Álvaro López Codina

The bacterial ESCRT-III PspA rods thin lipid tubules and increase membrane curvature through helix α0 interactions pubmed.ncbi.nlm.nih.gov/40758888/ #cryoEM

Beyond monomeric structures, accurate prediction of protein-protein interactions is crucial for understanding protein function. MSA Pairformer substantially outperforms all other methods in predicting residue-residue interactions at hetero-oligomeric interfaces

Scaling down protein language modeling with MSA Pairformer Recent efforts in protein language modeling have focused on scaling single-sequence models and their training data, requiring vast compute resources that limit accessibility. Although models that use ...

Excited to share work with
Zhidian Zhang, @milot.bsky.social, @martinsteinegger.bsky.social, and @sokrypton.org
biorxiv.org/content/10.1...
TLDR: We introduce MSA Pairformer, a 111M parameter protein language model that challenges the scaling paradigm in self-supervised protein language modeling🧵

Flexibility can be frustrating when processing a #cryoEM dataset. If your target has a wobbly domain, check out our new case study on FaNaC1 for continuous heterogeneity tips in #CryoSPARC!

guide.cryosparc.com/processing-d...

We are excited to announce the first in-cell structure of a LINC complex within a native nuclear envelope at subnanometer resolution!! #In-cell cryo-ET + #atomistic MD simulations! @tomdendooven.bsky.social et al!!
www.biorxiv.org/content/10.1...

FGF Signaling Promotes Lysosome Biogenesis in Chondrocytes via the Mannose Phosphate Receptor Pathway FGF signaling regulates lysosomal homeostasis in RCS chondrocytes by inducing TFEB/TFE3 nuclear translocation and activation. This promotes the expression of lysosomal genes and mannose 6-phosphate r...

FGF Signaling Promotes Lysosome Biogenesis in Chondrocytes via the Mannose Phosphate Receptor Pathway - Cinque - 2025 - Traffic - Wiley Online Library onlinelibrary.wiley.com/doi/10.1111/...

Lysosomal membrane homeostasis and its importance in physiology and disease Nature Reviews Molecular Cell Biology, Published online: 04 August 2025; doi:10.1038/s41580-025-00873-wLysosomes degrade cellular components, and their membrane is an important signalling hub. Recent insights into the mechanisms that maintain lysosomal membrane homeostasis — including the interplay between membrane damage, repair, lysophagy and lysosome biogenesis — highlight their importance in physiology, in disease and during ageing.

New Online! Lysosomal membrane homeostasis and its importance in physiology and disease

In-cell structure of a LINC complex reveals the molecular basis for membrane remodelling and head-to-tail coupling in sperm cells In eukaryotic cells, LINC complexes physically bridge the two nuclear membranes to cytoskeletal filaments, transmitting mechanical forces to the nucleus. Due to their dynamic and membrane-embedded nat...

Fantastic work by the group of @matteoall.bsky.social : a SUN5:Nesprin3 complex at the head:tail junction of sperm cells. 🤯 #teamtomo

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

The intrinsically disordered regions of organellophagy receptors are interchangeable and control organelle fragmentation, ER-phagy and mitophagy flux - Nature Cell Biology Rudinskiy et al. examine organellophagy receptor features, finding modules of functionally conserved intrinsically disordered regions and defining shared features despite sequence divergence, such as ...

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

Multi-scale Molecular Imaging of Human Cells reveals COPI and COPII Vesicles at ER Exit Sites Trafficking from the endoplasmic reticulum to the Golgi apparatus comprises the first steps toward the correct localization of 30% of eukaryotic proteins. Coat protein complexes COPII and COPI are inv...

Go check out the latest preprint from Giulia Zanetti's lab. @dr-downes.bsky.social used cryo-tomography to directly visualize COPI and COPII coated vesicles in situ at unprecedented resolution in human cells. Amazingly beautiful, rigorous, insightful work.
www.biorxiv.org/content/10.1...

🍹Li et al. uncover a lysosomal surveillance response whereby intestinal lumen deacidification induces a transcriptional program that boosts lysosomal activity and improves protein aggregate clearance in multiple worm disease models, extending #healthspan.
#lysosome
bit.ly/46G38dx

Structures of dynamic interactors at native proteasomes by PhIX-MS and cryoelectron microscopy www.biorxiv.org/content/10.1101/2025.07.31.667872v1 #cryoEM

Validated ligand geometries for macromolecular refinement restraints and molecular mechanics force fields www.biorxiv.org/content/10.1101/2025.08.01.668229v1 #cryoEM

very cool stuff and interesting note re the importance of linker length in isolation of the complex

Affinity-ligand purification of native human low-abundance multi-protein complexes for structure determination www.biorxiv.org/content/10.1101/2025.07.31.667873v1 #cryoEM

a woman in a red dress says " read honey " ALT: a woman in a red dress says " read honey "

#Autophagy and #mTOR papers from last week, lots of cool stuff, enjoy!

biomed.news/bims-auttor/...

Vacuolar Phosphatidylinositol 3,4,5-trisphosphate controls fusion through binding Vam7, and membrane microdomain assembly https://www.biorxiv.org/content/10.1101/2025.08.01.668199v1

CryoSift - An accessible and automated CNN-driven tool for cryo-EM 2D class selection www.biorxiv.org/content/10.1101/2025.07.28.667259v1 #cryoEM

Phosphoribosyl ubiquitination of SNARE proteins regulates autophagy during Legionella infection | The EMBO Journal imageimageAmong the hundreds of proteins that are secreted by Legionella pneumophila (the causative agent of Legionnaires’ disease) during infection, the SidE class of effectors modify host proteins b...

www.embopress.org/doi/full/10....

Pulsed-electron illumination does not reduce beam damage for imaging biological macromolecules www.biorxiv.org/content/10.1101/2025.07.29.667395v1 #cryoEM

Automated removal of corrupted tilts in cryo-electron tomography pubmed.ncbi.nlm.nih.gov/40741136/ #cryoEM

Nde1 promotes Lis1 binding to full-length autoinhibited human dynein 1 - Nature Chemical Biology Cryo-electron microscopy and biochemical reconstitution analysis reveals that Nde1 enhances Lis1 binding to autoinhibited dynein, promoting formation of a Phi-like–Lis1 intermediate during dynein acti...

Cryo-EM and biochemical reconstitution analysis reveal that Nde1 enhances Lis1 binding to autoinhibited dynein, promoting formation of a Phi-like-Lis1 intermediate during dynein activation

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

In situ cryo-ET visualization of mitochondrial depolarization and mitophagic engulfment pubmed.ncbi.nlm.nih.gov/40743392/ #cryoEM

Cryo-EM structures of amino acid sensors bound to the human GATOR2 complex pubmed.ncbi.nlm.nih.gov/40742811/ #cryoEM

Sub-3 Å resolution protein structure determination by single-particle cryo-EM at 100 keV pubmed.ncbi.nlm.nih.gov/40744008/ #cryoEM

Cryo-EM structures of amino acid sensors bound to the human GATOR2 complex Su et al. elucidated the cryo-EM structures of the CASTOR1-GATOR2, Sestrin2-GATOR2, and CASTOR1-Sestrin2-GATOR2 complexes. By integrating the structural findings with in vitro pull-down assays and HDX...

Cryo-EM structures of amino acid sensors bound to the human GATOR2 complex www.cell.com/cell-reports...

Cryo-EM captures early intermediate steps in dynein activation by LIS1 - Nature Communications The molecular motor dynein is modulated by several protein regulators, including LIS1. Here, authors use cryo-EM to show how LIS1 activates dynein by disrupting its autoinhibition and stabilizing inte...

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

In situ cryo-ET visualization of mitochondrial depolarization and mitophagic engulfment | PNAS www.pnas.org/doi/10.1073/...

RNF13 Regulates the Endolysosomal Pathway Through Interaction with the Small GTPase Arl8B The endolysosomal system is a dynamic intracellular network essential for cargo degradation, recycling and spatial compartmentalization. Precise coordination of endosome maturation and positioning is ...

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

Detecting Nuclear Pore Complex assembly in living cells The formation of nuclear pore complexes (NPCs) - vital gateways regulating nuclear-cytoplasmic transport - is a highly orchestrated process requiring the integration of hundreds of nucleoporins into t...

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