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Sagar Khavnekar
@cryosagar.subspatial.org

Hey #teamtomo checkout our #teamscience approach to #cellbio #cryoET I can’t thank @cellarchlab.com enough for this one 😍😍 Awesome team science from @mpibiochem.bsky.social @biozentrum.bsky.social Thermo Fisher Scientific and more #firstpost on Bluesky www.biorxiv.org/content/10.1...

biorxiv.orgTowards community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtiiIn situ cryo-electron tomography (cryo-ET) has emerged as the method of choice to investigate structures of biomolecules in their native context. However, challenges remain in the efficient production...

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Hiren Joshi
@glyco.me

This looks amazing - for a rube like me who has never touched this kind of data, what are the perspectives on searching this for specific proteins (assuming their AF models are mostly right)? Have people worked out search algorithms to search by PDB file?

Hiren Joshi
@glyco.me

We were involved in a paper earlier this year on C Reinhardtii, and I'm in particular wondering about one enzyme: CHLRE_01g031800v5, or whether there's resolution enough to see modifications on some of these proteins. www.nature.com/articles/s41...

nature.comMolecular-level architecture of Chlamydomonas reinhardtii’s glycoprotein-rich cell wall - Nature CommunicationsChlamydomonas reinhardtii produces a glycoprotein-rich cell wall. Using nuclear magnetic resonance and mass spectrometry approaches, this study reveals unprecedented details on its protein and carbohy...
Sagar Khavnekar
@cryosagar.subspatial.org

As @cellarchlab.com said template based approaches are powerful! However we are limited to roughly 200-300 kDa and abundant targets. Have a look at journals.iucr.org/d/issues/202... to get an idea and a systematic analysis from Beata’s team www.nature.com/articles/s41...

journals.iucr.orgSTOPGAP: an open-source package for template matching, subtomogram alignment and classificationSTOPGAP, an open-source package for subtomogram averaging that is designed to provide users with fine control over each of the steps in the image-processing workflow, is described.
Hiren Joshi
@glyco.me

Thanks Sagar - the one protein I am particularly interested in is about 140 kDa, although it would be cool to see if it pops up in a complex with anything (bumping it over 200 kDa). I'll have to take a look at how far I can get searching!

Ben Engel
@cellarchlab.com

Thanks Hiren! Yes, one approach is to perform template- or AI-based searches on this data using models generated from structure prediction (AF etc). That's an exciting frontier to explore. There's plenty of cell wall in this dataset, but I'm not sure if your protein is structured & abundant enough?🧪

Hiren Joshi
@glyco.me

Thanks for answering questions Ben :) I agree the modified proteins may be hard to see, but the enzyme doing this should be well ordered, and in the ER somewhere. I’ll park idea for now until the software matures for this! It blows my mind thinking about what we can currently image.