Julian Streit

Our recent investigation of the constriction in the bacterial ribosomal tunnel is online. Unbiased all-atom MD simulations of the entire ribosome and PDB analysis show, how flexible the constriction is. The flexibility is modulated by short nascent polypetides.

Looking forward to present our work on predicting protein side-chain rotamer distributions with AlphaFold2 Monday 8:30 at #bps0226

But you should also consider instead going to the The Future of Biophysics Symposium at 9:15 to hear Giulio Tesei talk about his work on data-driven modelling of IDPs

Happy to share our newest preprint on Parkin missense variants in work led by Erna Sol &
@vvouts.bsky.social in @rhp-lab.bsky.social

Using a multiplexed assay we determined the effects of 9,212 out of 9,300 single amino acid substitutions and nonsense Parkin variants. 1/n

doi.org/10.64898/202...

Really excited to share the latest work from my PhD with @giuliotesei.bsky.social and @lindorfflarsen.bsky.social!

New preprint with work led by @asrauh.bsky.social in which we explore how double mutant cycles could be used to study molecular interactions in condensates, and highlight difficulties in extracting information about interactions from mutational experiments

www.biorxiv.org/content/10.6...

Check out our newest preprint on how the chaperone BAG6 and E3 ligase RNF126 cooperate to target unstable and misfolded missense variants for degradation. Work led by Line Pedersen in @rhp-lab.bsky.social

doi.org/10.64898/202...

New preprint led by Fan Cao & Giulio Tesei

We present a data-driven “stickiness” scale for amino acids in intrinsically disordered proteins 🍝, learned from SAXS data on 115 proteins. The scale captures effective residue interactions without conflating size and strength

doi.org/10.64898/202...

Sampling IDPs is tough, but can be worth the effort!

OPES multithermal made it a little easier for us, hopefully you'll find it useful as well

New preprint with @invemichele.bsky.social, Sandro Bottaro, Kamil Tamiola, and @lindorfflarsen.bsky.social on transiently structured states of IDPs sampled in atomistic simulations with enhanced sampling and integrated with experimental data.

We’re thrilled to share our latest iTP-seq protocol for mapping bacterial translation landscapes in vitro — with a complete experimental workflow streamlined by Mélanie Gillard and an open source Python library for data analysis developed by Thibaud Renault.

First preprint of the year, led by Junjie Zhu from Haifeng Chen’s lab

Extending Conformational Ensemble Prediction to Multidomain Proteins and Protein Complex

doi.org/10.64898/202...

If anyone is interested in making bacterial ribosome-nascent chain complexes and studying them using HDX-MS, we have written up a detailed protocol.
rdcu.be/eYFx4
Characterise the conformational dynamics of the ribosome, nascent polypeptide and bound chaperones, label-free and at peptide-level

We (@sobuelow.bsky.social & @kejohansson.bsky.social) tested AF-CALVADOS using the recently described PeptoneBench SAXS benchmark that contains SAXS data for >400 proteins with different amounts of order and disorder. The results look pretty good 😇 so we are sharing here while updating the preprint📝

Our review on Integrative modelling of biomolecular dynamics 💃 is now live at COSB

We discuss approaches to integrate computational methods with time-dependent & time-resolved experiments to study protein dynamics

With @dariagusew.bsky.social & Carl G. Henning Hansen
doi.org/10.1016/j.sb...

New preprint! We measured temperature- and pH-induced aggregation for over 18,000 natural and de novo designed protein domains!

GroEL/ES chaperonin unfolds then encapsulates a nascent protein on the ribosome - Nature Communications The GroEL/ES chaperonin can act during protein synthesis to promote folding. Here, Roeselová et al. show how GroEL captures, remodels and sequesters nascent proteins in its central chamber, while they...

Our story on GroEL/ES action during cotranslational folding is now published @natcomms.nature.com. Led by former-student Alzbeta Roeselova, and in collaboration with Rado Enchev's lab @crick.ac.uk.
www.nature.com/articles/s41...

My first full contribution from my time in @opig.stats.ox.ac.uk is now out! Together with @fspoendlin.bsky.social (and with contributions from King Ifashe), we created FlAbDab and FTCRDab: two large-scale, open molecular dynamics datasets to study flexibility in immune receptors.

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...

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

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

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

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... 🧲🧪

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

doi.org/10.48550/arX...

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

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, ...

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

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

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....

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/...

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

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

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

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/...

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

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