Ernst Schmid

Identification of sporulation genes in Bacillus anthracis highlights similarities and significant differences with Bacillus subtilis How good is Bacillus subtilis as a model for the spore-forming pathogen Bacillus anthracis? Using high throughput genetics to identify B. anthracis sporulation genes and cytological analysis of the mu...

Fer’s tour de force in B. anthracis is out! Fer got Tn-seq running, built an ordered knockout library, defined all essential sporulation genes, and found a peptidoglycan deacetylase inhibitor critical for engulfment. Including our first one-by-all Alphafold screen! journals.plos.org/plosbiology/...

Rapid compensatory evolution within a multiprotein complex preserves telomere integrity Intragenomic conflict with selfish genetic elements spurs adaptive changes in subunits of essential multiprotein complexes. Whether and how these adaptive changes disrupt interactions within such comp...

How to keep in step when your (protein) partner speeds up…

Here we investigated the adaptive remodeling of a protein-protein interaction surface essential for telomere protection.

Congrats to whole team!

www.science.org/doi/10.1126/...

A metabolic atlas of mouse aging Pilley et al. describe how metabolite levels change in 12 organs from male and female mice across five ages, spanning adolescence to old age. They reveal that organs show distinct age- and sex-specific changes in metabolism. They also develop metabolic clocks that predict putative metabolic drivers of aging, including hydroxyproline.

Online now: A metabolic atlas of mouse aging

Protein domains have no single definition, so why stick to one segmentation? 🧩

Instead of forcing structures into rigid classifications, we built AFragmenter. It uses AlphaFold PAE networks for a tuneable approach to domain parsing.

You control the granularity. 👇
🔗 doi.org/10.1093/bioi...

Our lab is seeking a Postdoctoral Fellow. The position is intentionally broad, as we are looking for outstanding researchers from diverse scientific backgrounds to advance our understanding of cilia and ciliopathies: academicpositions.harvard.edu/postings/15526

No worries and valid point. I probably won’t be involved in future efforts but I know that Johannes is definitely looking to expand efforts. Happy to put you two in touch via email if you’d like.

Thanks! Through the NSF NAIRR pilot program we were paired with an industry partner to support our AI-related project. The program connected us with NVIDIA and they provided three months of access to a 256-GPU DGX cluster, which is where we ran all of the AlphaFold predictions.

Thanks Andrew!

Thanks Andreas!

Thanks Pedro! Our nomination procedure used evidence count from BioGRID as one of the features. We didn’t rely on it (or other dbs) exclusively because we wanted to preserve the ability to nominate interaction pairs that may have been missed by existing physical PPI databases.

Thanks to members of rhe @johanneswalter.bsky.social lab and our fantastic collaborators @alanbrownhms.bsky.social and Agata Smogorzewska, we experimentally verified several of these new PPIs. But don’t worry, there are plenty more to work on. Come explore the data and see what you find!

Proteome-wide in silico screening for human protein-protein interactions Protein-protein interactions (PPIs) drive virtually all biological processes, yet most PPIs have not been identified and even more remain structurally unresolved. We developed a two-step computational...

Thrilled to share that the final piece of my PhD work is now on bioRxiv! biorxiv.org/content/10.1... With support from @nvidia and the @NSF, we used AlphaFold to screen 1.6M+ protein pairs, revealing thousands of potential novel PPIs. All data can be viewed at predictomes.org/hp

The difference feels like it will be much more informative than overall values.

End-to-end protein design in the browser through evedesign. Generate and interactively explore designs in 2D/3D and export them as codon-optimized DNA. The underlying open source framework (released soon) is build to easily add new methods, more on that soon.
🌐 evedesign.bio

The Farnung Lab celebrates Martin Filipovski's thesis defense.

Martin Filipovski successfully defended his PhD thesis today! Congrats, Dr. Filipovski.

Just wanted to say that you making this MSA server available to the community is a true service to humanity. Thank you! Have you considered setting up a donation system? I expect many people would contribute!

If you use Boltz1/2, BioEmu, Chai1, or other MSA-dependent models, you’re likely using our ColabFold server. Please be considerate! Avoid large submissions across many IPs instead generate the MSA locally. Our server is an old-timer from 2014 and can’t handle that load.

YouTube video by MRC Laboratory of Molecular Biology Structure Prediction and Design using AlphaFold – Sami Chaaban

Great talk by @sami-c.bsky.social about the proper use and caveats of AlphaFold2/3 predictions, highly recommended to watch www.youtube.com/watch?v=z7vy...

Unexpectedly, @jurgjn.bsky.social found that running Alphafold3 predictions for protein interactions can yield ipTM scores that are more predictive of true interactions when run in pools of proteins instead of pairwise predictions. Presumably, this reflects some sort of "competition effect".

Folddisco finds similar (dis)continuous 3D motifs in large protein structure databases. Its efficient index enables fast uncharacterized active site annotation, protein conformational state analysis and PPI interface comparison. 1/9🧶🧬
📄 www.biorxiv.org/content/10.1...
🌐 search.foldseek.com/folddisco

Predictomes | AF3 ANALYSIS A free interactive resource for viewing predicted AlphaFold multimer structures for protein pairs in biological pathways.

Our AlphaFold 3 prediction analysis tool is now accepting the new version of the AlphaFold 3 server output files. Thanks to those who let me know about the output change and apologies for any inconvenience! predictomes.org/tools/af3/

Cyclic-di-AMP modulates cellular turgor in response to defects in bacterial cell wall synthesis - Nature Microbiology Brogan et al. uncover a signalling pathway in which levels of the nucleotide second messenger c-di-AMP increase in response to defects in cell wall synthesis. This regulatory pathway decreases turgor ...

Very happy to share that a large part of my thesis work is out today: B. subtilis uses the second messenger c-di-AMP to modulate its turgor pressure in response to the state of its cell envelope. www.nature.com/articles/s41...

EndoMAP.v1 charts the structural landscape of human early endosome complexes - Nature A study presents EndoMAP.v1, a resource that combines information on protein interactions and crosslink-supported structural predictions to map the interaction landscape of early endosomes.

Excited to share that our EndoMap project is now out! A fun collaboration with Miguel Gonzalez-Lozano from the @harperlabhms.bsky.social. Explore our #AlphaFold structural interactome of #XLMS complexes in endosomes-> endomap.hms.harvard.edu

and read about it here->
www.nature.com/articles/s41...

Last week I learned that all my NIH awards were terminated due to perceived acts of antisemitism by Harvard. My understanding (which may be incorrect) is that this has been extended to literally every grant to grad students, postdocs and faculty throughout the university.

What Happens When a Gene Quality-Control Mechanism Fails? Study solves riddle of how mutations in Integrator complex relate to neurodegeneration, cancer

Read all about Apoorva Baluapuri’s new work on Integrator (INT) in HMS News! @baluapuri.bsky.social @adelmanlab.bsky.social
tinyurl.com/y2fx22c2


🧬🎉Thrilled to share our new chromatin remodeling study! We reveal three states of human CHD1 and identify a novel "anchor element" that interacts with the acidic patch—conserved among remodelers. Our structures clarify mechanisms of remodeler recruitment! Link: authors.elsevier.com/a/1l2ik3vVUP...

Zero-shot design of drug-binding proteins via neural selection-expansion Computational design of molecular recognition remains challenging despite advances in deep learning. The design of proteins that bind to small molecules has been particularly difficult because it requ...

Super excited to share a new preprint from our lab on design of small-molecule binding proteins using neural networks! The paper has a bit of everything. A new graph neural network, new design algorithms, and experimental validation. www.biorxiv.org/content/10.1...
🧵🧪

ARMC1 partitions between distinct complexes and assembles MIRO with MTFR to control mitochondrial distribution ARMC1 partitions between distinct outer mitochondrial membrane complexes and the cytosol to control mitochondrial distribution.

How do cells achieve an optimal mitochondrial distribution? Excited to share a piece of this puzzle: www.science.org/doi/10.1126/...

🔬 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

The aPBP-type cell wall synthase PBP1b plays a specialized role in fortifying the Escherichia coli division site against osmotic rupture A multi-protein system called the divisome promotes bacterial division. This apparatus synthesizes the peptidoglycan (PG) cell wall layer that forms the daughter cell poles and protects them from osmo...

It has been coming a long way... happy to share our latest work with you: www.biorxiv.org/content/10.1...
Here, we show the importance of septal fortification by the Class A Penicillin Binding Protein, PBP1b, in E. coli and provide a molecular mechanism for this function. (1/12).