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Ivan Gushchin

@ivangushchin.bsky.social

230 followers 200 following 65 posts

Structural biology and protein engineering

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Ivan Gushchin @ivangushchin.bsky.social · Nov 22

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/...

Protein engineering details, chromatography profiles and spectroscopic characterization

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Ivan Gushchin @ivangushchin.bsky.social · 2d

Previously, we engineered 3 artificial CagLOV-derived proteins doi.org/10.1002/pro.... - so I'm glad to see that the approach works for other LOVs as well

Ivan Gushchin @ivangushchin.bsky.social · 2d

They even succeed in engineering an ultrastable photoactive protein based on Atphot2 LOV2

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Ivan Gushchin @ivangushchin.bsky.social · 2d

Interesting preprint by Herzog and colleagues where they investigate 21 diverse LOV domain - also beautiful illustrations throughout

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Ivan Gushchin @ivangushchin.bsky.social · 7d

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...

Reposted by Ivan Gushchin

Richard Sever @richardsever.bsky.social · 7d

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 @ivangushchin.bsky.social · 11d

And now prohibitins!
www.pnas.org/doi/pdf/10.1...

Reposted by Ivan Gushchin

piatkevich.bsky.social @piatkevich.bsky.social · 24d

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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Reposted by Ivan Gushchin

BejaLab @bejalab.bsky.social · Sep 8

Structural basis for no retinal binding in flotillin-associated rhodopsins www.cell.com/structure/fu...

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...

www.cell.com

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Reposted by Ivan Gushchin

Niko McCarty @nikomccarty.bsky.social · Sep 1

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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Reposted by Ivan Gushchin

Miguel Matilla - Matilla Lab @miguelmatilla.bsky.social · Sep 1

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 @ivangushchin.bsky.social · Aug 30

More beautiful stomatin structures!

Oli Clarke @olibclarke.bsky.social · Aug 30

Happy to share a new preprint from the Clarke & Vallese (@fravallese.bsky.social) labs reporting #cryoem structures of two RBC stomatin complexes – with AQP1 & UT-B - continuing the SPFH theme from our recent vault preprint! This was a fun one and has been cooking for a while - read on for more! ⬇️

Upper - cryo-EM reconstruction of stomatin AQP1 complex. Lower - reconstruction of stomatin-UT-B complex.

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Ivan Gushchin @ivangushchin.bsky.social · Aug 27

Congratulations! Great and inspiring work!

Reposted by Ivan Gushchin

Martin Pacesa @martinpacesa.bsky.social · Aug 27

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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Reposted by Ivan Gushchin

Boston Protein Design and Modeling Club @bpdmc.org · Aug 15

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

BindCraft: one-shot design of functional protein binders

YouTube video by Boston Protein Design and Modeling Club

youtu.be

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Ivan Gushchin @ivangushchin.bsky.social · Aug 11

Got an idea while reviewing a grant and a paper

Image courtesy: Qwen

A thought on using AI for peer review: instead of avoiding or discouraging it, the systems used for submission and evaluation should explicitly provide the authors, and then the reviewers with a thorough LLM evaluation. This will help in weeding out basic logical flaws and typos, and provide the human reviewers with a list of points which they can either confirm or disregard, and then add what was missed by the AI.

Yes, LLMs don't have access to subscription-based publications or field insider knowledge - that's what the human reviewers are needed for.

Also, everyone is using LLMs anyway, why not make it explicit and to the highest standard possible, with the best prompts and LLM models.

Ivan Gushchin @ivangushchin.bsky.social · Jul 26

This sequence, or sequence of some homologue, which is already released, would be great 🙏 [email protected]

Ivan Gushchin @ivangushchin.bsky.social · Jul 24

Could you share the accession ID for this or related proteins? Would love to play with it in AlphaFold (or Boltz-2)

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Ivan Gushchin @ivangushchin.bsky.social · Jul 21

Summer holidays @natcomms.nature.com ? 😕

Ivan Gushchin @ivangushchin.bsky.social · Jul 20

Great visual representation! Looks a little bit like a marketplace: choose the best organism for your specifications

Reposted by Ivan Gushchin

The Align Foundation @alignbio.bsky.social · Jul 8

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🚀 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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Reposted by Ivan Gushchin

polovinkinvitaly.bsky.social @polovinkinvitaly.bsky.social · Jul 14

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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Reposted by Ivan Gushchin

Diego del Alamo @delalamo.xyz · Jul 14

This paper is absolutely bananas and a tour de force of structural bioinformatics. Some random tidbits:

🧬Jacob L Steenwyk @jlsteenwyk.bsky.social · Jul 10

NEW pub: The role of metabolism in shaping #enzyme structures over 400 million years. Now out in @nature.com

Super grateful to have played a small role in this project - congrats to lead/corr authors Oliver, Benjamin, and Markus!

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

#alphafold #evolution #genomics

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Ivan Gushchin @ivangushchin.bsky.social · Jul 12

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

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Reposted by Ivan Gushchin

ibmb-csic.bsky.social @ibmb-csic.bsky.social · Jul 11

***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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Reposted by Ivan Gushchin

Martin Pacesa @martinpacesa.bsky.social · Jun 30

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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