Ivan Gushchin
@ivangushchin.bsky.social
📤 243
📥 206
📝 86
Structural biology and protein engineering
pinned post!
We engineered bacteriorhodopsin to be soluble. It binds retinal and can photocycle! X-ray structure reveals conserved binding pocket with 0.8 Å all atom RMSD to WT BR. All this became possible due to hard work by Andrey Nikolaev and the team 🙏
#proteindesign
biorxiv.org/cgi/content/...
over 1 year ago
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Ivan Gushchin
Kelvin Lau @klausenhauser on 🙅♂️🐘🪡
14 days ago
Started this project years ago, but now everything is deposited on
@addgene.bsky.social
and a short
@protocolsio.bsky.social
is online. Try it out to make your own (cheap) homemade nuclease/Benzonase!
dx.doi.org/10.17504/protocols.io.261ged7xov47/v2
Thank you
@jcoker10.bsky.social
and Michael Lim!
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New preprint: We checked whether AlphaFold and its great freely available analogs (including the recent Protenix) can predict the effects of ligand charge. Surprisingly, the predictions sometimes depended on the input format stronger than on the charge! (1/6)
15 days ago
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Ivan Gushchin
AI x Bio Discovery
15 days ago
Influence of molecular representation and charge on protein-ligand structural predictions by popular co-folding methods
[new] Input format impacts pred's more than protonation. Consistency & protonation steps vital for model improv.
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I found it very interesting to surf gene neighborhoods of homologs to the proteins we study
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22 days ago
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Ivan Gushchin
Igor Jouline
22 days ago
A ligand-binding sensor domain got a tiny insertion from cytochrome c, which contained a heme-binding motif, and now it is a nitric oxide sensor. As simple as that:
www.biorxiv.org/content/10.6...
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https://www.biorxiv.org/content/10.64898/2026.02.01.703092v1
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Ivan Gushchin
Alexey Amunts
28 days ago
We're launching a research lab at SMART. Shenzhen Medical Academy for Research and Translation is a newly established institute with long-term funding mechanisms for internal and external investigators. At full capacity SMART aims to support up to 400 labs.
www.scmp.com/news/china/s...
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Structural biologist Alexey Amunts launches new research lab in Shenzhen
‘Shenzhen adds another dimension; it is a place where ideas do not remain ideas for long,’ Amunts says of new position.
https://www.scmp.com/news/china/science/article/3339717/resolution-revolution-pioneer-alexey-amunts-leaves-max-planck-join-chinas-smart?utm_source=copy-link&utm_campaign=3339717&utm_medium=share_widget
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Ivan Gushchin
GAMA Miguel Angel
about 1 month ago
I recorded ~8h introducing the main algorithms for protein design: from classical approaches to protein language models, AlphaFold, ESMFold, MPNN, diffusion models and more :)
youtu.be/wKUYtAt87d4T...
Slides
drive.google.com/file/d/1EPLj...
English is available only via auto-translated subtitles
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Ivan Gushchin
BWJones
about 1 month ago
The bureaucracy of science has grown so much, the system is collapsing upon itself: Scientists have become administrators of grants rather than spending time on science. Paid administrators are demanding even more administrative work from scientists. Administrators are eating the science budget.
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Ivan Gushchin
GAMA Miguel Angel
about 1 month ago
I’ve recorded ~8h explaining the architectures of AlphaFold, AF2 & AF3, as well as the context needed to understand their development, applications and limitations :)
youtu.be/_jDRr5BcTaY
Slides
drive.google.com/file/d/1i4QE...
English is available only via auto-translated subtitles
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Ivan Gushchin
Verena Resch | 🧪🖥️
2 months ago
As the year winds down, I hope you all get the chance to slow down, spend time with family and loved ones, and enjoy the simple moments. I wish you a warm and peaceful holiday season 💫
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Ivan Gushchin
Johannes Vierock
2 months ago
Four years ago, the red-light–activated channelrhodopsin
#Chrimson
restored basic vision in a blind patient. Here, we uncover its
#multicolor_photoreactions
and show implications for optogenetic applications. Many interesting details and a wonderful team🥳!
www.pnas.org/doi/10.1073/...
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PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
https://www.pnas.org/doi/10.1073/pnas.2513375122
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Given the "positive inside" rule, many membrane proteins could potentially interact with negatively charged nucleic acids - I wonder if anyone done a whole proteome analysis
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3 months ago
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Ivan Gushchin
Oli Clarke
3 months ago
very unusual - a tRNA regulated anion channel
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Bacteriorhodopsin is not from bacteria 😅
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3 months ago
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Cryo-EM structure of sensor histidine kinase QseE with its activator QseG. Once again AlphaFold produced great model for the complex before the experimental data were available!
doi.org/10.1128/mbio...
3 months ago
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Hall of Fame for unexpected Boltz predictions, by Pavel Shishkin
3 months ago
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Joys of correcting proofs
3 months ago
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Ivan Gushchin
Misha Kudryashev
4 months ago
We got a large Helmholtz Bioengineering grant with Oliver Daumke, Artur Yakimovich, Alina Bazarova, and Dietrich Ruess to use protein design to target cancer. Five open postdoctoral positions in Generative AI & Protein Engineering. Share & apply!
jobrxiv.org/job/max-delb...
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Postdoctoral Positions in Protein Engineering
Post a job in 3min, or find thousands of job offers like this one at jobRxiv!
https://jobrxiv.org/job/max-delbrueck-center-for-molecular-medicine-27778-postdoctoral-positions-in-protein-engineering/
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Ivan Gushchin
Elodie Laine
4 months ago
Our new special collection "Protein-Nucleic Acid Interactions: From Origins to Design (2025)" is now published in Current Opinion in Structural Biology. I'm excited to have both co-edited it with Shandar Ahmad and contributed a review!
www.sciencedirect.com/special-issu...
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LinkedIn
This link will take you to a page that’s not on LinkedIn
https://lnkd.in/eDh62PSr
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Great work! Always wanted to do this myself
add a skeleton here at some point
4 months ago
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Ivan Gushchin
Alexey Amunts
4 months ago
What a gem from
@dudinlab.bsky.social
@gautamdey.bsky.social
@centriolelab.bsky.social
in Cell! Expansion microscopy atlas of >200 eukaryotes comparing cytoskeletal architectures revealing structures not seen before. Stunning visualisation! Exactly the kind of transformative cell biology we need.
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Ivan Gushchin
4 months ago
www.nature.com/articles/s41...
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Structural basis for agonist and heat activation of nociceptor TRPM3 - Nature Structural & Molecular Biology
TRPM3 is an ion channel that helps the body sense heat and contributes to pain. The authors show that both heat and small chemical molecules switch it on through similar changes inside the protein.
https://www.nature.com/articles/s41594-025-01692-5
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Ivan Gushchin
Joe Greener
5 months ago
I wrote a blog post about the future of structural bioinformatics. Where to go after AlphaFold? How do we avoid the field becoming a load of half-baked LLMs? Let me know what you think.
jgreener64.github.io/posts/struct...
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Where next for structural bioinformatics?
https://jgreener64.github.io/posts/structural_bioinformatics/
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5 months ago
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Interesting preprint by Herzog and colleagues where they investigate 21 diverse LOV domain - also beautiful illustrations throughout
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5 months ago
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Glad to contribute to this: in our most recent preprint, we describe peculiar ferritin-like proteins that have ferroxidase activity, but do not form shells, using encapsulin compartments instead:
doi.org/10.1101/2025...
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5 months ago
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Ivan Gushchin
Richard Sever
5 months ago
Another record month for bioRxiv - and further evidence the pandemic spike+dip was just that and growth continues. Thanks to all involved and that includes 🫵
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Ivan Gushchin
6 months ago
Major milestone for WeKwikGene!
wekwikgene.wllsb.edu.cn
now features 1,000+ ready-to-ship plasmids with 800+ more plasmids under QC. We've processed 1,000+ requests & distributed 3,000+ plasmids worldwide.
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Ivan Gushchin
BejaLab
6 months ago
Structural basis for no retinal binding in flotillin-associated rhodopsins
www.cell.com/structure/fu...
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Structural basis for no retinal binding in flotillin-associated rhodopsins
Kovalev et al. determined cryo-EM structures of a flotillin-associated rhodopsin (FAR) lacking retinal cofactor and its retinal-binding paralog, a classical light-driven proton pump from the same bact...
https://www.cell.com/structure/fulltext/S0969-2126(25)00222-9
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Ivan Gushchin
Niko McCarty
6 months ago
Out today: A useful review on AI-designed protein binders. It covers the history of this work + has lots of good case studies, including how these tools are being used to make snake anti-venoms. The tables are particularly valuable.
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Ivan Gushchin
Miguel Matilla - Matilla Lab
6 months ago
Neurotransmitters guide the chemotaxis behavior of the global human pathogen Pseudomonas aeruginosa. Discover more in our new article at
@microbiotech.bsky.social
@blastmeetings.bsky.social
@eezcsic.bsky.social
@csicdivulga.bsky.social
@krelllaboratory.bsky.social
dx.doi.org/10.1111/1751...
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Ivan Gushchin
Martin Pacesa
6 months ago
Exciting to see our protein binder design pipeline BindCraft published in its final form in @Nature ! This has been an amazing collaborative effort with Lennart, Christian,
@sokrypton.org
, Bruno and many other amazing lab members and collaborators.
www.nature.com/articles/s41...
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Boston Protein Design and Modeling Club
7 months ago
Have no fear if you weren't in the packed audience this week for
@martinpacesa.bsky.social
's awesome seminar, because you can check out the recording 👇
youtu.be/qQihl6If9vU
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BindCraft: one-shot design of functional protein binders
YouTube video by Boston Protein Design and Modeling Club
https://youtu.be/qQihl6If9vU
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Got an idea while reviewing a grant and a paper Image courtesy: Qwen
7 months ago
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Summer holidays
@natcomms.nature.com
? 😕
8 months ago
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Great visual representation! Looks a little bit like a marketplace: choose the best organism for your specifications
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8 months ago
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Ivan Gushchin
The Align Foundation
8 months ago
1/4 🚀 Announcing the 2025 Protein Engineering Tournament. This year’s challenge: design PETase enzymes, which degrade the type of plastic in bottles. Can AI-guided protein design help solve the climate crisis? Let’s find out! ⬇️
#AIforBiology
#ClimateTech
#ProteinEngineering
#OpenScience
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Ivan Gushchin
8 months ago
For high-resolution studies of intracellular crystals, in-house electron diffraction methods are shown to be orders of magnitude more efficient than serial X-ray crystallography regarding the total crystal material required and the radiation dose deposited.
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Ivan Gushchin
Diego del Alamo
8 months ago
This paper is absolutely bananas and a tour de force of structural bioinformatics. Some random tidbits:
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Interesting work from my former lab mate Vitaly Polovinkin and colleagues: solving a high resolution structure of a protein inside the cell using electron diffraction
add a skeleton here at some point
8 months ago
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Ivan Gushchin
8 months ago
***JOB OFFER*** The Protein Design and Modeling lab at IBMB offers a postdoc position at the intersection of computational protein design, biophysics and structural biology. Please share with colleagues and anyone you know that might be interested.
ibmb.csic.es/en/jobs/post...
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Ivan Gushchin
Martin Pacesa
8 months ago
We have written up a tutorial on how to run BindCraft, how to prepare your input PDB, how to select hotspots, and various other tips and tricks to get the most out of binder design!
github.com/martinpacesa...
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Ivan Gushchin
BejaLab
8 months ago
Selective Choice of the Efficient Carotenoid Antenna by a Xanthorhodopsin: Controlling Factors for Binding and Excitation Energy Transfer
pubs.acs.org/doi/10.1021/...
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Selective Choice of the Efficient Carotenoid Antenna by a Xanthorhodopsin: Controlling Factors for Binding and Excitation Energy Transfer
Despite extensive research on carotenoids and microbial rhodopsins in aquatic environments, a fundamental understanding of the binding requirements of carotenoids that serve as auxiliary light-harvest...
https://pubs.acs.org/doi/10.1021/jacsau.4c01243
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Adding fatty acids is indeed a great AF3 trick for many membrane proteins
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9 months ago
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Happy to present a new flavin-binding protein that unexpectedly displays a large Stokes shift due to excited state proton transfer. Not submitted yet - feedback is welcome!
doi.org/10.1101/2025...
9 months ago
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Terrific work from Nikita Egorkin, Nikolai Sluchanko and their colleagues, who discovered a protein binding two carotenoids and two bilins (also four PC lipids!), thus mimicking absorption spectrum of green plants and giving crickets their color. Link to the PNAS article:
doi.org/10.1073/pnas...
9 months ago
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Very happy to see our work published in Chemical Science! No new data compared to preprint, but the text is expanded for clarity and to cite all the relevant literature. Looking forward to engineering more rhodopsins and membrane proteins!
pubs.rsc.org/en/content/a...
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10 months ago
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Having recently submitted manuscripts to Nature Communications/Science Advances and the like, very surprised to see the data like this published, claiming magnesium interaction. The purported resolution is 2.5 Å
doi.org/10.1038/s414...
10 months ago
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Just learned that it turns out that flotillins form truncated cone-shaped compartments - beautiful structures from Fu and MacKinnon:
doi.org/10.1073/pnas...
10 months ago
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Ivan Gushchin
Max Fürst
10 months ago
If u ever had to depict proteins as schematics in papers, u know the dilemma: how to create a pretty “blob”? If structure ends up big & central, u’ll render it with PyMol et al, but for a truly schematic depiction u want a biorender-style icon, but for YOUR protein. Think I’ve finally found a way.
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