Matthieu Sainlos

Mapping targetable sites on the human surfaceome for the design of novel binders | PNAS The human cell surfaceome, integral to cell communication and disease mechanisms, presents a prime target for therapeutic intervention. De novo pro...

A new @pnas.org study caught the eye of our bioinformatics team with its identification of ~4,500 targetable binding sites & binding seeds across human cell surface proteins—giving IPI and other labs a protein design launch point.

The final version of our new paper is out now - and open access @acs.org Central Science!!

Such a fun collaboration!

pubs.acs.org/doi/10.1021/...

Directed Evolution of Enzymes for Bioorthogonal Chemistry Using Acid Chloride Proximity Labeling Combining bioorthogonal protecting groups with localized catalysts that can unmask them is a powerful approach to spatially and temporally modulate molecular activity. Enzymes are appealing catalysts ...

Enzyme catalyzed bioorthogonal chemistry published at ACS Cent Sci

pubs.acs.org/doi/10.1021/...

PANCS-spec-Binders: A system for rapidly discovering isoform- or epitope-specific binders Proteins that bind to a target protein of interest, termed "binders," are essential components of biological research reagents and therapeutics. Target proteins present multiple binding surfaces with ...

Check out our newest work! This is a story on how to get selectivity in binders - both isoform and site selectivity. Read the paper or enjoy this brief Skytorial of what we did!

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

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New preprint 🥳! We made photoclickable HaloTag ligands to precisely control protein labeling on living cells. With it, we can do some cool multicolor stuff. Huge congrats to Franzi and all co-authors! Check it out 👇

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

Chemical biology 2026

Registration for THE chemical biology conference of 2026 is now open! EMBO ChemBio 2026 in Heidelberg

DeGrado, Arikin, Picotti (Keynotes). @lmkdassama.bsky.social @brianliau.bsky.social @rhodamine110.bsky.social @benlehner.bsky.social @alitavassoli.bsky.social

www.embl.org/about/info/c...

A new, nerdy paper. We figured out (some) of the rules underlying cell-permeability of probes and designed ligands that light up, grab, and move proteins around. Awesome @hhmijanelia.bsky.social x @uwmadison.bsky.social x @stjuderesearch.bsky.social collaboration! www.pnas.org/doi/10.1073/...

ProteinDJ logo

I am thrilled to release ProteinDJ: a high-performance and modular protein design pipeline. Our open-source workflow incorporates #RFdiffusion, #ProteinMPNN, #FAMPNN, #AlphaFold2 and #Boltz-2. It is a fast, free, and fun way to design proteins (1/5)
doi.org/10.1101/2025.09.24.678028 #proteindesign

Paralog-specific intrabodies for PSD-93 and SAP102 expand the molecular toolkit to resolve excitatory synapse organization https://www.biorxiv.org/content/10.1101/2025.08.24.671450v1

Super-resolution live-cell mapping of protein-protein interactions using chemogenetic split reporters and STED microscopy The ability to map protein-protein interactions (PPI) within living cells at high spatial resolution is essential for unravelling their roles in cellular biology. Although several super-resolution mic...

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

Rational engineering of allosteric protein switches by in silico prediction of domain insertion sites - Nature Methods ProDomino is a machine leaning-based method, trained on a semisynthetic domain insertion dataset, to guide the engineering of protein domain recombination.

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

Also check out the associated News & Views by Masayasu Taki and Masayoshi Nakamura highlighting the work from @kjohnsson.bsky.social lab on SNAP-tag2

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

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 are thrilled to welcome Barbara Imperiali at #ChemBioParis2025 in Paris, October 6-9, 2025. Sign up here: chembioparis2025.com – Early bird ends June 10 with reduced fees for @icbschembio.bsky.social - euchems.eu - @eu-openscreen.bsky.social - @scf-chembio.bsky.social - #ChemBioEvent

Protein editing using a coordinated transposition reaction Protein engineering through the ligation of polypeptide fragments has proven enormously powerful for studying biochemical processes. In general, this strategy necessitates a final protein-folding step...

Employing engineered split inteins to replace the internal regions of target proteins in a single reaction. www.science.org/doi/10.1126/... #NBThighlight

Toward single-molecule protein sequencing using nanopores - Nature Biotechnology Maglia and colleagues discuss advances in nanopore technology en route to single-molecule protein sequencing

Maglia and colleagues discuss advances in nanopore technology en route to single-molecule protein sequencing go.nature.com/3FL0g3k
rdcu.be/efeZR

Toward single-molecule protein sequencing using nanopores - @unigroningen.bsky.social go.nature.com/3FL0g3k

Engineering a genomically recoded organism with one stop codon - Nature Ochre, a strain of Escherichia coli engineered to have a single stop codon, enables reassignment of four codons for non-degenerate functions, such as incorporation of non-standard amino acids into pro...

A genomically recoded E. coli with a single stop codon www.nature.com/articles/s41...

Rapid discovery of cyclic peptide protein aggregation inhibitors by continuous selection - Nature Chemical Biology A platform for the continuous selection of protein aggregation inhibitors from genetically encoded cyclic peptide libraries in Escherichia coli was developed. This platform was used to discover cyclic...

Continuous directed evolution of cyclic peptides in cells to inhibit protein aggregation. From Tina Wang et al. #chembio #ChemSky www.nature.com/articles/s41...

Super excited to finally share PANCS-Binders: our group's decade-long quest to accelerate protein binder discovery.

TLDR: PANCS-binders is fast (2 days), cheap (pennies), has extremely high fidelity (low false positive and negatives), and high-throughput.

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