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Reposted by Julian Streit

Paul Robustelli @paulrobustelli.bsky.social · 27d

Our work developing a maximum entropy reweighting method to refine all-atom ensembles of IDPs with extensive NMR and SAXS datasets is now out in @natcomms.nature.com:

rdcu.be/eKlK7

Led by @dartmouthchem.bsky.social graduate student Kaushilk Borthakur in collaboration with @bonomimax.bsky.social

Determining accurate conformational ensembles of intrinsically disordered proteins at atomic resolution

Nature Communications - This study demonstrates how to combine molecular dynamics computer simulations with experimental biophysical data to determine accurate atomic-resolution ensembles of...

rdcu.be

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Reposted by Julian Streit

Giulio Tesei @giuliotesei.bsky.social · Oct 2

I'm hiring for a PhD position at Malmö University, Sweden!

The project will focus on molecular modelling of proteins, lipids, and biomolecular condensates at cell membranes.

More details and application form: tinyurl.com/4zm92365

Please feel free to share!

@vetenskapsradet.bsky.social | @mau.se

Snapshot of a condensate near a lipid membrane with Swedish Research Council and Malmö University logos.

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Reposted by Julian Streit

Chris Waudby @chriswaudby.bsky.social · Sep 24

So excited that our lab's first home-grown paper is now available on ChemRxiv!

Kinetic NMR screening: rapidly quantifying fast ligand dissociation in fragment mixtures using ¹⁹F relaxation dispersion | doi.org/10.26434/che... 🧲🧪

Kinetic NMR screening: rapidly quantifying fast ligand dissociation in fragment mixtures using ¹⁹F relaxation dispersion

Ligand-observed NMR is a key tool for detecting weak protein-ligand interactions, but translating binding signals into meaningful affinity measurements remains difficult, limiting the ability to rank ...

doi.org

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Reposted by Julian Streit

Giulio Tesei @giuliotesei.bsky.social · Sep 18

Excited to see our review now on arXiv, written together with @fpesce.bsky.social and @lindorfflarsen.bsky.social

doi.org/10.48550/arX...

Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · Sep 17

New review on computational design of intrinsically disordered proteins 🖥️🍝 by @giuliotesei.bsky.social @fpesce.bsky.social & 👴

doi.org/10.48550/arX...

Figure 3 from the paper with the caption: "Role of machine learning in de novo design of IDRs. (A) Machine-learning models can be trained on diverse data sources, from molecular dynamics simulations to annotations of cellular localization and protein structures from the Protein Data Bank. (B) Often implemented as neural networks using sequence-encoded features as input, these models can initially be trained on a limited region of sequence space as surrogate models. Through active learning, additional simulations are performed during the design campaign to generate new data, and the surrogate model is retrained on the expanded dataset to progressively improve its accuracy. (C) Machine-learning models have been developed to predict biophysical observables, biological annotations, and protein structures. When combined, machine-learning models can be used to identify a set of sequences that strike a trade-off between multiple design objectives, defining a Pareto front."

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Reposted by Julian Streit

Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · Jul 22

Our paper on:

A coarse-grained model for simulations of phosphorylated disordered proteins

(aka parameters for phospho-serine and -threonine for CALVADOS)

is now published in Biophysical Journal

authors.elsevier.com/a/1lTcE1SPTB...

@asrauh.bsky.social @giuliotesei.bsky.social & Gustav Hedemark

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Julian Streit @julianstreit.bsky.social · Jun 28

New preprint with Benjamin Lang, Richard Kriwacki, John Christodoulou, and M. Madan Babu!
www.biorxiv.org/content/10.1...

Protein Dynamics at Different Timescales Unlock Access to Hidden Post-Translational Modification Sites
#bioinformatics #compchem #folding #proteindynamics

Protein Dynamics at Different Timescales Unlock Access to Hidden Post-Translational Modification Sites

Post-translational modifications (PTMs) alter the proteome in response to intra- and extracellular signals, providing fundamental information processing in development, homeostasis and disease. Here, ...

biorxiv.org

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Julian Streit @julianstreit.bsky.social · Jun 25

Now published in Advanced Science: our latest study combining NMR and MD to investigate a transient folding intermediate of human lysozyme #nmrchat #compchem

Janet Kumita @jrkumita.bsky.social · Jun 25

In press!! NMR & MD simulations reveal how non-native contacts stabilise a key transient intermediate in the lysozyme amyloid cascade. Well done Minkoo and all!! @phar.cam.ac.uk For CMD ❤️ advanced.onlinelibrary.wiley.com/doi/10.1002/...

Amyloid Forming Human Lysozyme Intermediates are Stabilized by Non‐Native Amide‐π Interactions

Mutational variants of human lysozyme cause fatal systemic amyloidosis by depositing kilograms of protein in the viscera of patients. Central to this process is a partially unfolded protein intermedi....

advanced.onlinelibrary.wiley.com

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Reposted by Julian Streit

Janet Kumita @jrkumita.bsky.social · Jun 25

In press!! NMR & MD simulations reveal how non-native contacts stabilise a key transient intermediate in the lysozyme amyloid cascade. Well done Minkoo and all!! @phar.cam.ac.uk For CMD ❤️ advanced.onlinelibrary.wiley.com/doi/10.1002/...

Amyloid Forming Human Lysozyme Intermediates are Stabilized by Non‐Native Amide‐π Interactions

Mutational variants of human lysozyme cause fatal systemic amyloidosis by depositing kilograms of protein in the viscera of patients. Central to this process is a partially unfolded protein intermedi....

advanced.onlinelibrary.wiley.com

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Reposted by Julian Streit

Wojciech Kopec @wojciechkopec.bsky.social · May 22

www.qmul.ac.uk/media/news/2...

Electrophysiology at atomic resolution: scientists simulate ion channel currents with unprecedented accuracy

www.qmul.ac.uk

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Reposted by Julian Streit

Stephanie Wankowicz @stephanieaw.bsky.social · May 16

The third episode of The Tortured Proteins Department is out now!

We chatted about grant cancellations, exciting regional meetings and reunions, two fun new preprints, community norms around code release, and the importance of giving kudos. @fraserlab.com

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Reposted by Julian Streit

Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · May 15

Led by @vvouts.bsky.social in @rhp-lab.bsky.social, we measured the degron potency of >200,000 30-residue tiles from >5,000 cytosolic human proteins and trained an ML model for degrons

📜 www.biorxiv.org/content/10.1...
🖥️ github.com/KULL-Centre/...

Rasmus Hartmann-Petersen @rhp-lab.bsky.social · May 15

In collaboration with the @lindorfflarsen.bsky.social group we release our map of degrons in >5,000 human cytosolic proteins with >99% coverage. A machine learning model trained on the data identifies missense variants forming degrons in exposed & disordered regions. Work led by @vvouts.bsky.social.

A complete map of human cytosolic degrons and their relevance for disease

Degrons are short protein segments that target proteins for degradation via the ubiquitin-proteasome system and thus ensure timely removal of signaling proteins and clearance of misfolded proteins fro...

www.biorxiv.org

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Reposted by Julian Streit

Sammy Chan @sammyhschan.bsky.social · May 8

Rationally designing 19F probe pairs was key to determining the structures of protein folding intermediates on the ribosome in our latest preprint.

Our design strategy is now published in @natcomms.nature.com

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

#NMRchat #compbio #compchem

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Julian Streit @julianstreit.bsky.social · May 8

Our latest is now in Nature Communications:
www.nature.com/articles/s41...
Rational design of fluorine NMR labelling sites (AlphaFold/molecular dynamics) to gain insights into protein structure and interactions for large complexes and in cells!
#NMRchat #compchem #AlphaFold #proteinfolding

This link will take you to a page that’s not on LinkedIn

lnkd.in

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Reposted by Julian Streit

Paul Robustelli @paulrobustelli.bsky.social · Apr 30

Presenting one of my favorite manuscripts I've ever worked on:

"Characterizing structural and kinetic ensembles of intrinsically disordered proteins using writhe"

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

by Tommy Sisk, with a generative modeling component done in collaboration with @smnlssn.bsky.social

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Reposted by Julian Streit

Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · Apr 17

AlphaFold is amazing but gives you static structures 🧊

In a fantastic teamwork, @mcagiada.bsky.social and @emilthomasen.bsky.social developed AF2χ to generate conformational ensembles representing side-chain dynamics using AF2 💃

Code: github.com/KULL-Centre/...
Colab: github.com/matteo-cagia...

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Julian Streit @julianstreit.bsky.social · Apr 11

Excited to share our new preprint presenting mechanistic details of how proteins fold on the ribosome. With co-first author @sammyhschan.bsky.social , @twlodarski.bsky.social , Alkistis Mitropoulou, Lisa Cabrita, and John Christodoulou.
www.biorxiv.org/content/10.1...
#proteinfolding #compchem #NMR

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Reposted by Julian Streit

bioRxiv Biophysics @biorxiv-biophys.bsky.social · Apr 11

Structures of protein folding intermediates on the ribosome https://www.biorxiv.org/content/10.1101/2025.04.07.647236v1

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Reposted by Julian Streit

Sammy Chan @sammyhschan.bsky.social · Apr 10

Cryo-EM, and integration with MD simulations, of nascent proteins on the ribosome.

Congrats Alki and @twlodarski.bsky.social and co-authors!

bioRxiv Biophysics @biorxiv-biophys.bsky.social · Apr 10

The ribosome directs nascent chains through two folding-dependent pathways https://www.biorxiv.org/content/10.1101/2025.04.08.647855v1

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Reposted by Julian Streit

Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · Mar 25

Our paper on prediction of phase-separation propensities of disordered proteins from sequence is now published:
www.pnas.org/doi/10.1073/...

The paper has been substantially updated compared to the preprint including new experimental data and using the neural network to finetune CALVADOS. 1/n

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Reposted by Julian Streit

Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · Mar 22

Gemma Solomon and I are looking for a postdoc to work across the two groups on modelling biological systems with a view to applications for quantum computing

More details about the project including how to apply in the link below. Deadline April 9 2025

candidate.hr-manager.net/ApplicationI...

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Reposted by Julian Streit

Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · Mar 21

CALVADOS now has parameters for phosphorylated amino acids

@asrauh.bsky.social @giuliotesei.bsky.social and Gustav Hedemark used a top-down approach in which we targeted experimental data to derive parameters or phosphorylated serine and threonine doi.org/10.1101/2025...

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Reposted by Julian Streit

Alisia Fadini @alisiafadini.bsky.social · Feb 24

Structural biology is in an era of dynamics & assemblies but turning raw experimental data into atomic models at scale remains challenging. @minhuanli.bsky.social and I present ROCKET🚀: an AlphaFold augmentation that integrates crystallographic and cryoEM/ET data with room for more! 1/14.

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Reposted by Julian Streit

Sammy Chan @sammyhschan.bsky.social · Feb 15

Preprint! The ribosome’s electro charge defines how proteins fold by all-atom MD and 19F NMR. Led by @julianstreit.bsky.social with @charles-burridge.bsky.social, Joel Wallace, @chriswaudby.bsky.social, Lisa Cabrita, John Christodoulou

#nmrchat #compchem #compbio

doi.org/10.1101/2025.02.10.637539

Long-range electrostatic forces govern how proteins fold on the ribosome

Protein biosynthesis and folding are tightly intertwined processes regulated by the ribosome and auxiliary factors. Nascent proteins can begin to fold on their parent ribosome but formation of the nat...

doi.org

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Julian Streit @julianstreit.bsky.social · Feb 14

With @sammyhschan.bsky.social, @charles-burridge.bsky.social, Joel Wallace, @chriswaudby.bsky.social, Lisa Cabrita, and John Christodoulou!

Julian Streit @julianstreit.bsky.social · Feb 14

Check out our latest preprint on the role of the ribosome in the folding of its nascent polypeptides - an integrative study combining NMR experiments and atomistic simulations!
#NMRchat #compchem #CompBio #ribosome #proteinfolding
www.biorxiv.org/content/10.1...

Long-range electrostatic forces govern how proteins fold on the ribosome

Protein biosynthesis and folding are tightly intertwined processes regulated by the ribosome and auxiliary factors. Nascent proteins can begin to fold on their parent ribosome but formation of the nat...

www.biorxiv.org

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