Álvaro López Codina

AGPAT2 acts at the crossroads of lipid biosynthesis and DRP1-mediated ER morphogenesis
www.nature.com/articles/s41...

Reversible One-way Lipid Transfer at ER-Autophagosome Membrane Contact Sites via Atg2 Bridge-like lipid transfer proteins (LTPs) contain a repeating β-groove domain and long hydrophobic grooves that act as bridges at membrane contact sites (MCSs) to efficiently transfer lipids. Atg2 is...

Reversible One-way Lipid Transfer at ER-Autophagosome Membrane Contact Sites via Atg2 www.biorxiv.org/content/10.1...

Structure of human cytoplasmic Pol II complex explains global transcription repression by Gdown1 www.biorxiv.org/content/10.64898/2025.12.10.693371v1 #cryoEM

The aging of the AlphaFold database Nature Structural & Molecular Biology, Published online: 10 December 2025; doi:10.1038/s41594-025-01725-zThe AlphaFold database, released in 2022, modeled UniProt sequences from April 2021 and now provides 200 million predicted protein structures. Of the 20,504 full-length predicted human structures, 631 entries conflict with the June 2025 UniProt release. Similar conflicts across species highlight how bioinformatics resources can rapidly age.

ICYMI: New online: The aging of the AlphaFold database

Comparing Multislice Simulations of MD Simulations with CryoEM Exposes Membrane Prediction Errors www.biorxiv.org/content/10.64898/2025.12.09.693260v1 #cryoEM

Integrating endogenous TurboID and data-independent acquisition mass spectrometry for in vivo proximity labeling - The EMBO Journal Proximity labeling has emerged as a powerful approach for identifying protein–protein interaction networks within living systems, particularly those involving weak or transient associations. Here, we ...

New methods article:
David Fay et al integrate endogenous TurboID labeling and data-independent acquisition mass-spectrometry for in vivo proximity labeling
link.springer.com/article/10.1...

Glad to hear real cells can be Goodsell-esque 😁

Cryo-EM Analysis in CASP16 pubmed.ncbi.nlm.nih.gov/41380080/ #cryoEM

😍 Zhou Lab on fire!!! 🔥🔥🔥 #cryoet #teamtomo

Overview of the LDR. Lysosomal stress & membrane damage are triggered by diverse harmful factors, including physical stressors, oxidative stress, lipid peroxidation, amyloid fibrils and bacterial infection. Lysosomal damage leads to the leakage of lysosomal contents such as cathepsins and protons into the cytosol. The LDR involves at least three pathways – membrane repair, removal of damaged lysosomes, and lysosome biogenesis and regeneration. The activation of these pathways depends on the extent, duration and severity of the damage . Mild or transient stress or damage is rapidly resolved within seconds to minutes through lysosomal membrane repair mechanisms. When the damage exceeds the repair capacity, indicated by persistent rupture or exposure of luminal glycoproteins, the cell initiates selective autophagy of damaged lysosomes (called lysophagy). In addition, when damage is widespread or chronic, and functional lysosomes are depleted, lysosome biogenesis and regeneration occur.

In their Review, Shuhei Nakamura, Takayuki Shima and Tamotsu Yoshimori summarise our current knowledge of the lysosomal damage response, its significance in aging and diseases, and future perspectives.
journals.biologists.com/jcs/article/...

Thanks for sharing your research (and beautiful images) with us!
Check out @lysoluis.bsky.social and team’s research on lysosome tubulation using AiryScan, SoRa and CLEM FIB-SEM ⤵️
focalplane.biologists.com/2025/12/11/d...

China leads research in 90% of crucial technologies — a dramatic shift this century The United States tops the remaining areas in an assessment of 74 technologies.

China is leading research in nearly 90% of the crucial technologies that “significantly enhance, or pose risks to, a country’s national interests”, according to a technology tracker run by an independent think-tank.

go.nature.com/3YtbmA4

Loss of ErbB3 redirects Integrin β1 from endosomal recycling to secretion in extracellular vesicles, say Dorival Mendes Rodrigues-Junior, Ana Rosa Sáez-Ibáñez, Ingvar Ferby and colleagues @uu.se: rupress.org/jcb/article/...

#Cancer #Biochemistry #Trafficking #CellSignaling

Parsing Contributions of Physical Phenomena to smFRET Statistical Inhomogeneity via Multiparameter Stochastic Simulations https://www.biorxiv.org/content/10.64898/2025.12.09.692639v1

IsoNet2 determines cellular structures at submolecular resolution without averaging www.biorxiv.org/content/10.64898/2025.12.09.693325v1 #cryoEM

RELION 5 3D refinement on tomo data often seems to struggle to align objects that old school STA packages handled no problem... does this match everyones experience or is this a me problem?

Holy cow the Zhou lab at UCLA is cooking with Isonet 2 - www.biorxiv.org/content/10.6...

Averaging-free direct visualization of ribosome translational state! #teamtomo #cryoet

Ancestral Chaperonins Provide the First Structural Glimpse into Early Multimeric Protein Evolution Abstract. Chaperonins are essential protein-folding machines, classified into three structural and phylogenetic groups: Group I (bacterial GroEL), Group II

Ancestral Chaperonins Provide the First Structural Glimpse into Early Multimeric Protein Evolution

Magnifique papier et en plus qui va dans le même sens que ce qu'on disait en 2021 dans un de mes papiers sur la topologie et l'émergence du Groupe 3 des chaperonines.

academic.oup.com/mbe/article/...

Integrating endogenous TurboID and data-independent acquisition mass spectrometry for in vivo proximity labeling - The EMBO Journal Proximity labeling has emerged as a powerful approach for identifying protein–protein interaction networks within living systems, particularly those involving weak or transient associations. Here, we ...

Hot off the press at EMBO Journal. The culmination of several years of work and hopefully useful to people in the field!

BIG Shout-out to Review Commons, who handled the submission. It's a sensible and efficient model and all the journals I like (Society and NFP) are already participating. 🙏

Encoding and Decoding Ubiquitin Chain Architectures: Fine-Tuning the Fate of Proteins pubmed.ncbi.nlm.nih.gov/41368807/ #cryoEM

Decreased cytoplasmic crowding via inhibition of ribosome biogenesis can trigger Candida albicans filamentous growth pubmed.ncbi.nlm.nih.gov/41372638/ #cryoEM

Mechanoenhancers are key regulators of how cells translate mechanical cues into gene activity and functional behaviors @science.org @dukeu.bsky.social @cgersbach.bsky.social
www.science.org/doi/10.1126/...

Comparing Multislice Simulations of MD Simulations with CryoEM Exposes Membrane Prediction Errors https://www.biorxiv.org/content/10.64898/2025.12.09.693260v1

Image-based morphological profiling of autophagy phenotypes in Zika virus infected cells https://www.biorxiv.org/content/10.64898/2025.12.09.693313v1

Resolving structural heterogeneity in situ through cryogenic electron tomography pubmed.ncbi.nlm.nih.gov/41370988/ #cryoEM

🤯

This movie shows lysosomes (orange) and keratin (gray) in a cultured cell over 10 minutes.

This week, check out a new #Primer on #cryogenic electron tomography (cryo-ET) used for visualizing 3D structures of cells with sub-nanometer resolution. 🔬🧫
www.nature.com/articles/s43...

Rashmi Budhathoki et al. @blankenshiplab.bsky.social show that nuclear dispersion relies on a transition from centrosomal to embedded nucleus-associated, non-centrosomal #microtubules during #Drosophila tissue extension. rupress.org/jcb/article/...
#Cytoskeleton #Development #Organelles

💥I am excited to present our first research paper from the lab about caveolae lipid trafficking 🎉 Led by my fantastic PhD candidate @estherocket.bsky.social

Here we looked into caveolae mediated dietary lipid uptake and how this process is mechanistically facilitated 👇 1/n