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Stanisław Dunin-Horkawicz

@staszekdh.bsky.social
335 followers 604 following 23 posts

Max Planck Institute for Biology, Tübingen & University of Warsaw. Using computational tools to study protein evolution and function.

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Stanisław Dunin-Horkawicz @staszekdh.bsky.social · 28/08/2026
7/7 X-ray structures: www.rcsb.org/structure/9TRK www.rcsb.org/structure/9TRJ Paper: onlinelibrary.wiley.com/doi/10.1002/...
rcsb.org
RCSB PDB - 9TRJ: First four HAMP domains of a soluble histidine kinase from Myxococcus xanthus fused to a GCN4 adaptor
First four HAMP domains of a soluble histidine kinase from Myxococcus xanthus fused to a GCN4 adaptor
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Stanisław Dunin-Horkawicz @staszekdh.bsky.social · 28/08/2026
6/7 Our speculation: poly-HAMP arrays may not switch all at once. Instead, signals could propagate through local conformational rearrangements traveling along the chain.
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Stanisław Dunin-Horkawicz @staszekdh.bsky.social · 28/08/2026
5/7 Consecutive HAMP domains tend to adopt compatible states, reinforcing the zig-zag pattern seen in the crystal structures. In other words, the array behaves as a coupled chain rather than as independent switches.
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Stanisław Dunin-Horkawicz @staszekdh.bsky.social · 28/08/2026
4/7 We compared each HAMP domain modeled within a complete poly-HAMP array with the same domain modeled in isolation. The result: conformational states depend on neighboring domains.
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Stanisław Dunin-Horkawicz @staszekdh.bsky.social · 28/08/2026
3/7 The C-terminal HAMP domains were also partly influenced by the stabilizing GCN4 fusion. Years later, we turned to AlphaFold2 to explore a broader conformational landscape.
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Stanisław Dunin-Horkawicz @staszekdh.bsky.social · 28/08/2026
2/7 After a long experimental effort, Carolin Ewers, Reinhard Albrecht & Marcus Hartmann obtained X-ray structures revealing an alternating zig-zag of consecutive HAMP conformations. Yet these were only static snapshots.
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Stanisław Dunin-Horkawicz @staszekdh.bsky.social · 28/08/2026
1/7 HAMP domains are conformational switches found in many multidomain sensory proteins, coupling input signals to alternative output states. But what happens when dozens of HAMP domains are chained together in poly-HAMP arrays?
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Tanmay Bharat @tbharat-lab.bsky.social · 23/08/2026
Molecular architecture of colossal surface layers from hyperthermophilic archaea Led by @idocaspy.bsky.social (Ido) In collaboration with @mkrupovic.bsky.social and @vikramalva.bsky.social labs doi.org/10.64898/202...
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Oko.press RSS @okopressrss.plsky.eu · 11/08/2026
Nadzieja na koniec chowu klatkowego? KE publikuje strategię i obiecuje lepszy los kur i świń - oko.press/chow-klatkowy-ke-publikuj…
oko.press
Nadzieja na koniec chowu klatkowego? KE publikuje rolniczą strategię i obiecuje lepszy los kur i świń
Komisja Europejska obiecuje, że w ciągu najbliższych miesięcy przedstawi propozycje zakazu trzymania niosek w klatkach i loch w kojcach. Takie zapowiedzi znalazły się w Strategii dotyczącej hodowli zwierząt. Tylko czy to wystarczy? O chów klatkowy pytamy Małgorzatę Szadkowską
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Stanisław Dunin-Horkawicz @staszekdh.bsky.social · 30/07/2026
Web server: plast.lbs.cent.uw.edu.pl Code, local package and documentation: github.com/labstructbio... Paper: doi.org/10.1093/bioi... Feature requests. Please place your orders here: github.com/labstructbio...
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Stanisław Dunin-Horkawicz @staszekdh.bsky.social · 30/07/2026
If you are into plasmid research, try pLAST. By representing plasmids as ORF chains, it enables fast searches of 700k PlasmidScope sequences in global (find similar plasmids) or local (find recurring gene modules) mode. Available as server or local package. Feedback welcome! Links below ⬇️
Similarity map of hits for a single query plasmid, with the query and selected hit highlighted.Global alignment of a single query-target plasmid pair, showing corresponding ORFs and conserved gene blocks.
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 30/01/2026
FoldMason is out now in @science.org. It generates accurate multiple structure alignments for thousands of protein structures in seconds. Great work by Cameron L. M. Gilchrist and @milot.bsky.social. 📄 www.science.org/doi/10.1126/... 🌐 search.foldseek.com/foldmason 💾 github.com/steineggerla...
science.org
Multiple protein structure alignment at scale with FoldMason
Protein structure is conserved beyond sequence, making multiple structural alignment (MSTA) essential for analyzing distantly related proteins. Computational prediction methods have vastly extended ou...
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Iñaki Ruiz-Trillo @multicellgenome.bsky.social · 01/01/2026
The real drama of life happened "backstage" in the unicellular world. 🎭🧬 #protistsonSky Our postdoc Vika Shabardina is co-organizing this symposium with Annia (@ankarn.bsky.social). Two brilliant minds leading the evocell way! Plus, a talk by @vikramalva.bsky.social. 👇
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Stanisław Dunin-Horkawicz @staszekdh.bsky.social · 02/12/2025
We envisioned pLAST as a BLAST-like tool, but tailored for plasmid sequences. pLAST can be run online (plast.lbs.cent.uw.edu.pl) or locally (github.com/labstructbio...) to search, classify and explore plasmid diversity. We would greatly appreciate your feedback! ➡️ www.biorxiv.org/content/10.1...
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Retraction Watch @retractionwatch.com · 12/08/2025
"Exclusive: Medical journal rejects Kennedy's call for retraction of vaccine study"
reuters.com
Exclusive: Medical journal rejects Kennedy's call for retraction of vaccine study
An influential U.S. medical journal is rejecting a call from Health Secretary Robert F. Kennedy Jr. to retract a large Danish study that found that aluminum ingredients in vaccines do not increase health risks for children, the journal's editor told Reuters.
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Stanisław Dunin-Horkawicz @staszekdh.bsky.social · 09/08/2025
I got followed by exactly the same dog from two different accounts. Are fake accounts becoming a problem on BS?
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Year Progress Bot @yearprogress.bsky.social · 07/08/2025
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Stanisław Dunin-Horkawicz @staszekdh.bsky.social · 05/08/2025
It should also be illegal to force cats to wear collars with bells :)
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Year Progress Bot @yearprogress.bsky.social · 02/08/2025
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Stanisław Dunin-Horkawicz @staszekdh.bsky.social · 28/07/2025
a fire truck's diesel engine?
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Stanisław Dunin-Horkawicz @staszekdh.bsky.social · 07/07/2025
A 6-year internship? that’s something! ;)
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Dr Javier Sánchez Utgés @javierutges.bsky.social · 19/05/2025
I am #exhilarated to share that our new paper "LIGYSIS-web: a resource for the analysis of protein-ligand binding sites" is now published in @narjournal.bsky.social! After almost two years of development and more than 600 commits, LIGYSIS-web is out! 📜 : tinyurl.com/utges-LIGYSI...
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Claudia Alvarez Carreño @claudiaalcar.bsky.social · 01/05/2025
We are pleased to announce that the next speaker in the ProSE seminar series will be Dr. Klara Hlouchova with a talk on "Protein Structure Before LUCA" May 13, 4PM CET Registration link: tinyurl.com/prose-seminar4 Please share!
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Stanisław Dunin-Horkawicz @staszekdh.bsky.social · 16/03/2025
We have benchmarked the AF2 multimer on coiled-coil domains and the results are also very good (even outperforming dedicated tools). Interestingly, the performance does not depend on the use of MSA: onlinelibrary.wiley.com/doi/full/10.....
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Stanisław Dunin-Horkawicz @staszekdh.bsky.social · 18/01/2025
This chopped alignment does not look meaningful. Or do I miss something?
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Stanisław Dunin-Horkawicz @staszekdh.bsky.social · 17/12/2024
Coiled coils (CCs) are protein domains in which alpha helices assemble into regular supercoiled bundles. In our new paper, we investigate how accurately AlphaFold2 predicts the oligomeric state, topology, and fine structural details of CC domains: onlinelibrary.wiley.com/doi/10.1002/....
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Infectious Disease Tracker @hmpxvt.bsky.social · 15/12/2024
Large livestock facilities in states across the country have become epicenters of bird flu, and some researchers say that’s no surprise: Putting thousands of animals together in confined, cramped barns or corrals creates a petri dish for virus to spread, according to WIRED.
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Stanisław Dunin-Horkawicz @staszekdh.bsky.social · 13/12/2024
Maybe “Logicomix: An epic search for truth”?
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Dan Jagger @auditorynerves.bsky.social · 08/12/2024
If talent and opportunity were equally distributed, the average #NobelPrize winner would come from a middle income background. The reality? The average laureate grew up in a household just below the top 10%. More than 50% come from the top 5%. 🧪🎩💰 www.theguardian.com/commentisfre...
theguardian.com
The science behind winning a Nobel Prize? Being a man from a wealthy family | Torsten Bell
A lot of talent is wasted in a world where more than half of laureates come from households in the richest 5%
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Eric Topol @erictopol.bsky.social · 05/12/2024
New @science.org from my Scripps Research colleagues on H5N1 A single mutation can increase the virus's binding to human receptors, highlighting the need for rigorous surveillance science.org/doi/10.1126/...
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Kevin Waldron @waldronlab.bsky.social · 03/12/2024
I have a PhD position available in my group, to start in March 2025. If you have a keen interest in biochemistry and would like to study an exciting and novel class of copper proteins (aka weird Cu tubes) from bacteria, I'd love to hear from you. You should apply here: ibb.edu.pl/app/uploads/...
Figure from Vita et al., 2016, Sci Rep: https://www.nature.com/articles/srep39065
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Stanisław Dunin-Horkawicz @staszekdh.bsky.social · 01/12/2024
We’ve seen such cases among coiled-coil domains. Fig. 8 here www.biorxiv.org/content/10.1...
biorxiv.org
Applicability of AlphaFold2 in the modeling of dimeric, trimeric, and tetrameric coiled-coil domains
Coiled coils are a common protein structural motif involved in cellular functions ranging from mediating protein-protein interactions to facilitating processes such as signal transduction or regulatio...
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Judith Bernett @judith-bernett.bsky.social · 28/11/2024
Related to that, there is a fun PPI prediction challenge by @chembiobryan.bsky.social, which I'd like to advertise to everyone developing PPI prediction models. Tests like that are crucial for assessing model generalization capabilities! www.dickinsonlab.uchicago.edu/ppi-challenge
dickinsonlab.uchicago.edu
PPI Challenge 1 | dickinson-group
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Stanisław Dunin-Horkawicz @staszekdh.bsky.social · 27/11/2024
"If only there was some way to remove viruses from milk" - it's easy, just drink plant-based milks :)
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Stanisław Dunin-Horkawicz @staszekdh.bsky.social · 24/11/2024
Not only is this an illusion, but it is a western culture-oriented illusion.
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Stanisław Dunin-Horkawicz @staszekdh.bsky.social · 23/11/2024
This reminds me of www.cell.com/fulltext/S00...
cell.com
Protein Sectors: Evolutionary Units of Three-Dimensional Structure
Proteins display a hierarchy of structural features at primary, secondary, tertiary, and higher-order levels, an organization that guides our current understanding of their biological properties and e...
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Elisa Fadda @elisafadda.bsky.social · 18/11/2024
If you are interested or working in #structuralbiology, as you see any protein (yes, *any*), you should be thinking: is it glycosylated? The answer is likely to be yes! You can predict N-glycosylation sites and rebuild all types of glycans with ReGlyco glycoshape.org 😌 Check out the example ⬇️ 1/2
Left, cry-EM structure of the complex between MIK2 (green), the immunoregulatory peptide SCOOP (yellow) and the LRR of the co-receptor BAK1 (white) with only the most rigid part of the N-glycans resolved (1 or 2 or none) and represented with sticks. Right, reconstruction of the N-glycosylation with plant N-glycans G90477LS,selected to be all the same as glycoproteomics data is not available (as far as I know)
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Stanisław Dunin-Horkawicz @staszekdh.bsky.social · 05/01/2024
How do you study a family of protein domains whose function depends on their dynamics? Let's model 5000 homologs with AlphaFold2 and see what happens. The case of dimeric HAMP domains of prokaryotic signal transduction proteins: onlinelibrary.wiley.com/doi/full/10....
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Rafal Mostowy @rafalmostowy.bsky.social · 28/11/2023
Our paper looking into the phenomenon of domain mosaicism in phages is now out in Nature Communications. Work led by Bogna Smug together with Krzysztof Szczepaniak, @epcrocha.bsky.social and @staszekdh.bsky.social. See a short thread. 1/7 www.nature.com/articles/s41...
nature.com
Ongoing shuffling of protein fragments diversifies core viral functions linked to interactions with ...
Proteins are composed of distinct functional domains, each serving a specific role. Here, Smug et al. show that phages are able to shuffle fragments of their proteins and this predominantly occurs in ...
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