Marcin J. Suskiewicz

Mapping the yeast atructural interactome with AlphaFold3: an open call for collaboration We are excited to announce the early-stage release of our S. cerevisiae  structural interactome mapping project. Using AlphaFold3 (AF3), w...

We have started a project trying to predic the interactions/structures of all yeast protein pairs using an AlphaFold pooling approach. We are making the current dataset open and we welcome collaborations.
www.evocellnet.com/2026/03/mapp...

Exapted CRISPR–Cas12f homologues drive RNA-guided transcription - Nature Specialized σ factors interact with nuclease-dead, CRISPR–Cas12f proteins to form potent, RNA-guided gene activation systems that function independently of fixed promoter motifs.

Just amazing what evolution can come up with. Naturally occurring nuclease deficient Cas12 family members use gRNAs to bind DNA and recruit sigmaE family members that drive txn initiation proximally. 2 papers! 1- describes 2- structure!
www.nature.com/articles/s41... www.nature.com/articles/s41...

Stunning new structural analysis and mechanism for Tmn anti-phage defense by @fnobrega.bsky.social

www.biorxiv.org/content/10.6...

A pharmacological modality to sequester homomeric proteins - Nature Chemical Biology Polymerization-inducing chimeras are a novel bifunctional modality that uses protein symmetry to sequester targets by forming insoluble supramolecular assemblies. This approach overcomes reliance on a...

Polymerization-inducing chimeras (PINCHs) are a novel bifunctional modality that sequesters target homodimers in a polymeric state, thereby inhibiting their function

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

Image of FAF2's predicted helical domain interacting with the UFD1 UT3 domain. Next to this are similar images showing the predicted binding of de novo designed protein binders to the same region. Above is a sequence alignment indicating the key residues involved in the interaction.

🚨⚠️ New Preprint Alert! ⚠️ 🚨
www.biorxiv.org/content/10.6...

Screening p97 cofactors, @prithadg.bsky.social identified FAF2 as the strongest activator of the p97-UFD1-NPL4 complex. Leveraging her mechanistic descoveries, we designed 𝘥𝘦 𝘯𝘰𝘷𝘰 binders that could also enhance p97 substrate unfolding.

Degrons and degradation signals beyond short linear motifs - Nature Chemical Biology Degrons are degradation signals in target proteins to direct recognition and degradation by the ubiquitin–proteasome system. Wang et al. introduce degrons of different types, with an emphasis on high-...

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

Papers are like buses... You wait for ages, then two come along at once.

Huge congrats to @bornanovak.bsky.social and @jefflotthammer.bsky.social for pushing and driving every aspect of this work, preprinted ~1 year ago to the day (Friday before BPS), now published!

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

A mathematical exploration of some increasingly worrying trends in peer review. Some sensible recommendations, including encouraging AEs to STOP sending out just about everything for re-review after the first round. It's become systematic and annoying. Editors should make decisions.

A sequel to 'Groovy science'...

Except literally every data analysis or model I've ever asked AI to build has contained at least one error: www.nature.com/articles/d41...

Common response: "But someone just needs to give AI detailed instructions..."

But who is the "someone" in that sentence? And how did they get their expertise?

the estimated 1 billion biochemical reactions that occur every second in every cell of our bodies 🤯

Since last year, I've been making a RELION GUI that supports viewing, navigating and running jobs in a way completely compatible with the original RELION pipeline. Now it's working nicely for both SPA and tomography! Please try it out - github.com/hanjinliu/hi...

Unbalanced chromatin binding of Polycomb complexes drives neurodevelopmental disorders Borges, González-Blanco, Arigela, et al. report new missense mutations in the PRC1 genes RNF2 and RING1 in individuals with neurodevelopmental disorders. Functional dissection of a deleterious variant reveals that balanced co-recruitment of Polycomb complexes to chromatin is essential for proper neurogenesis and for normal brain function and behavior.

Unbalanced chromatin binding of Polycomb complexes drives neurodevelopmental disorders

Ancient co-option of LTR retrotransposons as yeast centromeres - Nature Evolutionarily related ‘proto-point’ centromeres providing resolution to the evolutionary origins of point centromeres are identified in yeast, and comparison shows they evolved in an ancestor with re...

Our paper is now out in Nature:

“Ancient co-option of LTR retrotransposons as yeast centromeres”

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

A short thread on how retrotransposons helped give rise to yeast point centromeres.

1/14

Bacteria deliver a microtubule-binding protein into mammalian cells to promote colonization Pathogenic Bordetella bacteria use protein adhesins to infect the ciliated respiratory epithelia of vertebrate hosts. In this work, we show that the filamentous hemagglutinin FhaB adhesin of Bordetell...

Just published in @science.org with related Perspective by Françoise Jacob-Dubuisson.
Bacteria deliver a microtubule-binding protein into mammalian cells to promote colonization | Science www.science.org/doi/10.1126/...

Ribosomal RNA expansion segments mediate the oligomerization of inactive animal ribosomes Cells down-regulate protein synthesis when stressed to conserve energy and shift resources toward repair. We found that in some mammalian cells, including neurons, stress also resulted in the formatio...

Out now in @science.org
Ribosomal RNA expansion segments mediate the oligomerization of inactive animal ribosomes | Science www.science.org/doi/10.1126/...

#microsky
Massive update of preprint with @polardlab.bsky.social!
Bacteria have evolved two systems to recombine extracellular DNA
www.biorxiv.org/content/10.1...
Kudos to lead authors Léo Hardy, Violette Morales and Clothilde Rousseau, and to outstanding Dalia's lab and @epcrocha.bsky.social
🧵⬇️

... modeling E2 with 2×Ub (one backside, one covalently linked either open or closed) could avoid forcing AF to choose between the two. Just a slight suggestion that came to my mind, @rolanddunbrack.bsky.social . But a very nice and useful work and a nice read!

One comment - it seems to me that the models where the Ub C-terminus is far from the catalytic Cys may represent Ub docked noncovalently on the E2 backside. Since most E2s can bind a second Ub there, compatible with the covalent Ub in a closed/open conformation...

Just finished reading this pre-print. A really nice computational exploration of RING_E3–E2 pairs, and whether AlphaFold might help to predict which RING E3s go with which E2s and model the structures of the resulting complexes.

🎉🎉 Our paper on temperature-dependent protein control using AsLOV2 variants is now published at @natchembio.nature.com: www.nature.com/articles/s41... including some new insights from extend variant characterizations.

AlphaFold Database welcomes community datasets Latest AlphaFold Database update adds high-value datasets for microbial and viral proteins, generated by specialist communities

Delighted to see over 17 million new protein structure predictions from novel proteins in AllTheBacteria are now integrated into the AlphaFold Database at @ebi.embl.org !
Huge work from @gbouras13.bsky.social @oschwengers.bsky.social and friends to generate these.

www.ebi.ac.uk/about/news/u...

A very interesting thread!

Engineering intrinsically disordered regions for guiding genome navigation Liu et al. design and test synthetic IDRs based on simple design rules derived from mutation-based analysis of 25 native TF IDRs. They show that hydrophobic amino acids endow activity, acidic ones pre...

Engineering intrinsically disordered regions for guiding genome navigation: Molecular Cell www.cell.com/molecular-ce...

We posted a biorxiv preprint on structural bioinformatics, AlphaFold modeling & machine learning on predicting specificity of E3 ligase ring domains for different E2 enzymes. 1/4

Preprint: www.biorxiv.org/content/10.6...

Models/data (UbiqCore website): dunbrack.fccc.edu/ubiqcore

Engineering a human-based translational activator for targeted protein expression restoration Abstract. Therapeutic modalities to programmably increase protein production are in critical need to address diseases caused by deficient gene expression v

Excited to share our new work in @narjournal.bsky.social ! We engineered a human-based translational activator that rescued phenotypes in a Dravet syndrome mouse model by boosting protein expression from haploinsufficient genes. A thread on targeting translation 🧵
academic.oup.com/nar/article/...

Join us in Palermo!
FEBS Workshop Protein Termini 2026: the power of protein termini across bacteria, plants, and animals—from ribosome biology to proteostasis and applications. Deadline: 3 March 2026
proteintermini.org/meeting
#ProteinTermini #Proteostasis #FEBS #EMBO @iubmb.bsky.social

Human DNA polymerase η is regulated by mutually exclusive mono-ubiquitination and mono-NEDDylation Abstract. DNA polymerase eta (Pol η) is a Y-family translesion polymerase responsible for synthesizing new DNA across UV-damaged templates. It is recruited

Pleased to share that our latest paper is out now in NAR. We demonstrate that Pol η binds to and is a substrate of NEDD8. @ncmoreno.bsky.social @txelah.bsky.social @barneslab.bsky.social @irinabezsonova.bsky.social
academic.oup.com/nar/article/...

🧬 Molecular glue discovery at scale

CeMM, @aithyra.bsky.social & @scripps.edu have developed a scalable method for molecular glue discovery. Their approach identified a selective degrader of ENL, a key driver of aggressive #leukemia.

➡️ More: bit.ly/4re95Wu
📄 Paper: bit.ly/4r404iy

COMBINE-lab - The skeptic’s guide to generative AI assisted coding An easy-to-use, flexible website template for labs, with automatic citations, GitHub tag imports, pre-built components, and more.

I’ve written a post about my recent experiences (successes) with AI coding models; the experiences that caused me to re-evaluate my initial judgements, the surprise I had at what can be accomplished, & some fears I have about these tools. Discussion welcome! combine-lab.github.io/blog/2026/02...