Single-molecule peptide sequencing through reverse translation of peptides into DNA - Nature Biotechnology Peptides are sequenced by converting each amino acid into amplifiable DNA barcodes.

Single-molecule peptide sequencing through reverse translation of peptides into DNA - @bioe-stanford.bsky.social go.nature.com/4sRPr2K

This is who runs this account

PDB101: Molecule of the Month: Histones Across the Tree of Life Uncovering the evolutionary diversity of histones

pdb101.rcsb.org/motm/314 histones outside of the eukaryotic domain are the 'molecule of the month'! nice!

WE ARE #HIRING: [reposting=👌 🙏 ]
2 funded positions for #nanopore related projects @unibas.ch 🇨🇭:
1️⃣ #PhD Candidate in Single-Molecule Biophysics using Nanopore Trapping.
2️⃣ #PhD Candidate in Microplastic Detection Using Micropores and Microfluidics.
More info: schmid.chemie.unibas.ch/en/join-us-1/

The ribosome synchronizes folding and assembly to promote oligomeric protein biogenesis Large oligomeric proteins constitute a major fraction of proteomes, but are difficult to refold in vitro, raising the question of how cells direct their biogenesis. Roeselová and Shivakumaraswamy et a...

Our latest cotranslational folding story is now published @cp-molcell.bsky.social. Really cool (I think) new ideas about how exactly the ribosome directs folding and assembly to make sure complicated proteins mature efficiently in cells.
www.cell.com/molecular-ce...

Perceptions can be often misleading

Latest #CDlab paper on nanopore protein sequencing now published in JACS: pubs.acs.org/doi/full/10....

Here, Justas Ritmejeris, Xiuqi Chen, collaborator Bauke Albada, and me developed a conjugation chemistry strategy for nanopore sequencing of natural peptides!

Computational design of conformation-biasing mutations to alter protein functions Conformational biasing (CB) is a rapid and streamlined computational method that uses contrastive scoring by inverse folding models to predict protein variants biased toward desired conformational sta...

Can we design mutations that bias proteins towards desired conformational states?

Today in @science.org, we introduce Conformational Biasing (CB), a simple and scalable computational method that uses contrastive scoring by inverse folding models to identify conformation-biasing mutations.

The value of publishing negative data - News Scientific journals love news-worthy results. Editors want to publish studies with novel data that scientists will eagerly read and cite in their own work. Because of this desire for novelty, studies ...

Giving the gift of negative data 🥰

Since I joined @lsajournal.org I have handled several stellar manuscripts that report null results. These papers do very well and reviewers almost always appreciate them!

Thanks @rockefeller.edu news team for the article!

www.rockefeller.edu/news/38829-t...

Quite unhinged format 🤯

An integrated view of the structure and function of the human 4D nucleome - Nature The 4D Nucleome Project demonstrates the use of genomic assays and computational methods to measure genome folding and then predict genomic structure from DNA sequence, facilitatin...

A major output of the 4D Nucleome project appeared today. This is the joint effort of many scientists working together and (publicly) sharing data and results for several years. We hope this is of interest to many genome biologists!

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

Latest #CDlab paper on nanopore protein sequencing on @biorxivpreprint.bsky.social: www.biorxiv.org/cgi/content/...

Here, Justas Ritmejeris, @xiuqichen.bsky.social, collaborator @albadalab.bsky.social and me developed a conjugation chemistry strategy for nanopore sequencing of natural peptides!

I recently wrote a 1page "Highlight" article for the Swiss Journal @chimiajournal.bsky.social about the #single-molecule perspective on biomolecular dynamics and experiments:

Beyond 3D Structures: New Ways to Study Biomolecular Gymnastics
www.chimia.ch/chimia/artic...

Temperature–dependent reaction rates of quinone-alkene cycloaddition reveal that only entropy determines the rate of SPOCQ reactions Second-order rate constants and thermodynamic activation parameters for the strain-promoted oxidation-controlled quinone (SPOCQ) click reaction of an ortho-quinone with various trans-cyclooctene and c...

#paperalert

Very happy to share our new paper in Chemical Science @chemicalscience.rsc.org

Great work by Yuri Damen (now at BioChem in Oss), @joresfu.bsky.social, Judith Firet, and Han Zuilhof @w-u-r.bsky.social

Especially for those of you who use strained alkynes in their click reactions!

I am thrilled with the news that our ERC Synergy proposal GeneMotors was granted!!

This prestigious grant allows Leonid Mirny (MIT), Wendy Bickmore (Edinburgh), Benjamin Rowland (NKI) and me to study the DNA-looping SMC motors proteins that control our chromosomes in the next 6 years

Lab’s first paper is out!! We show the first structures of #Asgard #chromatin by #cryo-EM 🧬❄️
Asgard histones form closed and open hypernucleosomes. Closed are conserved across #Archaea, while open resemble eukaryotic H3–H4 octasomes and are Asgard-specific. More here: www.cell.com/molecular-ce...

🤯

Are these the happiest PhD students in the world? Brazil, Australia and Italy have the highest satisfaction scores in Nature’s global 2025 PhD survey — but are these nations really the best places to do a doctorate?

Additional conclusions are available here
www.nature.com/articles/d41...

What makes PhD students happy? Good supervision Supervisors who invest in positive mentoring relationships with their PhD candidates also reap the benefits for their own research.

Results from Nature’s 2025 global survey of more than 3,700 doctoral students:

Supervisors who make a conscious effort to support and mentor their PhD candidates have more-satisfied students

www.nature.com/articles/d41...

Check out our paper from @christ3na.bsky.social in G+D. DIO3, which degrades thyroid hormone/TH, is expressed in progenitors and turns off in neurons. As the progenitor:neuron ratio decreases, DIO3 decreases and TH increases, triggering photoreceptor generation.
genesdev.cshlp.org/content/earl...

How do SMC complexes load onto DNA to get ready for loop extrusion?

@roisnehamelinf.bsky.social & co discovered that Wadjet, an SMC complex involved in bacterial DNA immunity, performs some impressive molecular gymnastics 🤸‍♂️🤸‍♂️🤸‍♂️.

Check out the new paper: www.cell.com/molecular-ce...

Next week GIIN webinar will feature @fmattiroli.bsky.social and Marco Tigano. Join us on Tuesday, October 7th at 5 PM Rome / 11 AM NYC via zoom: uniroma1.zoom.us/j/95149984403
Register here to become part of our community: docs.google.com/forms/d/e/1F...

Join us at the Hubrecht Institute in Utrecht to start your research group! Fantastic scientific environment, strong support, and nice colleagues :) Apply and please share broadly in your network.

Phosphorylation modulates secondary structure of intrinsically disorder regions in RNA polymerase II The intrinsically disordered C-terminal domain (CTD) of RNA polymerase II contains tandem repeats with the consensus sequence YSPTSPS and coordinates …

Now published! Phosphorylation patterns modulate transient secondary structures of the intrinsically disordered CTD of RNA polymerase II www.sciencedirect.com/science/arti...

The human ribosome modulates multidomain protein biogenesis by delaying cotranslational domain docking Nature Structural & Molecular Biology, Published online: 19 September 2025; doi:10.1038/s41594-025-01676-5By studying dynamic folding intermediates on the human ribosome, Pellowe et al. show that newly made domains help each other to fold but do not stably interact until synthesis is complete, avoiding interdomain misfolding.

ICYMI: New online: The human ribosome modulates multidomain protein biogenesis by delaying cotranslational domain docking

Fragile Nucleosome Fall Seminars: September 10 Grace Bower, Kvon Lab @ UC Irvine, USA Jennifer Phillips-Cremins, UPenn, USA September 24 Ali Wilkening, Sanulli Lab @ Stanford, USA Juanma Schvartzman, Columbia University, USA October 8 Sanim Rahman, Greenberg Lab @ UPenn, USA Alex Federation, Talus Bio, USA October 22 Alice Laigle, Croll Lab @ University of Neuchâtel, Switzerland Seungsoo Kim, UC Irvine, USA November 5 Hannah Long, University of Edinburgh, UK Jeff Vierstra, Altius Institute, USA November 19 Ishtiaque Hossain, Pastor Lab @ McGill, Canada Sarah Teichmann, University of Cambridge, UK December 3 María Mariner Faulí, Rada Iglesias Lab @ IBBTEC, Spain Jonathan Henninger, Carnegie Mellon, USA December 17 Rebecca Berrens, Oxford University, UK Jean-Benoit Lalanne, University of Montreal, Canada

We're super excited to announce the entire lineup for the Fall season of Fragile Nucleosome Seminars, starting on Sept 10th at 1200 EDT / 1600 UTC with @gracebower.bsky.social and @creminslab.bsky.social!

register here for the entire series: us06web.zoom.us/webinar/regi...

💥 We have 3 positions open in my lab in Basel, Switzerland🇨🇭:
#nanopores #smFRET #biomolecular #dynamics #singleMolecules

We’re looking for talented & ambitious new colleagues enthusiastic about biomolecular dynamics & single-molecule tech.

Please share broadly, thank you!🤝

schmid.chemie.unibas.ch

Open position in @ceesdekker.bsky.social lab! Apply if you are interested in nanopore sequencing!