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Katja Luck

@katjaluck.bsky.social

Group Leader at Institute of Molecular Biology, Mainz, Germany

4 Posts87 Follower40 Folgt
Katja Luck@katjaluck.bsky.social · 5d ago

Check out our new article if you are interested in disorder-mediated protein interactions, AlphaFold-based structural modeling and variant characterization: Https://rdcu.be/fw2oz Dx.doi.org/10.1038/s41594-026-01846-z

Variant characterization in the intrinsically disordered human proteome - Nature Structural & Molecular Biology

Proteome-wide prediction and structural modeling of disordered protein interaction interfaces advance characterization of disease-associated variants in disordered protein regions.

dx.doi.org

Ylva Ivarsson@ivarssonlab.bsky.social · 11mo ago

Finally out! Thrilled to share our collaboration with @kulathu.bsky.social, @orafurman.bsky.social, and N Davey. We screened auxiliary domains of USP family #deubiquitinases, revealing short linear motifs (SLiMs), contributing to specificity in complex assembly. www.biorxiv.org/content/10.1...

Systematic Discovery of Motif-based Interactions of the Auxiliary Domains of USP Family Deubiquitinases

The ubiquitin-specific proteases (USPs) family is the largest family of human deubiquitinating enzymes (DUBs). While most USPs are agnostic to polyubiquitin linkage-type, their substrate specificity i...

biorxiv.org

Kresten Lindorff-Larsen@lindorfflarsen.bsky.social · 10mo ago

The proteasome-substrate-shuttle protein UBQLN2 contains—like other quality control system proteins—a long region devoid of lysine (a lysine desert) Martin Grønbæk-Thygesen (from @rhp-lab.bsky.social) et al show that introducing K here causes ubiquitylation and degradation doi.org/10.1101/2025...

Fig. 1 – UBQLN2 is a conserved lysine-depleted protein. (A) Sequence comparison of UBQLN2 orthologs in the indicated species. Intrinsically disordered regions in human UBQLN2 based on MobiDB are shown as a blue bar. The domain organization based on the SMART database is marked. Lysine residues are marked as black squares. (B) ESM-2 predictions of all possible single amino acid substitutions of human UBQLN2 presented as a heat map. The wild-type residues are marked in blue. ESM-2 scores close to zero (light yellow colors) indicate that the amino acid substitution is compatible with the ESM-2 language model, whereas negative scores (dark orange colors) indicate that the variant is incompatible with the ESM-2 model. The domain organization (based on SMART) is aligned above the map. Note that substitutions to lysine or cysteine in general appear detrimental, in particular downstream of the UBL domain. (C) The AlphaFold2 predicted structured of human UBQLN2 (AF-Q9UHD9-F1) (left panel). The UBL domain is colored blue, and the UBA domain is colored orange and the STI1 regions green. Zoom in on the UBL domain (right panel) with the lysine residues highlighted as stick representations and colored based on the relative accessible surface area (rASA, dark red exposed; grey, buried).
bioRxivpreprint@biorxivpreprint.bsky.social · 10mo ago

The importance of UBQLN2 ubiquitylation for its turnover and localization https://www.biorxiv.org/content/10.1101/2025.10.02.679934v1

Pedro Beltrao@pedrobeltrao.bsky.social · 10mo ago

new preprint: Ubiquitin is a protein modification linked with degradation but known to regulate other functions. Over 100k ubiquitination sites have been discovered and here we (@julianvangerwen.bsky.social + others) try to prioritize those most critical to the cell www.biorxiv.org/content/10.1...

The functional landscape of the human ubiquitinome

Protein ubiquitination regulates cell biology through diverse avenues, from quality control-linked protein degradation to signaling functions such as modulating protein-protein interactions and enzyme...

biorxiv.org

jackie pelham@pelhamjackie.bsky.social · 11mo ago

New IDPSeminars season on deck 🤩 We hope you can join us to learn about some exciting science! More info in the post below👇

IDPSeminars@idpseminars.bsky.social · 11mo ago

🚨🚨IDPSeminars is BACK 🚨🚨 Season 19 (!) gets underway next week with @rohitpappu68.bsky.social and Meredith Jackrel! Date: Thur. Sept 4th Time: 1 pm EST [USA] / 7 pm CET [Europe] If you've previously signed up, you should be good to go, otherwise, please sign up at idpseminars.com

Katja Luck@katjaluck.bsky.social · last yr.

Variant characterization in the intrinsically disordered human proteome - here is how we did it using short linear motif prediction, AlphaFold, and experimentation. Check out our preprint: www.biorxiv.org/cgi/content/...

Variant characterization in the intrinsically disordered human proteome

Variant effect prediction remains a key challenge to resolve in precision medicine. Sophisticated computational models that exploit sequence conservation and structure are increasingly successful in t...

biorxiv.org

SFB 1551 - Collaborative Research Centre 1551@sfb1551.bsky.social · last yr.

🚨Publication alert🚨 "Molecular simulations of enzymatic phosphorylation of disordered proteins and their condensates" by Emanuele Zippo, @lstelzl.bsky.social, @dormannlab.bsky.social & Thomas Speck. Congratulations!! 📄 www.nature.com/articles/s41... #TDP43 #CK1δ #ALS #biophysics #proteincondensates

Molecular simulations of enzymatic phosphorylation of disordered proteins and their condensates - Nature Communications

Here, the authors implement molecular dynamics simulations to model ATP-driven enzymatic reactions, revealing how the enzyme CK1δ phosphorylates condensates of the neurodegeneration linked protein TDP...

nature.com

ME Torres-Padilla@metorrespadilla.bsky.social · last yr.

Are you @ the late stages of your postdoc ? Want to pursue a PI career ? Then this 👇👇 is for you ! Apply for a spot @ our Talent Forum www.helmholtz-munich.de/en/stem-cell... Peer-networking / Career orientation and more !!! Please distribute :) 🙂

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Epigenetics at Helmholtz Munich@epihmgu.bsky.social · last yr.

🎤 Postdocs: want to take the next step and become a #PI? Apply to speak at the TALENT FORUM @www.helmholtz-munich.de, showcase your research in Epigenetics & Nucleic Acids, and connect with top scientists. 🧳 Travel & accommodation covered if selected! 📝 Apply by 31July. 🔗 Info: lnkd.in/drkRvz7N

Pedro Beltrao@pedrobeltrao.bsky.social · last yr.

New lab preprint - Delora Baptista tested AlphaFold 2 and 3 for the prediction of structures of host-pathogen interactions and then applied these to study convergence of binding and molecular mimicry in host-pathogen vs. host-host interactions. www.biorxiv.org/content/10.1...

AlphaFold models of host-pathogen interactions elucidate the prevalence and structural modes of molecular mimicry

Pathogens exploit host cellular machinery through protein-protein interactions (PPIs), often using molecular mimicry to hijack host cellular processes. While there have been thousands of host-pathogen...

biorxiv.org

Martin Steinegger 🇺🇦@martinsteinegger.bsky.social · last yr.

We've updated our AFESM website to now include biome filtering, allowing exploration of protein structures adapted to specific environments. 🌐 afesm.foldseek.com Read more about the work in the skeetorial 🦋 bsky.app/profile/mart... or our preprint 📄 www.biorxiv.org/content/10.1...

Martin Steinegger 🇺🇦@martinsteinegger.bsky.social · last yr.

AFESM: a metagenomic guide through the protein structure universe! We clustered 821M structures (AFDB&ESMatlas) into 5.12M groups; revealing biome-specific groups, only 1 new fold even after AlphaFold2 re-prediction & many novel domain combos. 🧵 🌐 afesm.foldseek.com 📄 www.biorxiv.org/content/10.1...

Evangelia Petsalaki@epetsalaki.bsky.social · last yr.

We present SELPHI 2.0 a machine learning model integrating >40 sequence, omics and structural features to predict kinase-substrate interactions between 420 kinases and 240K phosphosites and improve interpretation of global phosphoproteomics data www.sciencedirect.com/science/arti...

Data-driven extraction of human kinase-substrate relationships from omics datasets

Phosphorylation forms an important part of the signalling system that cells use for decision making and regulation of processes such as cell division …

sciencedirect.com

Kresten Lindorff-Larsen@lindorfflarsen.bsky.social · last yr.

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 · last yr.

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.

Michael Bronstein@mmbronstein.bsky.social · last yr.

Join us in Vienna on Sep 8-10 with an incredible speaker lineup!

AITHYRA Research Institute of the Austrian Academy of Sciences@aithyra.bsky.social · last yr.

Please save-the-date for the #AITHYRA Symposium “AI for Life Science”, which will take place in Vienna at the House of Industry from 8-10 September 2025. Great speakers, interesting framework programme and beautiful location. Registration will open mid May. More info: www.oeaw.ac.at/aithyra/news...

Arne Elofsson@handle.invalid · last yr.

In this evaluation of AlphaFold3 (and other methods), we show that (i) accurate predictions are limited to RNA structures/complexes with structural similarity to PDB and (ii) that current methods are bad at estimating the accuracy of the predictions. www.biorxiv.org/content/10.1...

Limits of deep-learning-based RNA prediction methods

Motivation: In recent years, tremendous advances have been made in predicting protein structures and protein-protein interactions. However, progress in predicting the structure of RNA, either alone or...

biorxiv.org

Gräter lab @graeterlab.bsky.social · last yr.

Job alert: Join us in Mainz as Max Planck Research Group Leader (W2) in Molecular Design ...and make your own research dreams happen on de novo design, generative models, proteins, materials ... tinyurl.com/r2xjxnuk @mpip-mainz.mpg.de

Max Planck Research Group Leader (W2) in Molecular Design

We are looking for exceptional early-career scientists conducting computational research with a proven record of accomplishment. The primary focus of this call is on candidates proposing research on b...

tinyurl.com

PMC Protein Modules Community@pmc-modularity.bsky.social · last yr.

Remember to join us at 6pm CET April 14 for the next seminar in our series with Prof. Anne-Claude Gingras (@uoft.bsky.social) and Dr. Veronica Venafra. Register to attend: tinyurl.com/register-pmc-seminar You can find recordings of previous seminars here: www.youtube.com/@PMCModularity

PMC Modularity

youtube.com

PMC Protein Modules Community@pmc-modularity.bsky.social · last yr.

Join us at 6pm CET April 14 for the next seminar in our series with Prof. Anne-Claude Gingras (@uoft.bsky.social) and Dr. Veronica Venafra. Register to attend: tinyurl.com/register-pmc-seminar (1/2)

BioMassSpec@realbiomassspec.bsky.social · last yr.

Holdup Multiplex Assay for High-Throughput Measurement of Protein-Ligand Affinity Constants Using a Mass Spectrometry Readout #JACS pubs.acs.org/doi/10.1021/...

Holdup Multiplex Assay for High-Throughput Measurement of Protein–Ligand Affinity Constants Using a Mass Spectrometry Readout

The accurate description and subsequent modeling of protein interactomes require quantification of their affinities at the proteome-wide scale. Here we develop and validate the Holdup Multiplex, a versatile assay with a mass spectrometry (MS) readout for profiling the affinities of a protein for large pools of peptides. The method can precisely quantify, in one single run, thousands of affinity constants over several orders of magnitude. The throughput, dynamic range, and sensitivity can be pushed to the performance limit of the MS readout. We applied the Holdup Multiplex to quantify in a few sample runs the affinities of the 14–3–3s, phosphoreader proteins highly abundant in humans, for 1000 different phosphopeptides. The seven human 14–3–3 isoforms were found to display similar specificities but staggered affinities, with 14–3–3γ being always the best binder and 14–3–3ε and σ being the weakest. Hundreds of new 14–3–3 binding sites were identified. We also identified dozens of 14–3–3 binding sites, some intervening in key signaling pathways, that were either stabilized or destabilized by the phytotoxin Fusicoccin-A. The results were corroborated by X-ray crystallography. Finally, we demonstrated the transferability of the Holdup Multiplex by quantifying the interactions of a PDZ domain for 5400 PBM peptides at once. The approach is applicable to any category of protein-binding ligands that can be quantifiable by mass spectrometry.

pubs.acs.org