Virus Addict

Happy to share our lab's recent #cryoEM studies that show how a SPIN90 dimer activates Arp2/3 complex to form either uni or bidirectional actin filaments. Congrats🎉👏 @justusfrancis.bsky.social @achyutha-kp.bsky.social @tejashyamk.bsky.social @sridharskulkarni.bsky.social @kiranvyshnav.bsky.social

In situ cryo-ET redefines HPV disassembly and transport paradigms pubmed.ncbi.nlm.nih.gov/40949969/ #cryoEM

Improved cryo-EM reconstruction of sub-50 kDa complexes using 2D template matching www.biorxiv.org/content/10.1101/2025.09.11.675606v1 #cryoEM

Epstein–Barr virus exploits desmocollin 2 as the principal epithelial cell entry receptor | @natmicrobiol.nature.com

sco.lt/6i4kd6

Genetic tuning of retinal ganglion cell subtype identity to drive visual behavior Nature Communications - This study reveals that graded expression of the transcription factor BRN3B fine-tunes the identity and function of melanopsin-expressing ipRGC subtypes in the retina....

Our paper is out today! In @tiffmschmidt.bsky.social lab, we identified a single transcription factor, BRN3B, that shapes multiple, key features that define diverse ipRGC subtypes🧬👁️🐭

Novel insights into the molecular underpinnings of islet cell dysfunction in #T1D highlighting pathways that may be leveraged to preserve residual β-cell function and modulate α-cell activity @bcellorg.bsky.social www.jci.org/articles/vie...

A modular platform for bioluminescent RNA tracking - Nature Communications Studying RNA dynamics in vivo often relies on fluorogenic approaches, but these can be hampered by factors such as limited sensitivity and sample autofluorescence. Here, the authors describe an ultrasensitive platform for RNA imaging, which features RNA tags that recruit light-emitting luciferase fragments.

Great talk by Jenn Prescher at the Virtual @chembiotalks.bsky.social. She talked about her group's many contributions to expanding the toolbox of bioluminescent tools. Cool insights into tracking RNA. www.nature.com/articles/s41...
#ChemBio #ChemSky

SRBD1, a highly conserved gene required for chromosome individualization Raaijmakers et al. study S1 domain containing protein 1 (SRBD1), a previously uncharacterized essential protein. The loss of SRBD1 results in a complete failure in anaphase chromosome segregation due to defects established in prophase. The phenotype…

SRBD1, a highly conserved gene required for chromosome individualization

Screening de novo designed protein binders in unpurified lysate using flow induced dispersion analysis Computational protein design can create binders against targets of interest, but identifying binders with sufficient affinity still requires biochemical screening of many designs. In this work, we te....

Experimental verification is increasingly the bottleneck in protein design projects.

In this paper, we develop a new mini-binder screening pipeline based on the microfluidic sizing technique called flow-induced dispersion analysis (FIDA).

doi.org/10.1002/pro....

Figure 3 from the paper with the caption: "Role of machine learning in de novo design of IDRs. (A) Machine-learning models can be trained on diverse data sources, from molecular dynamics simulations to annotations of cellular localization and protein structures from the Protein Data Bank. (B) Often implemented as neural networks using sequence-encoded features as input, these models can initially be trained on a limited region of sequence space as surrogate models. Through active learning, additional simulations are performed during the design campaign to generate new data, and the surrogate model is retrained on the expanded dataset to progressively improve its accuracy. (C) Machine-learning models have been developed to predict biophysical observables, biological annotations, and protein structures. When combined, machine-learning models can be used to identify a set of sequences that strike a trade-off between multiple design objectives, defining a Pareto front."

New review on computational design of intrinsically disordered proteins 🖥️🍝 by @giuliotesei.bsky.social @fpesce.bsky.social & 👴

doi.org/10.48550/arX...

Type VI inhibitor targeting both the catalytic site and the tunnel of Autotaxin (ATX). PDB ID: 9FXW

🚨New Article Out!!

📢 In our latest work, we propose a Three-Point Lock binding mode for ATX inhibitors 🔒

🚀 This approach may represent the final piece in the puzzle of known binding mode types — and could have therapeutic relevance

♥️ Thanks for your support
Read more here: doi.org/10.1016/j.bm...

Excited to share our latest work in expanding AI-based protein design into targeting PTMs! I’m particularly excited in this work as there is so much we don’t know about PTMs despite their central role in signaling and hopefully we can start to decode their rules and functions.

ProteinDJ logo

I am thrilled to release ProteinDJ: a high-performance and modular protein design pipeline. Our open-source workflow incorporates #RFdiffusion, #ProteinMPNN, #FAMPNN, #AlphaFold2 and #Boltz-2. It is a fast, free, and fun way to design proteins (1/5)
doi.org/10.1101/2025.09.24.678028 #proteindesign

Design of a potent interleukin-21 mimic for cancer immunotherapy A de novo IL-21 mimic, 21h10, exhibits improved stability and potent antitumor activity in vivo compared with native IL-21.

David Baker & colleagues develop an #IL21 mimic (21h10) that is more stable & shows x-reactivity against both human & murine #IL21R. 21h10 promotes potent antitumor responses in mice and in human #melanoma tumor explants, expanding low-affinity CD8 #TCells & #TH1 cells & reducing #Tregs in #tumors!

GSK-3 and BCL-XL inhibition mitigates the competitive advantage of APC-mutant colorectal cancer cells - Oncogenesis Oncogenesis - GSK-3 and BCL-XL inhibition mitigates the competitive advantage of APC-mutant colorectal cancer cells

🚨 New strategy against colorectal cancer!

Dual GSK-3 & BCL-XL inhibition kills APC-mutant cells in organoid models, tipping the balance towards healthy cells—a promising way to halt early tumor growth 💪🧪

➡️Read more: www.nature.com/articles/s41...

A metallic arm holding a protein, simulating a GPI-anchored protein attached to the surface of a membrane.

📢 Excited to announce that our Opinion paper on GPI-anchored proteins is now Published! 🎉

👀 If you're working in this field, be sure to check out our paper — we've highlighted some truly outstanding questions on the topic! ⚠️

www.cell.com/trends/cell-...

Part of something that we have been working on for a while-A 3.1 Å map of a flexibly tethered 38 kDa domain. Hopefully preprinted soon along with a few other structures. #CryoEM

I am excited to share our new preprint on the CAGE complex, a mysterious hollow protein complex that I first saw years ago while surveying Tetrahymena ciliary lysate www.biorxiv.org/content/10.1... #cilia #protistsonsky 🧬🧪

September Map of the Month: Small Data, Big Insights ⚡️

From just 233 movies, CryoCloud delivered a 3.2 Å SARS-CoV-2 spike map in 3.5 h.

Fast and efficient #cryoEM, exactly what vaccine design teams need when screening dozens of antigen variants per day.

📬 DM or hi@cryocloud.io for more info!

gapTrick - Structural characterisation of protein-protein interactions using AlphaFold pubmed.ncbi.nlm.nih.gov/40985612/ #cryoEM

Initial attempt at replicating in relion (parameters in next post). This is for Aca2-RNA, using a 100k subset of the 2D-classified particles (no prior 3D cleanup).

A 1-class ab initio in relion, then local refinement in relion (1.8deg searches+blush) gives a nominally 3.3Å map; 3.5 Å w/out blush.

Rounding off an incredibly busy week with the excellent third installment of the Dutch Structural Biology Meeting! Many thanks to Arjen for the kind invitation to present our lab’s work.

Latest preprint from the lab, many years in the making!

By combining #cryoEM with #AlphaFold3 modelling, we propose that norovirus NS3 forms a transmembrane RNA translocase.

This could have big implications for our understanding of viral replication & assembly (🧵)

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

Zincore, an atypical coregulator, binds zinc finger transcription factors to control gene expression Zinc finger proteins (ZNFs) are the largest family of transcription factors, yet how they activate gene expression remains unclear. In this study, we identified Zincore, a protein complex consisting o...

In today’s publication in Science we introduce Zincore: a novel protein of QRICH1 and SEPHS1 and functions as a transcriptional coregulator dedicated to zinc finger transcription factors. Here’s how we found it: 🧵 www.science.org/doi/10.1126/... 1/11

👀 Just updated my Google Scholar and... can’t believe one of my papers reached 100 citations! 🚀

💪🏼 It might not seem like much, but as a PhD student, it feels like a big achievement.

❤️ To all fellow PhDs, keep going, stay strong, and celebrate every milestone!🔁

Read it: www.jbc.org/article/S002...

Very happy to see this online! 🥂

A starter pack for all virologists out there on the blue side ! Might be missing some people but it’s a good start ! go.bsky.app/DmphBCT

Hi new science&art friends! it seems that science-skies has grown quite a bit from the last time! 👀👀👀

I need to be more active here, so here's a render I made a while ago: "phi29 bacteriophage"

#SciArt #Blender #Molecularnodes #artwork #digitalart

AlphaFold can predict protein, DNA, or RNA complexes.. BUT is it easy to determine the reliable interactions?🤔

➡️ AlphaBridge will identify the most confident interactions, making your analysis easier!

🌐Try it here: alpha-bridge.eu
👀Read more: www.biorxiv.org/content/10.1...