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Yousuf A. Khan

@yousufakhan.bsky.social

1.4K followers 250 following 40 posts

Group Leader @Stanford. RNA focused ML/AI, cryoEM/ET, and biophysics. Formerly:DeepMind AlphaFold,EvoscaleAI, Churchill Scholar@Cambridge_Uni & seen on Netflix

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Yousuf A. Khan @yousufakhan.bsky.social · Aug 27

I'm extremely thrilled to announce that I will be starting as a group leader at Stanford this upcoming fall! My lab will be studying how RNAs exert themselves in the cell to induce a multitude of biological phenomena using ML, cryoEM/ET, and biochemistry!

www.yousufakhan.com

Yousuf A. Khan (YAK) Lab - RNA Research at Stanford University

Yousuf A. Khan (YAK) Lab - Studying RNA folding, interactions, and cellular effects using Molecular and Cellular Physiology, Structural Biology, and Machine Learning at Stanford University

www.yousufakhan.com

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Yousuf A. Khan @yousufakhan.bsky.social · Aug 27

Excited to collaborate and have people join us! Please checkout the lab website above if you are interested!

Yousuf A. Khan @yousufakhan.bsky.social · Aug 27

Yousuf A. Khan (YAK) Lab - RNA Research at Stanford University

Yousuf A. Khan (YAK) Lab - Studying RNA folding, interactions, and cellular effects using Molecular and Cellular Physiology, Structural Biology, and Machine Learning at Stanford University

www.yousufakhan.com

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Reposted by Yousuf A. Khan

Ahmad Jomaa @jomaalab.bsky.social · Aug 1

Check out our new preprint on the discovery of a molecular switch in NAC that mediates nascent chain sorting on the ribosome and prevents mitochondrial protein mistargeting by SRP. A great collaboration with the Shan Lab @Caltech and the Qi Lab @UVA: www.biorxiv.org/content/10.1...

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Yousuf A. Khan @yousufakhan.bsky.social · Jul 29

Don’t leave us hanging Hiten!

Reposted by Yousuf A. Khan

Alex Rubinsteyn @alexr.bsky.social · Jul 23

Going deep on 2A peptides:

www.cell.com/cell-reports...

(Trying to pick between GSG:T2A, GSG:P2A, and furin site:GSG:T2A)

Systematic identification and characterization of eukaryotic and viral 2A peptide-bond-skipping sequences

Rao et al. identified thousands of previously unknown 2A peptides across both viruses and eukaryotes using an HMMER analysis. The authors further identified a unique class of 2A peptides, class B, who...

www.cell.com

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Reposted by Yousuf A. Khan

Sergey Ovchinnikov @sokrypton.org · Jul 22

PSA = Google Colab Pro free for one year for academic use (US only):
blog.google/outreach-ini...

New Google Colab features for higher education

Google Colab offers free Colab Pro for students, interactive slideshows and AI controls in notebooks.

blog.google

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Reposted by Yousuf A. Khan

Nikolai Slavov @slavov-n.bsky.social · Jul 9

Key numbers in cell biology

Having a sense of scale helps to think more rigorously and realistically about biological systems.

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Reposted by Yousuf A. Khan

Nature Structural & Molecular Biology @natsmb.nature.com · Jul 3

ICYMI: New online: SNARE disassembly requires Sec18/NSF side loading

SNARE disassembly requires Sec18/NSF side loading

Nature Structural & Molecular Biology, Published online: 02 July 2025; doi:10.1038/s41594-025-01590-wKhan et al. show that Sec18 uses both D1 and D2 AAA+ rings cooperatively, opening them laterally for SNARE substrate loading and for subsequent release of SNAREs.

go.nature.com

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Reposted by Yousuf A. Khan

Hiten Madhani @hitenmadhani.bsky.social · Jul 2

Cool paper on bacterial amyloids as protection from predatory bacteria from the Whitely lab at CU Boulder.

There are predatory fungi, so one wonders if a similar system exists in eukaryotes.

www.nature.com/articles/s41...

Functional amyloid proteins confer defence against predatory bacteria - Nature

Escherichia coli uses curli fibres, oligomers of the functional amyloid CsgA, as a barrier to protect against the predatory bacteria Bdellovibrio bacteriovorus and Myxococcus xanthus in a mechanism th...

www.nature.com

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Yousuf A. Khan @yousufakhan.bsky.social · Jul 2

Thus, any kind of SNARE can be processed universally by this single molecule machine. Check out the paper for more in-depth structural work! (5/5)

Yousuf A. Khan @yousufakhan.bsky.social · Jul 2

Combining in-vivo mass-spec, single molecule FRET, and time resolved cryoEM, we were able to determine that this NSF/Sec18 ring actually splits itself open from the side to accomodate SNAREs, thus completely bypassing any substrate topology issues! (4/5)

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Yousuf A. Khan @yousufakhan.bsky.social · Jul 2

The complex that recycles these SNAREs is called NSF/Sec18. However, our mehanistic understanding of how these complex SNARE proteins are pulled through the NSF/Sec18 complex is poor. SNAREs are like a knotted thread that must somehow be threaded by a NSF/Sec18 needle (3/5)

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Yousuf A. Khan @yousufakhan.bsky.social · Jul 2

SNARE proteins are the engines for membrane fusion; they cause neurotransmitters to be released in a synpatic cleft all the way to the relase of hormones. After these SNAREs perform their job, they must naturally be recyled and prepared for additional rounds of fusion (2/5)

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Yousuf A. Khan @yousufakhan.bsky.social · Jul 2

Sharing some of my PhD work that just came out today.

TLDR; We found a universal mechanism for all the many kinds of SNAREs are processed and recycled by a single molecular machine that is conserved in all eukaryotic life as we know it (1/5)

www.nature.com/articles/s41...

(1/5)

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Reposted by Yousuf A. Khan

Chris H. Hill @chillzaa.bsky.social · Jun 20

I'm thrilled and honoured to receive the 2025 Lister Prize, along with seven other fantastic biomedical scientists 🔬🦠🧬

This award will enable us to determine high-resolution structures of viral protein synthesis inside infected cells

The Lister Institute of Preventive Medicine @thelisterinstitute.bsky.social · Jun 19

We are very proud to introduce our brand new 2025 #ListerFellows! This year there are eight Prize recipients. lister-institute.org.uk/a-warm-welco...

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Reposted by Yousuf A. Khan

Oli Clarke @olibclarke.bsky.social · Jun 12

1/x New story - the structure of the Vault cap, at 2.3Å! Matching a beautiful preprint from @sjorsscheres.bsky.social, we show that the cap of the vault particle has C13 symmetry, in contrast to the 39-fold symmetry of the body. Study lead by talented postdoc @huanli00.bsky.social from my group! ⬇️

At left, a reconstruction of the vault cap with C39 symmetry imposed; at right, the reconstruction after identifying the correct symmetry, with the three non-equivalent protomers highlighted.

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Reposted by Yousuf A. Khan

Lena Steckelberg @lenasteckelberg.bsky.social · Dec 20

Hi Bluesky, just in time for the holidays I am excited to share the latest pre-print from my group! We solved the 3D structure of a mysterious viral RNA that resists degradation by host nucleases. A short 🧵 &link below – please also check out the full video! #RNA #RNAbiology #RNASky #lovevirology

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Reposted by Yousuf A. Khan

Gina El Nesr @ginaelnesr.bsky.social · May 12

someone said we need a meme

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Yousuf A. Khan @yousufakhan.bsky.social · May 10

The structure of the human sweetness receptor bound to sucralose, and aspartame!!! Who will design the protein binder that mimics this conformation? Protein sweetneer??

www.cell.com/cell/fulltex...

The structure of human sweetness

A single taste receptor initiates our reactions to both sugars and artificial sweeteners, triggering a signaling process that drives our intense attraction to sweet foods. Single-particle cryo-EM reve...

www.cell.com

Reposted by Yousuf A. Khan

Arne Elofsson @bioinfo.se · May 5

In this evaluation of AlphaFold3 (and other methods), we show that (i) accurate predictions are limited to RNA structures/complexes with structural similarity to PDB and (ii) that current methods are bad at estimating the accuracy of the predictions. www.biorxiv.org/content/10.1...

Limits of deep-learning-based RNA prediction methods

Motivation: In recent years, tremendous advances have been made in predicting protein structures and protein-protein interactions. However, progress in predicting the structure of RNA, either alone or...

www.biorxiv.org

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Reposted by Yousuf A. Khan

Grigorieff Lab @UMassChan and @HHMI @grigoriefflab.bsky.social · Mar 31

www.biorxiv.org/content/10.1...

NEW PREPRINT ALERT!
Thanks to all involved!

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Reposted by Yousuf A. Khan

Juan S. Bonifacino @juanbonifacino.bsky.social · Apr 13

Our lab at the NIH (Bethesda, MD) is looking for postdoctoral fellows to join our team studying the molecular mechanisms of protein trafficking and their links to neurodevelopmental disorders starting on or after 10-1-2025. Send your application to [email protected]. Please share and repost!

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Akshay Agrawal @akshaykagrawal.bsky.social · Apr 10

🚀 We achieved a big milestone today: marimo just crossed 12200 GitHub stars — crossing Jupyter notebook, too.

We launched marimo to the public just over a year ago. People are clearly hungry for a better environment for working with data, and we have a lot more planned still.

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Reposted by Yousuf A. Khan

Haselbach Lab @haselbachlab.bsky.social · Apr 9

New Preprint: We have solved the structure of the proteasome in complex with two different ubiquitin chains: www.biorxiv.org/content/10.1... This work is spearheaded by PhD Student Sascha Amann
Let me walk you through it 🧵 1/9

Structural basis for the ubiquitin chain recognition of the human 26S proteasome

Proteasomal degradation is a fundamental process for all eukaryotic life. A protein destined for degradation is first tagged with a polyubiquitin chain, which is selected by the proteasome. Different ...

www.biorxiv.org

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Yousuf A. Khan @yousufakhan.bsky.social · Apr 9

A 100 BILLION protein language model has dropped...

www.nature.com/articles/s41...

xTrimoPGLM: unified 100-billion-parameter pretrained transformer for deciphering the language of proteins - Nature Methods

xTrimo protein general language model (xTrimoPGLM) is a unified pretraining framework and foundation model designed for various protein-related tasks, including protein understanding and generation or...