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Amelie Stein @amelierocks.bsky.social · 22h

Kiel

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Amelie Stein @amelierocks.bsky.social · 4d

Very similar experience moving to Spain 🇪🇸 (20 years ago, might have changed)

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Amelie Stein @amelierocks.bsky.social · 4d

I maintain that the most important is the coffee machine

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Reposted by Amelie Stein

Izzy Jayasinghe @ijayas.bsky.social · 4d

Ah, a classic moment of @nature.com recognizing the scientific contributions of both genders: man and machine.

Prof Anna Watts @profannawatts.bsky.social · 4d

Lol the Nobels can't even acknowledge women's contribution to discovery. But sure let's acknowledge The Machines.

Headline from an article in Nature this week that states "Prizes must recognize machine contributions to discovery. The future of science will be written by humans and machines together. Awards should reflect that reality."

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Reposted by Amelie Stein

Marcel Dickmanns | 🌿❄️🔬 @madic.bsky.social · 6d

You can get MSAs directly from AlphaFold DB now (alphafold.ebi.ac.uk). I also missed the FoldSeek implementation, which lets you search for structurally similar proteins direktly.

This saves some clicking around. Neat!

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Reposted by Amelie Stein

Andrew Iwaniuk @evoneuro.bsky.social · 4d

As I tell my students, if you arrived at a simple answer in biology you have done one of two things: arrived at the wrong answer or asked the wrong question

Claus Wilke @clauswilke.com · 6d

Biology is much more complicated than most non-biologists can imagine. And AI is not going to change this anytime soon.
blog.genesmindsmachines.com/p/we-still-c...

We still can’t predict much of anything in biology

Biology is hard. Yes, even for AI.

blog.genesmindsmachines.com

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Amelie Stein @amelierocks.bsky.social · 4d

Kindergarten teacher asks what I teach (biological sequence analyses), I try to explain.
She turns to the 3yo and asks „What do you want to be when you grow up?“

Prompt and confident answer: „A butterfly 🦋!“

Reposted by Amelie Stein

Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 6d

The proteasome-substrate-shuttle protein UBQLN2 contains—like other quality control system proteins—a long region devoid of lysine (a lysine desert)

Martin Grønbæk-Thygesen (from @rhp-lab.bsky.social) et al show that introducing K here causes ubiquitylation and degradation

doi.org/10.1101/2025...

Fig. 1 – UBQLN2 is a conserved lysine-depleted protein. (A) Sequence comparison of
UBQLN2 orthologs in the indicated species. Intrinsically disordered regions in human
UBQLN2 based on MobiDB are shown as a blue bar. The domain organization based on the
SMART database is marked. Lysine residues are marked as black squares. (B) ESM-2
predictions of all possible single amino acid substitutions of human UBQLN2 presented as a
heat map. The wild-type residues are marked in blue. ESM-2 scores close to zero (light
yellow colors) indicate that the amino acid substitution is compatible with the ESM-2
language model, whereas negative scores (dark orange colors) indicate that the variant is
incompatible with the ESM-2 model. The domain organization (based on SMART) is aligned
above the map. Note that substitutions to lysine or cysteine in general appear detrimental, in
particular downstream of the UBL domain. (C) The AlphaFold2 predicted structured of
human UBQLN2 (AF-Q9UHD9-F1) (left panel). The UBL domain is colored blue, and the
UBA domain is colored orange and the STI1 regions green. Zoom in on the UBL domain
(right panel) with the lysine residues highlighted as stick representations and colored based
on the relative accessible surface area (rASA, dark red exposed; grey, buried).

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Reposted by Amelie Stein

Elizabeth Wood, PhD @lizbwood.bsky.social · 8d

For every Nobel that goes to a criminally under-recognized woman scientist (Brunkow, Karikó), or fails to go (Candy Lee), a week of mourning and reform for an academic system wherein you can do Nobel-prize-worthy-work and still end up without a conceivable path to being a professor.

Nature @nature.com · 8d

BREAKING: The Nobel Prize in Physiology or Medicine has been awarded jointly to Mary E. Brunkow, Fred Ramsdell, and Shimon Sakaguchi "for their discoveries concerning peripheral immune tolerance"

Stay tuned for more.
#NobelPrize

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Amelie Stein @amelierocks.bsky.social · 8d

Fun & action the local science museum

#experimentarium

Small child standing by a goods transport model (essentially a very large rolling ball sculpture), next to a sign labelled København, putting orange balls onto the rails.

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Reposted by Amelie Stein

Irina Bezsonova @irinabezsonova.bsky.social · 11d

This October I’m drawing one molecule a day inspired by proteins in pdb @rcsbpdb.bsky.social

Day 2/31
Prompt WEAVE

N-terminal domain of a Fibrion - a building block of silk fiber produced by silkworms.

Pdb: 3UA0

Next prompt is CROWN and I would love your suggestions!

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Amelie Stein @amelierocks.bsky.social · 10d

Alternatively, we could just run a random number generator. Burns far less rainforest.

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Amelie Stein @amelierocks.bsky.social · 11d

Yes, that’s the poster child!

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Amelie Stein @amelierocks.bsky.social · 11d

Evolutionarily buffering of minor damage could be a good idea, to allow for intermediates along trajectories to other functions. Dan Tawfik looked into this trade-off between stability and evolvability quite a bit.

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Amelie Stein @amelierocks.bsky.social · 11d

Depending on the specific protein in question, if it has a dedicated transcription factor that senses whether its function/presence is needed, there could be dynamic regulation, but - as far as I know - this doesn't generally happen just for levels.

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Amelie Stein @amelierocks.bsky.social · 11d

I think, for protein stability (which I feel most qualified to comment on), the main proposed masking mechanism is that chaperones can help refold moderately affected proteins, so there is no apparent phenotype. Up to a certain level of damage, then it's down the degradation pathway.

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Amelie Stein @amelierocks.bsky.social · 11d

Ouch 😢 I’d guess it has been studied some, but not systematically enough yet to cross over to modellers?

Amelie Stein @amelierocks.bsky.social · 11d

Some interesting thoughts on the Perspective Harper Raiken and I wrote over the summer

Philip Ball @philipcball.bsky.social · 11d

We can identify genetic associations with disease, but the hard part is figuring out what effects the variants at those loci actually do, including how penetrant they are. This is hard. But one phrase in this piece struck me in particular... /1
www.science.org/doi/10.1126/...

Penetrance and variant consequences—Two sides of the same coin?

To get more out of genome sequences, the effects of variants need to be quantified

www.science.org

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Amelie Stein @amelierocks.bsky.social · 11d

and what isn’t, and why. I think e.g. organoid models can provide insight here.
This is a very mechanistic perspective, sequence models informed by evolution and mutagenesis may be able to tell whether a variant is likely detrimental (patient at risk?), just not why/how (treatment development). 4/4

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Amelie Stein @amelierocks.bsky.social · 11d

to problems with oxygen transport and blood flow. Can we model each of these layers and scales individually? Perhaps. And this is a very well-studied, monogenic case. For polygenic diseases or environmental factors, we’ll need to learn how to integrate them. What is buffered by dynamic regulation 3/

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Amelie Stein @amelierocks.bsky.social · 11d

point towards gaps in our understanding of biology. As for whether we can model it, to me it depends on whether we can model emergent properties. Take sickle cell anemia. Broadly, the extra bulge on the protein surface leads to stacking, which leads to distortion of red blood cells, which leads 2/

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Amelie Stein @amelierocks.bsky.social · 11d

Thank you! I would say that us protein people are aware that we can’t explain everything bottom-up from the molecular level. But there are some things we can explain, like loss of stability, and that can be helpful. Sometimes we turn it around & say that the effects observed that we can’t explain 1/

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Reposted by Amelie Stein

Dr. Jens Foell @jensfoell.de · Mar 23

I don’t know who wrote this, but it’s absolutely perfect

• X-Men is about civil rights. If you didn't get that, you didn't get X-Men.
• Black Panther is about civil rights. If you didn't get that, you didn't get
Black Panther.
• Captain America literally fought the Nazis. He is the embodiment of fighting the alt-right. If you didn't get that, you didn't get Captain America.
• The Empire in Star Wars is fascist. The Rebel alliance is Anti-Fascist. If you didn't get that, you didn't get Star Wars.
• The Punisher isn't meant to be a role model for police or armed forces.
So much so that the writers of The Punisher made him actively speak out against it in a comic. If you didn't get that, you didn't get The Punisher.
• Deadpool is queer. He's pansexual. Fact. If you didn't get that you didn't get Deadpool.
• Star Trek is about equality for all genders, races, and sexualities. As early as the mid-60s it was taking a pro-choice stance and defending women's right to choose. One of its clearest themes is accepting different cultures and appearances

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Amelie Stein @amelierocks.bsky.social · 11d

Congrats 🙌 🎉 🎓

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Reposted by Amelie Stein

Sarah Shammas @sarahshammas.bsky.social · 12d

Why are transcription factors disordered? Come join us in Oxford as a postdoc and we'll find out together!

Help publish 3 mature projects, AND develop cool new single molecule fluorescence binding assays!

biophysics
transcription
protein:DNA interactions

my.corehr.com/pls/uoxrecru...

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