De novo designed oligomers that respond to copper, small molecules, and phosphorylation... Using a single design strategy? 🧬⚙️ 🎉 Excited to share our new bioRxiv preprint—a collaboration between the Khmelinskaia, Correia, Schoeder and a Tinnefeld labs! www.biorxiv.org/content/10.6...

A generalizable interface-seeded framework for de novo design of functional oligomers

Protein oligomers are ubiquitous in biological systems and essential for function. However, the de novo design of oligomers that controllably assemble in response to exogenous stimuli remains challeng...

biorxiv.org

Our PhD Aanchal Mishra @origichals.bsky.social will defend this December. We'll be sad to see her go - she's been heart & soul of the team in many ways. Soon a highly recomm. *postdoc candidate* with good skills in protein biochem., crystal growth, ITC, advanced AlphaFold, passionate about science.

This is what accessible science looks like: lowering barriers, sharing knowledge, and enabling more people to participate in discovery.

Sergey Ovchinnikov@sokrypton.org · 2mo ago

New Experimental Google Colab Notebook now integrates AlphaFold3 with OpenFold3 and py2Dmol: colab.research.google.com/github/sokry... (1/3)

Crystallography’s first law: crystal beauty is inversely proportional to structural insight. Sad to see no diffraction of these crystals. P.S. First encounter with Eppendorf-shaped crystals. Natural selection has apparently been replaced by lab selection 😄

'If a control experiment fails, does that mean that the entire experiment is poorly designed and you must restart from scratch? Often, yes— but not always. I present five examples where failed control experiments triggered entirely new fields of research.' link.springer.com/article/10.1...

The controls that got out of control - EMBO Reports

EMBO Reports - When experimental controls go wrong, it does not necessarily mean your experiment is flawed. It might well be the first sign of something unexpected.

link.springer.com

Experimental ingenuity: The peak performance of our collective scientific brain cells under pressure- a highly sophisticated, temporarily engineered solution to prevent our 0.5 mL tubes from launching themselves off the rotator. Special thanks to panic n the last surviving fragment of creativity🤣🤣

You know the most destructive molecule for my experiments is Air? ITC thermogram shifts? Bubble. Gel refuses to run properly? Bubble. Crystallization ruined? Bubble. Mysterious signal artifacts? Also bubble. My troubleshooting career = fighting microscopic air pockets with a pipette tip. #origichals

Academia has many shades; today I’m thinking about one we don’t talk about enough: the life of a PI (coming from the perspective of a PhD student). It’s easy to assume that PhD/PostDocs do the heavy lifting of an entire project. But the reality is far more layered.

Days like these... Protein: expressed Transformation: done Cells: alive, thriving, judging Preculture: done Culture: done Pellet: secured like a tiny biological treasure Next day Lysis: done HisTrap: run… but, no protein!!! Gel: shows protein in the soluble extract Where's the protein, then?

To cleave or not to - especially for de-novo ones!?

Kelvin Lau @klausenhauser on 🙅‍♂️🐘🪡@klausenhauser.bsky.social · 4mo ago

Refined after adding the histidines, from both monomers of the assymetric unit. Very similar coordination spheres. If anyone is interested the tag is : GSGSHHWGSTHHHHHH. Dont ask me why it was designed that way 🙃 Im pretty sure the W is there to ensure absorbance at 280 nm

Why do intrinsically disordered proteins appear larger than they are in SDS-PAGE? We investigate how sequence properties affect SDS-PAGE mobility using synthetic IDRs. Conclusion: We need to consider both SDS binding and the compaction of protein-SDS complexes. www.biorxiv.org/content/10.6...

Our deepest fear is not that we are inadequate. Our deepest fear is that we are powerful beyond measure. It is our light, not our darkness that most frightens us. We ask ourselves, 'Who am I to be brilliant, gorgeous, talented, fabulous?' Actually, who are you not to be?

One of us is absolutely obsessed with capybaras. Another can’t stop talking about dachshunds. One lives and breathes anime. Another is powered entirely by romance novels. One expresses personality through funky socks. Another could survive on potatoes alone.

A gentle, fun reminder that science isn’t just about answers, but about the long, curious wandering that gets you there. Prof. Kleanthous shares his lab’s journey with warmth, making bacteriocins feel like companions along the way rather than just subjects of study.

Syma Khalid@sykhalid.bsky.social · 6mo ago

A gift of an article from the inimitable Colin Kleanthous as he says a moving farewell to his laboratory. A brave, unrepentant and scientifically brilliant journey is described - please have a read, friends. www.jbc.org/article/S002...

How does molecular valency shape condensate assembly and function? We used the CO2-fixing organelle in algae—the pyrenoid—to find out… 🧵 Preprint here!: www.biorxiv.org/content/10.6... @cellarchlab.com @phaips.vd.st @biologyatyork.bsky.social #Rubisco #PhaseSeparation #Condensates #Pyrenoid

Stop scrolling and post two characters that bring you happiness :)

a cartoon of a man and a white dog holding up sticks with squares on them

ALT: a cartoon of a man and a white dog holding up sticks with squares on them

media.tenor.com

Indie Book Spotlight@bookspotlight.bsky.social · 7mo ago

Stop scrolling and post two characters who bring you happiness.

Evolution’s cheat code in action: www.nature.com/articles/s41...

I updated ipSAE code to handle Boltz2 files properly -- non-standard chainIDs/order, PDB input as well as mmCIF; other pull requests. github.com/DunbrackLab/.... Also updated preprint--fixed Latin grammar error in title - very embarrassing and added new figure. www.biorxiv.org/content/10.1...

Roland Dunbrack 🏳️‍🌈@rolanddunbrack.bsky.social · 11mo ago

pip install ipsae from www.linkedin.com/in/ullah-sam... www.youtube.com/watch?v=A5ph... PyPI pypi.org/project/ipsae/ His github fork github.com/ullahsamee/I... My github github.com/DunbrackLab/... Paper www.biorxiv.org/content/10.1... For designed protein binders www.biorxiv.org/content/10.1...

Magic incoming from our team soon....

CBM CNRS UPR4301@cbm-upr4301.bsky.social · 8mo ago

And on December 15 @ 2 PM we will follow Lucija Mance

There are moments in life when certain people nearby just show up for you- no fanfare, no fuss, just pure goodness. And honestly? These people deserve a standing ovation, confetti cannons, and maybe even a parade.

Thrilled to share our PI’s new publication exploring filament ambition of FAM118A/FAM118B in NSMB. These proteins show remarkable self-assembly with clear implications for their biological roles, proving once again that structure n function go hand in hand or in this case, subunit by subunit.

Marcin J. Suskiewicz@msuskiewicz.eurosky.social · 9mo ago

Very happy to share our collaborative project on FAM118 proteins - noncanonical sirtuins that form filaments and process NAD in human and other vertebrate cells.

Science just pulled up a chair at the kitchen table: a new paper explores the physics behind droplet outbursts when slicing onions www.pnas.org/doi/10.1073/...

Grateful to be listed as an author in this insightful review. All credits to Marcin Sir for his generosity, considering my contribution was more of a cameo than a lead role.

Marcin J. Suskiewicz@msuskiewicz.eurosky.social · 9mo ago

SUMO interactions: the 1st of two reviews which Aanchal (@origichals.bsky.social), El Hadji, and I have recently written on non-covalent interactions of SUMO is now out. The 1st covers interactions with E1, E2, and deSUMOylating enzymes; the 2nd - on interactions with SIMs etc. - will appear soon.

Let's connct Biology to real life examples Cooperativity: Like applause spreading through a crowd Transient complexes: Like birds flying in formation, then dispersing Affinity: like gravity between planets (weak individually, but strong and inevitable when surfaces complement)

Amazing insights to the phosphorylation world

Miguel Correa@m-correa-m.bsky.social · 9mo ago

Hot off the press! Our paper, “Global comparative structural analysis of responses to protein phosphorylation”, is now out in Nature Communications! www.nature.com/articles/s41...

Beauty of academia- you spend your days with minds trying to understand a basic concept, seeking solutions and not working for profit. That quiet pursuit changes the air you breathe and, eventually, you.

As a PhD student, I've been buried in bits and bytes of structural biology and biochemistry for the past two years and yet honestly I feel like I know absolutely nothing. Take an amino acid residue, for instance.

Science literally got its own taste: doi.org/10.1063/5.02... Einstein would’ve loved this dish. Time, temperature, and relativity- all served al dente!

Phase behavior of Cacio e Pepe sauce

“Pasta alla Cacio e pepe” is a traditional Italian dish made with pasta, pecorino cheese, and pepper. Despite its simple ingredient list, achieving the perfect

doi.org

Trust me, success is finding a team with whom you can laugh with.

Alex Holehouse@alexholehouse.bsky.social · 10mo ago

Also needs to be said that (as some folks know) our software packages are named after birds, so while I was away, the lab filled my office with birds... ...but honestly... *very* tastefully. Will stay for the foreseeable future!

Cryo-EM captures the elusive moment when E1 hands off SUMO to E2- a molecular relay that’s been mostly guesswork until now. The structures reveal E1 doing dramatic shape-shifting to line up perfectly for the transfer, like enzyme origami in action.

Nature Structural & Molecular Biology@natsmb.nature.com · 10mo ago

New online: Cryo-EM structures reveal the molecular mechanism of SUMO E1–E2 thioester transfer