I’m thrilled to be able to announce that we were granted a NWO Summit grant entitled ‘Evolving Life from Nonlife’ (EVOLF) with 40 million euro for a 10-year project aimed to cross the gap between non-life and life by assembling a living synthetic cell from lifeless biomolecules! This project aims to address some of the biggest questions: What is life? How do living systems differ from non-living ones? Can we create living cells from lifeless molecules? EVOLF will take an experimental approach and build synthetic cells from the bottom up, from molecules.

DNA loop extrusion by SMC motor proteins is an intriguing process that is the key organizer of our chromosomes

As I explained to you before (see our NAR 2022 paper), magnetic tweezers are a powerful single-molecule method to measure single loop extrusion steps (~40nm, 200bp)

0/ But here's a new twist!

Today, we put a new #CDlab paper on @biorxivpreprint where we developed a new tweezer assay to directly measure how much supercoiling twist is induced into the extruded loop by an individual SMC in each loop-extrusion step!



1/ biorxiv.org/content/10.110…

Latest #CDlab paper online now in @ScienceMagazine:

In this important hypothesis paper we sketch a possible mechanistic model for SMC motor proteins that make loops in DNA.
This is a collaborative effort of @HaeringLab, JM-Peters, B-Rowland,. and us

1/ science.org/doi/epdf/10.11…
Background of this paper is interesting as the 4 authors met at a Titisee conference. Given that each of us had a favorite model (scrunching, swing&clamp, hold&feed), we disagreed.
But we discussed, ending up with this joint paper on a ‘reel-and-seal’ model that fits most data
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a while ago I posed this question...

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https://twitter.com/cees_dekker/status/1630580415483265024

As a follow up:

Yesterday we posted a #CDlab paper on @biorxivpreprint that describes careful single-molecule experiments that measure the supercoiling generated by a RNA polymerase during transcription.

Great work by @JanissenRichard @RomanBarth2 @MincoPolinder JacovdTorre

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Protein sequencing is a big deal and goes way beyond DNA sequencing. While we have ~20000 protein-coding genes, we have _millions_ of protein variants, mainly because of post-translational modifications that attach a side group to amino acids.

1/ Phosphorylation is the most frequent PTM, and of particular interest, as dysregulation of phosphorylation pathways is linked to many diseases including cancers, Parkinson’s, Alzheimer’s, and heart disease.

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Today, we put 2 new #CDlab papers on the @arxiv preprint server – which both report, in different ways, on demonstrating nanoscale rotary motors that are driven by a flow through a nanopore.

arxiv.org/pdf/2206.06612…

arxiv.org/pdf/2206.06613…

1 / @arxiv Such rotors are inspired by the awesome F0F1 ATPase motor protein in our cells. Here, a proton gradient drives rotation of F0 which induces conformational changes in F1 that catalyze production of ATP, which is the fuel for most processes in our body.

Video credit Biovisions

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Today we publish a paper in @ScienceMagazine that expands nanopore readings to the proteome:
a nanopore-based scanner to read off PROTEINS at the single-molecule level! 🤩

Awesome experiments by postdoc Henry Brinkerhoff of our #CDlab, with MD simulations of @aksimentievLab

1/x @ScienceMagazine @aksimentievLab Here’s the link to this paper in @ScienceMagazine entitled “Multiple re-reads of single proteins at single-amino-acid resolution using nanopores”: science.org/doi/10.1126/sc…

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