Ivan Gushchin
@ivangushchin
Structural biology and protein engineering
In particular, simulations of microbial rhodopsin-carotenoid complexes become possible, and dynamic behavior of carotenoids is reproduced well
The new parameter set was carefully validated and compares favorably to the General Amber Force Field (GAFF) and other common parameter sets
If you want to do molecular dynamics simulations of carotenoids, look no further: Andrey&Co developed AMBER-compatible parameters for the most common carotenoid moieties
The same for acetate and acetic acid (the protein is more challenging given that no experimental structure is available and that the acetic acid probably binds in the protonated form) (4/6)
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)
Great to see a nice computational study also complemented by experiments, and impressive that the approach works overall!
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...
"Study of the effect of acoustic treatment on freezing point and boiling point of tap water" - way to go for a scientific journal www.nature.com/articles/s41...
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
They even succeed in engineering an ultrastable photoactive protein based on Atphot2 LOV2
Interesting preprint by Herzog and colleagues where they investigate 21 diverse LOV domain - also beautiful illustrations throughout
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...
Got an idea while reviewing a grant and a paper Image courtesy: Qwen
Great visual representation! Looks a little bit like a marketplace: choose the best organism for your specifications
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
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...
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...
It looks like Reviewer 1 was happy from the start, Reviewer 2 criticized crystallography and got the paper rejected, but said okay after revision. Still, this data collection and refinement statistics raises quite a number of questions.