Álvaro López Codina

Cooperative Native Contact Formation Facilitates Free Energy Barrier Crossing in Protein Folding High-temporal-resolution fluorescence measurements reveal how quickly proteins cross energy barriers separating unfolded and folded states.

Very cool paper on folding rates for small single protein domains: journals.aps.org/prl/abstract...

Now that we know these domains fold very fast (0.7-4 microseconds), it should be possible to simulate this by MD and compare, right? This might be helpful in improving MD force field accuracy.

Dynamin-2 promotes Atg9A retrieval from phagophores during autophagy. https://www.biorxiv.org/content/10.64898/2026.03.11.711183v1

In-Chamber Sublimation: A Practical Approach for Mitigating Ice and Curtaining in Cryo-Electron Tomography Lamellae Preparation https://www.biorxiv.org/content/10.64898/2026.03.12.711158v1

Drebrin forms a cortical hub that connects actin, microtubules, and clathrin for endocytic transport of β2 integrin https://www.biorxiv.org/content/10.64898/2026.03.12.711275v1

A membrane insertion code for intrinsically disordered proteins https://www.biorxiv.org/content/10.64898/2026.03.12.711444v1

Emerging landscape of KRAS inhibitors in cancer treatment RAS mutations drive ∼20% of human cancers. This review summarizes clinical outcomes and resistance mechanisms of KRASG12C inhibitors and highlights emerging classes of next-generation (K)RAS inhibitors, focusing on their mechanisms of action, selectivity, early efficacy, and potential to overcome resistance in RAS-driven tumors.

Emerging landscape of KRAS inhibitors in cancer treatment

Cullin–RING receptors in rare disease biology The ubiquitin–proteasome system governs selective protein turnover in all eukaryotes, and its cullin–Really Interesting New Gene (RING) ligases represent the largest class of E3 ligases. Their substrate receptors (SRs) act as the ‘specificity engines’ of degradation, yet their contribution to human genetic disease has only recently come into focus. In this review, we provide the first systematic catalogue of 267 SRs, of which 93 are now linked to germline disorders. We synthesise emerging mechanisms, from altered degron recognition to noncanonical SR functions, and highlight how patient variants illuminate pathways for diagnosis and therapy. By connecting proteostasis, rare-disease genetics, and targeted protein degradation, SRs emerge as central nodes with broad implications for precision medicine.

Cullin–RING receptors in rare disease biology

Targeting UGCG sensitizes AML cells to venetoclax through RAB32-mediated endoplasmic reticulum-mitochondria communication Sun et al. demonstrate that targeting UGCG in combination with venetoclax is an alternative combinatory strategy to treat AML and provide insights for ceramide-mediated cell death in anti-cancer therapies.

Targeting UGCG sensitizes AML cells to venetoclax through RAB32-mediated endoplasmic reticulum-mitochondria communication

Drebrin forms a cortical hub that connects actin, microtubules, and clathrin for endocytic transport of β2 integrin

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

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

Dynamin-2 promotes Atg9A retrieval from phagophores during autophagy.

3DDF-VAE: Dual-frequency variational autoencoder with pose-consistency validation for rare cryo-EM conformation discovery pubmed.ncbi.nlm.nih.gov/41819391/ #cryoEM

GAP mimetic activity of pan-Ras TCI daraxonrasib synergizes with K-Ras Switch-II pocket inhibition https://www.biorxiv.org/content/10.64898/2026.03.11.711097v1

To accompany the #Autophagy #GRC, explore our recent autophagy special collection, incl. the role of ATG 9 in autophagosome formation & the regulation of lysosomal function, and the regulation of selective autophagy, incl. #mitophagy and #pexophagy 👉 rupress.org/jcb/collecti...

easymode

New Title Alert: easymode- a collection of general pretrained networks for cellular cryoET.

Learn more here: buff.ly/mLbcUbZ

#SBGrid #SBGridSoftware

Exciting new discovery from @jimwellsucsf.bsky.social and coworkers, a new class of potential cancer antigens flipped onto the cell surface via autophagy-associated exocytosis, featuring first author and former PhD student Corleone Delaveris! #proudofalumni

How do we build realistic cellular environments for simulations?

@cg-martini.bsky.social, @ma3ke.bsky.social, @janstevens.bsky.social answer this with Bentopy, an integration tool for proteomics, metabolomics, and structural data that rapidly assembles simulation-ready molecular models.

#OpenSoftwareAcceleratesScience! 😍

New OpenFold3 preview out! (OF3p2)

It closes the gap to AlphaFold3 for most modalities.

Most critically, we're releasing everything, including training sets & configs, making OF3p2 the only current AF3-based model that is functionally trainable & reproducible from scratch🧵1/9

started using --𝐬𝐢𝐠𝐦𝐚_𝐚𝐧𝐠 𝟑 in RELION5 Refine3D and all of a sudden every subtomogram average goes to high resolution 🤯
#TeamTomo

Bacterial CipB is an exogenous receptor to drive the #mitophagy-TFEB axis and promote pathogenesis. From Shuai Liu, Shan Li and colleagues (Huazhong Agricultural University): rupress.org/jcb/article/...

📕 Part of #Autophagy 2026 👉 rupress.org/jcb/collecti...
#GRC

Excited to share Sampleworks led by @karsonchrispens.bsky.social with @diffuseproject.bsky.social. It's a modular framework connecting structure predictors to experimental data and guidance methods. Swap predictors or guidance methods. All open and made to be built upon. t.co/fvNHH3gfVu

Arp2/3 complex-dependent actin remodeling is required for efficient RSV uncoating in A549 cells https://www.biorxiv.org/content/10.64898/2026.03.11.711013v1

Autophagolysosomal exocytosis inverts Src kinase onto the cell surface in cancer Overexpression of the proto-oncogene Src is common to a wide variety of cancers. In this work, we found that Src is noncanonically translocated and inverted onto the cell surface in cancer, both in vi...

Autophagolysosomal exocytosis inverts Src kinase onto the cell surface in cancer | Science www.science.org/doi/10.1126/...

An efficient clear-native PAGE-based workflow for cryo-electron microscopy sample preparation of large protein complexes pubmed.ncbi.nlm.nih.gov/41808182/ #cryoEM

Targeting the senescence–autophagy axis for idiopathic pulmonary fibrosis therapy Idiopathic pulmonary fibrosis (IPF) is a progressive, age-associated interstitial lung disease with limited therapeutic options. Current antifibrotics modestly slow the decline but fail to halt or reverse fibrosis. Emerging evidence implicates two central hallmarks of aging—cellular senescence and impaired autophagy—in IPF pathogenesis. Senescent epithelial and stromal cells secrete proinflammatory and profibrotic mediators, while defective autophagic flux exacerbates protein and organelle accumulation, mitochondrial dysfunction, and maladaptive stress responses. Increasingly, these processes are recognized as reciprocally regulated, converging on signaling pathways such as transforming growth factor-β, adenosine monophosphate-activated protein kinase/mechanistic target of rapamycin, nuclear factor kappa-light-chain enhancer of activated B cells, and reactive oxygen species. This review examines the senescence–autophagy axis, outlines conceptual frameworks to reconcile its paradoxical functions, and highlights emerging therapeutic strategies, including drug repurposing and next-generation interventions.

Targeting the senescence–autophagy axis for idiopathic pulmonary fibrosis therapy

Modulation of mitochondria-ER contacts decrease inflammasome formation and restores amyloid β-peptide phagocytosis in adult mouse microglia https://www.biorxiv.org/content/10.64898/2026.03.10.710773v1

Today I presented a fresh paper (out 2 days ago in @jcb.org) during our lab literature session.
Really nice work from Suzuki’s Lab using the R18 lipid dye to map ATG2-dependent lipid transfer from the ER to autophagy structures in vivo ☺️ revealing a how R18 reaches ER-IM contacts
shorturl.at/hZR8k

Samsung 3D display showing a molecule, 3D mouse pointer, and atom identification label.

ChimeraX works with Acer, Sony and Samsung 3D eye-tracking displays that do not use glasses. Thanks to Andre Michaelis for adding Samsung support and a 3D mouse pointer (menu Tools / More Tools... / XR3D).
www.rbvi.ucsf.edu/chimerax/dat...

SLC4A1 mutations that cause distal renal tubular acidosis alter cytoplasmic pH and cellular autophagy Distal renal tubular acidosis induced by some SLC4A1 variants is characterized by cytosolic pH alkalization, reduced ATP synthesis and defective autophagy degradative flux.

SLC4A1 mutations that cause distal renal tubular acidosis alter cytoplasmic pH and cellular autophagy

CryoEM structure of mGlu6 captures receptor activation prior to G protein coupling pubmed.ncbi.nlm.nih.gov/41803130/ #cryoEM