Kiarash Jamali

Could lithium stave off Alzheimer’s disease? The metal is depleted in brains of people with disease and can reverse memory symptoms in mice, new study shows

Researchers found that low lithium levels are linked to Alzheimer's disease in humans, and restoring it can reverse cognitive decline in mice. For a field still searching for cure, this paper may offer a clever new approach 🧠

Read more about it in @science.org
www.science.org/content/arti...

Glowing E. coli bacteria in green and blues on a background of DNA bases

Rewriting the language of life: Jason Chin’s group in the LMB’s PNAC Division have synthesised E. coli with just 57 codons instead of the usual 64.
Syn57 required 101000+ codon changes & represents a bold step towards programmable life.
Read more: www2.mrc-lmb.cam.ac.uk/syn57-repres...
#LMBResearch🧪

Good luck Martin! I’m sure you will do great 😊

I am super excited to announce that I will be starting my lab at the Department of Pharmacology of the University of Zurich in Switzerland next year!

Very excited about our latest all-atom generative model proteina, check out the project page (research.nvidia.com/labs/genair/...) and stay tuned for the code release soon!

You designed binders for your favourite protein and wish there was a way to experimentally screen them within 24h w/ only a set of pipettes and a plate reader?

Check out our Cell-Free 2-Hybrid approach (CF2H)

Full post: tinyurl.com/48cz5nb6

Preprint: www.biorxiv.org/cgi/content/...

Hi Randy, sorry about that. This should work: openreview.net/forum?id=8tQ...

Our entrance into protein design! Inverse folding steered by external sources of information, and for multiple conformations. By the amazing @kaiyi94.bsky.social and @kjamali.bsky.social!
Download our code and try it yourself. 🥳

Thank you so much Randy 😊 It was lots of fun

Many congratulations to Dr Kiarash Jamali @kjamali.bsky.social for successfully defending his PhD thesis today! 🥳 Also many thanks to Jonas Adler and Randy Read for examining him. I expect great things from Dr Jamali in his career, so do keep an eye on him. #ModelAngelo

Temporal and spatial coordination of DNA segregation and cell division in an archaeon. Cells must coordinate DNA segregation with cytokinesis to ensure that each daughter cell inherits a complete genome. Here, we explore how DNA segregation and division are mechanistically coupled in ar...

We are excited to share our preprint describing how Sulfolobus cells coordinate DNA segregation with cell division! In eukaryotes this type of regulation involves checkpoints and CDK-cyclins. But how does this work in archaea? This is the question we ask in our paper: www.biorxiv.org/content/10.1...

LocScale-SURFER is now also available for quick install via the ChimeraX toolshed:

cxtoolshed.rbvi.ucsf.edu

Adapting ProteinMPNN for antibody design without retraining The neural network ProteinMPNN designs protein sequences capable of folding into predefined tertiary structures and quaternary assemblies. It has become widely used due to its high success rates when ...

"Adapting ProteinMPNN for antibody design without retraining"

Our several-years-old fix to ProteinMPNN's tendency to make weird antibody CDR sequences is finally preprinted

1/5: Over the last few months, I have been working on an update for the #FollowRelionGracefully dashboard, which offers improved real-time job previews for #cryoEM #Relion jobs.

AFESM: a metagenomic guide through the protein structure universe! We clustered 821M structures (AFDB&ESMatlas) into 5.12M groups; revealing biome-specific groups, only 1 new fold even after AlphaFold2 re-prediction & many novel domain combos. 🧵
🌐 afesm.foldseek.com
📄 www.biorxiv.org/content/10.1...

We are looking for a postdoctoral fellow to join us to explore telomerase regulation by histones. Please get in touch if this may interest you.

Postdoc @emma.sedivy.bsky.social determined the structure of the Neck complex that joins the capsid head to the tail. We only knew the identity of 4 out of 8 of the proteins in the Neck, but we were able to identify the remaining 4 using ModelAngelo by @kjamali.bsky.social. /3

Meme describing types of headaches, with the most all encompassing headache being the stress of holding copious amounts of DNA in a phage head.

Did you know that there is so much DNA packed inside a phage capsid that the pressure is 10X higher than in a bottle of champagne? In our latest preprint, we wondered how that is contained in a phage that lives at extremely high temperatures. /1
www.biorxiv.org/content/10.1...

Shigella flexneri evades LPS ubiquitylation through IpaH1.4-mediated degradation of RNF213 - Nature Structural & Molecular Biology Naydenova, Boyle and Pathe et al. report that Shigella uses the ubiquitin E3 ligase IpaH1.4 to evade lipopolysaccharide ubiquitylation in infected cells by degrading the host E3 ligase RNF213. Using c...

RNF213, a host E3 ligase, ubiquitylates LPS to mark cytosol-invading bacteria for autophagy. But how do cytosol-adapted bacteria escape? We found that Shigella's E3 ligase IpaH1.4 blocks LPS ubiquitylation by degrading RNF213 via the proteasome.
www.nature.com/articles/s41...

Comparison of Salmonella and Shigella host cell invasion. Salmonella are targeted by the host E3 ligase RNF213, which ubiquitylates bacterial lipopolysaccharide (LPS), marking bacteria for autophagic destruction. Shigella employs its effector proteins IpaH1.4 - an E3 ubiquitin ligase itself - to ubiquitylate RNF213, leading to its proteasomal degradation and thus preventing the host from tagging Shigella for destruction.

Cryo-EM structure showing how the leucine-rich repeat (LRR) domain of IpaH1.4 binds to the RING domain of RNF213

How do cytosol-invading bacteria evade LPS ubiquitylation by the host's defence machinery?

@felixrandow.bsky.social's group determined that Shigella flexneri uses IpaH1.4 to degrade the LPS ligase RNF213, inhibiting the cell's ubiquitylation abilities.
Read more: tinyurl.com/3y4kv2bp

#LMBResearch🧪

This has been a long journey, but it's now out in final form. @kjamali.bsky.social

academic.oup.com/bioinformati...

🔬 New from the Farnung Lab: We established a fully in vitro reconstituted chromatin replication system and report the first cryo-EM snapshots of the human replisome engaging nucleosomes. Brilliant work by @felixsteinruecke.bsky.social with support from @jonmarkert.bsky.social! tinyurl.com/replisome

saw this piece being shared around on the bird site and sharing it here cuz it's so good genomebiology.biomedcentral.com/articles/10....

Excited to share our new preprint on co-transcriptional splicing! U1 snRNP is recruited to RNA polymerase II through multiple interaction sites, with elongation factor SPT6 binding directly to the U1 snRNP protein.

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

#cryoEM #transcription #splicing

Woohoo! Such awesome structures 😮

In a new Science study, cryo–electron tomography captures the in-cell architecture of the mitochondrial respiratory chain, illuminating how the coordinated action of molecular machines drives life’s fundamental energy conversion.

Learn more in this week's issue: scim.ag/3FA3Ygq

Thrilled to share the structure of dimerised human PINK1 docked to an endogenous translocase array on the mitochondrial surface, composed of two TOM complexes, bridged by a VDAC2 dimer! Published today in Science www.science.org/doi/10.1126/...

@wehi-research.bsky.social @komanderlab.bsky.social

Our preprint is now published www.science.org/doi/10.1126/...

Did you know that two jumping sequences (LINE-1 and Alu) make up nearly 30% of our genomes? Ever wonder how they jump into new genomic sites? We have some exciting discoveries to share new in @science.org on the structural mechanisms of LINE-1 retrotransposition (aka jumping 🧬➡️🧬) 🧪 #ScienceResearch