about our work from lead author @sijiewang.bsky.social using phage display to find covalent inhibitors of protein-protein interactions. #ChemBio
www.nature.com/articles/s41...

Fluorescence Lifetime Multiplexing with Environment‐Sensitive Chemigenetic Probes HaloTag (HT) is a versatile self-labeling protein that has been widely adopted in fluorescence microscopy. Besides its established use as an intensity-based marker and sensor, interest in using HT fo....

Happy to share the results of a fun side project in which we used the COUPY dye and mutants of HaloTag7 to show that changes in fluorescence lifetime correlate with the polarity of the protein binding pocket!
chemistry-europe.onlinelibrary.wiley.com/doi/abs/10.1...
#FLIM #fluorescence #HaloTag

High-performance genetically-encoded green and red fluorescent biosensors for pyruvate Pyruvate is the end-product of glycolysis and a central metabolite involved in many biochemical pathways. However, a lack of high-performance (i.e., Δ F / F > 10) single fluorescent protein (FP)-base...

New tools! GreenPy and ApplePy are fluorescent biosensors for pyruvate with huge responses (20–40x in vitro) and a range of affinities (10s of μM to mM). These should be game changers for imaging of metabolism! Great work by Shosei Imai @sikmys.bsky.social and team 👏. www.biorxiv.org/content/10.1...

Chemical strategies for targeting lipid pathways in bacterial pathogens Microbial pathogens continue to plague human health and develop resistance to our current frontline treatments. Over the last few decades, there has b…

If you are interested in lipids in bacteria, check out this awesome new review written by my talented student Alyssa Carter, super postdoc Emily Woods and me. #chembio
www.sciencedirect.com/science/arti...

Congratulation :)

Far-red chemigenetic kinase biosensors enable multiplexed and super-resolved imaging of signaling networks - Nature Biotechnology Far-red kinase biosensors are applied to image kinase signaling networks at super resolution.

Happy to see my Postdoc work out @natbiotech.nature.com. Using HaloTag and synthetic fluorophores instead of FPs enables us to shift the spectral properties of kinase activity reporters (KARs) to the far-red 🔬. Huge thanks to everyone involved @jinzhanglab.bsky.social!
www.nature.com/articles/s41...