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Oli Clarke @olibclarke.bsky.social · 10h

I think the fact the authors made figures with the same map suggests it was not an accident sadly

Reposted by Oli Clarke

TJ McCorvie @allostericstate.bsky.social · 12h

Yikes! In this paper the AlphaFold model of human plasminogen (PDB-8uq6) has been refined into noise (EMD-42462) using Phenix & ISOLDE. For some reason the authors even interpret side-chain interactions:
#cryoEM

Image from the EMD entry EMD-42462 for human plasminogen bound to streptococcal surface enolase. Projections of the map are shown demonstrating no protein features and radial streaks due to overfitting.

EMD-424262 and PDB-8UQ6 opened in ChimeraX. Though the map is stated to be of Human Plasminogen bound to streptococcal surface enolase the authors have modelled only plasminogen in their PDB. The map shows radial streak at the surface indicative of overfitting and no clear density in the centre of the map corresponds to the model.

Figure 5 from the paper describing side chain interactions of human plasminogen from the PDB 8uq6.

Image showing the model to map FSC curve from Phenix which is the software used by the authors to real space refine their PDB into their cryo-EM map. The model to map FSC curve is a flat line showing no correlation exists between the cryo-EM map EMD-42462 and the PDB 8uq6.

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Oli Clarke @olibclarke.bsky.social · 11h

Cytoplasmic

Oli Clarke @olibclarke.bsky.social · 23h

Yeah that was my guess - I guess I didn’t realize it was found in the cytoplasm too?

Oli Clarke @olibclarke.bsky.social · 1d

Oh yes of course! Thx

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Oli Clarke @olibclarke.bsky.social · 1d

To me they look kind of reminiscent of apolipoprotein particles (see 2d classes in here: www.nature.com/articles/s41...) but I wouldn’t expect to find them here

The structure of apolipoprotein B100 from human low-density lipoprotein - Nature

The structure of apolipoprotein B100 provides insights into how the various domains of apoB100 act in concert to maintain low-density lipoprotein shape and cohesion across a range of particle sizes.

www.nature.com

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Oli Clarke @olibclarke.bsky.social · 1d

Oh interesting!

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Reposted by Oli Clarke

Derek Lowe @dereklowe.bsky.social · 1d

One week from now I plan to be out marching against the idiotic criminals running our government. I'm not "getting paid" and I'm not part of any "Pro-Hamas" group. I'm just mad as hell.

I will not be punching any police officers, nor setting fires, nor breaking any glass. Why will I turn out? (1/2)

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Reposted by Oli Clarke

Alister Burt @alisterburt.bsky.social · 1d

Don Fawcett’s big red book The Cell is available for free online!!

There are a bajillion cryo-ET projects in there, recommend a physical copy if you can find one - it’s my favourite coffee table book

Oli Clarke @olibclarke.bsky.social · 1d

And it's available to borrow/view at archive.org, nice!

archive.org/details/cell...

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Oli Clarke @olibclarke.bsky.social · 1d

Already ordered! found one for 60 USD with free shipping which seemed like a fair price for a hardcover of this kind

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Oli Clarke @olibclarke.bsky.social · 1d

And it's available to borrow/view at archive.org, nice!

archive.org/details/cell...

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Oli Clarke @olibclarke.bsky.social · 1d

ooh that looks excellent! going on the shopping list

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Oli Clarke @olibclarke.bsky.social · 1d

Also this hexagonal thing, and these short bow-ties (kind of reminiscent of TPP2 but shorter?). Also 400Å circle here

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Oli Clarke @olibclarke.bsky.social · 1d

here with a 400Å circle you can see a little more detail on the sides

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Oli Clarke @olibclarke.bsky.social · 1d

possibly stupid question - does anyone in #teamtomo or #cryoem recognize these little stacks (from EMPIAR-12549, U2OS cell lamellae)? The green circle is 300Å, and the spacing between the layers is ~50Å. The fourth, bell-shaped thing is something else, also not sure of that one..

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Reposted by Oli Clarke

Yamuna Krishnan @krishnanyamuna.bsky.social · 1d

Nobel Laureate Joachim Frank: "I will not be bookended by two fascist regimes." An impactful must-read. www.usnews.com/opinion/arti...

www.usnews.com

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Reposted by Oli Clarke

Aaron Reichlin-Melnick @reichlinmelnick.bsky.social · 1d

My first thought was “wow I hope this guy didn’t give out his name because he could absolutely be charged” and yup, he is correct to stay anonymous.

This man’s account is shocking. His neighbors’ situation is shocking. The entire Chicago raid is shocking.

On the other side was a mom and her 7-year-old daughter, pleading for his help.
"I wasn't planning on letting her stay, but I didn't know what the hell was going on," the man said of his Venezuelan migrant neighbors. But he quickly relented. The little girl was inconsolable and hid under his bed.
"I didn't want them to take her," said the man, who didn't want to be named because he fears he'll be targeted by federal authorities for his actions.
"I gave her my bedroom, and I just told her,
'Just stay there. Don't open, don't, shh, just stay quiet," he recalled telling the mom and daughter as he choked back tears.

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Reposted by Oli Clarke

Aaron Reichlin-Melnick @reichlinmelnick.bsky.social · 1d

Can you think of a single movie in which there is a video from the government denouncing its political opponents playing on a loop in public spaces in which that government was the good guy?

Ron Filipkowski @ronfilipkowski.bsky.social · 1d

A new Noem video is being played at airports trashing Democrats.

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Reposted by Oli Clarke

Carolyn Bertozzi @carolynbertozzi.bskyverified.social · 2d

Pres. Kornbluth articulates such moral clarity in this rejection of the proposed “compact”:

“the premise of the document is inconsistent with our core belief that scientific funding should be based on scientific merit alone”

orgchart.mit.edu/letters/rega...

Regarding the Compact | MIT Organization Chart

orgchart.mit.edu

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Reposted by Oli Clarke

Frances Separovic @francesbiophys.bsky.social · 2d

Congratulations to our esteemed colleague, Richard Robson, whose work highlights the strong nexus between teaching and research. #chemistry
www.linkedin.com/posts/univer...

#unimelb | University of Melbourne | 71 comments

Congratulations to #UniMelb's Professor Richard Robson, who has been awarded the 2025 Nobel Prize in Chemistry alongside Professor Susumu Kitagawa of Kyoto University and Professor Omar M. Yaghi of th...

www.linkedin.com

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Reposted by Oli Clarke

Stephan Gruber @gruberlab.bsky.social · 3d

How do SMC complexes load onto DNA to get ready for loop extrusion?

@roisnehamelinf.bsky.social & co discovered that Wadjet, an SMC complex involved in bacterial DNA immunity, performs some impressive molecular gymnastics 🤸‍♂️🤸‍♂️🤸‍♂️.

Check out the new paper: www.cell.com/molecular-ce...

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Oli Clarke @olibclarke.bsky.social · 3d

no wonder - the Fab-antigen interaction in that structure is only resolved at very low resolution, not at the level of sidechain detail. Probably the starting model is to blame...?

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Reposted by Oli Clarke

Alejandro Llorente, Ph.D. @llorentealejandro.bsky.social · 3d

1/9 🚀 Big news! As a result of 5 years of my PhD, building on a 30-year dream of my PI Dr. Nancy Carrasco, we think we've found a new way to treat cancer! We’ve released our preprint & I'm so excited to share this story! 🧵
www.biorxiv.org/content/10.1...
#Science #proteinengineering #proteindesing

Engineering substrate selectivity in the human sodium/iodide symporter (NIS)

Iodide (I-) uptake mediated by the Na+/I- symporter (NIS) is the first step in the biosynthesis of the thyroid hormones, of which I- is an essential constituent. NIS couples the inward transport of I-...

www.biorxiv.org

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Reposted by Oli Clarke

ttsukaza @ttsukaza.bsky.social · 4d

Our MurJ/LysM paper has been published in Science Advances.

Kohga et al., Sci. Adv. (2025).

This study elucidates, through cryo-electron microscopy, the mechanism by which the small bacteriophage-derived protein LysM inhibits the lipid II flippase MurJ.

t.co/u5ZibBF0kA

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Oli Clarke @olibclarke.bsky.social · 4d

Congrats!!! 🍾 🎉

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