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Aniruddha Das

@aniruddhad.bsky.social
226 followers 97 following 22 posts

Postdoctoral Fellow at University of Utah, Ph.D. in Biochemistry | Interested in Proteostasis Network, Ubiquitin-Proteasome System, Protein Quality Control Pathways, Proteasome Complex

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Reposted by Aniruddha Das
Michelle Fry @myfry.bsky.social · 02/10/2026
1/ 🧵 Two classic mitochondrial pathways the TCA cycle and OXPHOS are taught as linked but distinct pathways. I’m happy to share our new work out in @cp-cell.bsky.social showing that in Acanthamoeba they're physically linked—with a TCA enzyme incorporated in ATP synthase. www.cell.com/cell/fulltex...
cell.com
Acanthamoeba ATP synthase structure reveals the TCA cycle is tethered to OXPHOS
Acanthamoeba castellanii, a pathogenic amoeba, belongs to an evolutionary branch distinctly removed from humans and fungi. Cryo-EM of the organism’s ATP synthase enzyme using raw mitochondrial lysates...
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cryoEM papers @cryoempapers.bsky.social · 02/10/2026
Cryo-tides: synthetic peptides for cryo-EM grid preparation of multi-subunit protein complexes sensitive to the air-water interface www.biorxiv.org/content/10.64898/2026.09.30.755610v1 #cryoEM
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Craig M. Crews @craigmcrews.bsky.social · 22/09/2026
cendigitalmagazine.acs.org/2026/08/14/f...
cendigitalmagazine.acs.org
First human trials of designer protein therapies stun US neuroscientists
Chinese researchers are testing DREADDs, a gene therapy to turn down neuronal activity, in the clinic
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Reposted by Aniruddha Das
MRC Laboratory of Molecular Biology @mrclmb.ac.uk · 16/09/2026
How do cells remove abnormal glycogen? Led by Matthew Yip, using mouse models, cell engineering & cryo-ET, Felix Randow's group found that RNF213 ubiquitylates aberrant glycogen to trigger autophagy. mrclmb.ac.uk/news-events/articles/h… #LMBResearch
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Reposted by Aniruddha Das
Leo Kiss @leokiss.bsky.social · 14/09/2026
Very cool article by @rachelbrazil.bsky.social on Ubiquitin, Degradation and the potential for Targeted Protein Degradation inducing Drugs in Medicine! www.chemistryworld.com/features/cra...
chemistryworld.com
Cracking the ubiquitin code to unlock new drug targets
The approval of the first Protac cancer drug marks a turning point in medicine - but scientists are only beginning to decode the complex molecular language that makes it possible
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Reposted by Aniruddha Das
Nature Structural & Molecular Biology @natsmb.nature.com · 11/09/2026
ICYMI: New online: ATP-independent unfolding of ubiquitin by Ufd1 initiates Cdc48/p97-mediated substrate processing
dlvr.it
ATP-independent unfolding of ubiquitin by Ufd1 initiates Cdc48/p97-mediated substrate processing
Nature Structural & Molecular Biology, Published online: 10 September 2026; doi:10.1038/s41594-026-01884-7Wang et al. show that the UT3 domain of Ufd1 binds to and unfolds K48-linked polyubiquitin chains without ATP. Simultaneous binding of two ubiquitins to UT3 is key to overcome the energy barrier. This ubiquitin unfolding is critical for Cdc48/p97’s function.
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Stella Hurtley @smhsci.bsky.social · 21/08/2026
Out now in @science.org Virome-wide ubiquitin ligase discovery reveals diverse mechanisms of immune evasion | Science www.science.org/doi/10.1126/...
science.org
Virome-wide ubiquitin ligase discovery reveals diverse mechanisms of immune evasion
Viruses are intracellular parasites that reprogram the host proteome to promote replication and evade immune recognition. We applied a virome-wide library of ~10,000 open reading frames to discover vi...
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Reposted by Aniruddha Das
Francis O'Reilly @fjoreilly.bsky.social · 14/08/2026
PhIX-MS is out in Molecular Cell! Rapid in situ photo-crosslinking traps transient proteasome interactions before purification; crosslinking MS, cryo-EM and AlphaFold tell us where they bind. Paper: doi.org/10.1016/j.mo... Preview: doi.org/10.1016/j.mo...
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The EMBO Journal @embojournal.org · 11/08/2026
What’s the function of embryonic ‘cytoplasmic lattices’? Using cryo-ET, @kashishsingh.bsky.social @carter-lab.bsky.social and coworkers reveal them as megadalton-size hubs of ubiquitination proteins/ubiquitin transfer link.springer.com/article/10.1...
link.springer.com
In-situ cryo-ET of mouse embryos reveals cytoplasmic lattices contain ubiquitin-charged E2-E3 ligase assemblies - The EMBO Journal
Cytoplasmic lattices (CPLs) are filamentous assemblies essential for mammalian embryonic development. They are known to regulate organelle organization, spindle assembly, and protein homeostasis, but ...
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Reposted by Aniruddha Das
The Francis Crick Institute @crick.ac.uk · 16/06/2026
Join @davidbalchin.bsky.social, group leader here at the Crick, as he describes the fascinating ways our cells ensure that proteins fold correctly, and what happens when this goes awry in disease. youtu.be/gEgK1JDNlZ8
youtu.be
How Are We So Good at Folding Proteins? - With David Balchin
YouTube video by The Francis Crick Institute
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Reposted by Aniruddha Das
Clausen Lab @clausenlab.bsky.social · 21/05/2026
Open Postdoc Position - Giant E3 ligases: mysterious mechanisms & non‑protein substrates. Interested? Join us to uncover how these molecular giants tag lipids, RNAs, sugars beyond proteins, on organelles and pathogens, to defend the cell. Details & Application here www.imp.ac.at/career/open-...
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Mathieu M.J.E. Rebeaud @chercheurjuteux.com · 20/05/2026
The twisted tale of cotranslational protein complex assembly My friend Saurav wrote this with Ayala Shiber and this is a great review. www.sciencedirect.com/science/arti...
sciencedirect.com
The twisted tale of cotranslational protein complex assembly
Macromolecular complexes are cells’ functional units, and their correct and efficient assembly is critical to life’s processes. Complex assembly was c…
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Reposted by Aniruddha Das
Lorenz Lab @sonjalorenzlab.bsky.social · 14/05/2026
Over the past 5 years, 50 structures of full-length HECT-type ligase constructs have been deposited in the PDB. What have we learned from these studies, and what key questions remain open? Check out our new review on this exciting and fast-moving field: www.jbc.org/article/S002...
jbc.org
HECT-type ubiquitin ligases: Emerging principles in the era of full-length structures
Ubiquitin coordinates a complex network of cellular pathways through covalent modification of substrates. Specificity in substrate recognition and modification choice is largely conferred by ubiquitin...
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Reposted by Aniruddha Das
The EMBO Journal @embojournal.org · 06/05/2026
Phosphorylation tunes p62 condensates to drive autophagic degradation of ubiquitinated proteins Masaaki Komatsu and collaborators link.springer.com/article/10.1...
link.springer.com
Phosphorylation tunes p62 condensates to drive autophagic degradation of ubiquitinated proteins - The EMBO Journal
p62/SQSTM1 self-assembles with polyubiquitin into liquid-like condensates (“p62 bodies”) that function as stress-signaling hubs and selective autophagy cargo. We show that TBK1-dependent phosphorylati...
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Reposted by Aniruddha Das
bioRxiv Cell Biology @biorxiv-cellbio.bsky.social · 26/04/2026
Proteasome-dependent degradation and nucleus-vacuole junctions sustain proteostasis during acute glucose starvation www.biorxiv.org/content/10.64898/20…
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IMP @impvienna.bsky.social · 23/04/2026
Cells have a built-in cleanup system to remove unwanted proteins, and scientists can hijack it to destroy cancer drivers. Now, researchers from our Haselbach lab and collaborators reveal how this works in near-atomic detail: www.nature.com/articles/s41467-026-…
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Marco Jochem @marcojochem.bsky.social · 23/04/2026
Interested in non-proteinaceous ubiquitination, induced proximity or glycogen? Then you should have a look at our newest article, “Ubiquitination of glycogen and metabolites in cells and tissues”, just published in Nature: www.nature.com/articles/s41...
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Reposted by Aniruddha Das
Komander Lab @komanderlab.bsky.social · 10/04/2026
Out now! The latest paper from the lab, spearheaded by Philipp Schenk, describing a new USP9X inhibitor with a unique DUB binding site.
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Craig M. Crews @craigmcrews.bsky.social · 29/03/2026
www.biorxiv.org/content/10.6...
biorxiv.org
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Kelly Nguyen @kellythd-nguyen.bsky.social · 26/03/2026
Proud to share the yeast telomerase structure, led by the talented @hongmiaohu.bsky.social in collaboration with the Wellinger and Chartrand labs. Discovered 37 years ago and took us nearly 7 years but totally worth the wait 😍. www.science.org/doi/10.1126/... www.youtube.com/watch?v=gFE4...
youtube.com
Cryo-EM structure of yeast telomerase
YouTube video by MRC Laboratory of Molecular Biology
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Reposted by Aniruddha Das
David Bartel's Lab @bartellab.bsky.social · 06/01/2026
We are thrilled to share our latest work uncovering the mechanistic basis of target-directed microRNA degradation (TDMD). This work was driven by @jakobfarnung.bsky.social and @elenaslo.bsky.social in a fantastic collaboration with Brenda Schulman's lab. tinyurl.com/E3TDMD (1/5)
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Castañeda Lab at SU @castanedalab.bsky.social · 19/03/2026
Postdocs Nirbhik Acharya and @jessniblo.bsky.social worked awesomely together to show how disordered regions regulate folded domain interactions that affect UBQLN structure, dynamics, and binding. Illustrating the power of experimental (NMR, SAXS) and computational collabs on full-length proteins!!!
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Reposted by Aniruddha Das
Hellerschmied Lab @hellerschmiedlab.bsky.social · 06/02/2026
Very happy to share our recent preprint describing #Golgi protein quality control #PQC in mammalian cells. #proteasome #ubiquitin #ChemBio Fantastic work by @joaodiamantino.bsky.social and team! #proudPI @unidue-zmb.bsky.social @imprs-lm.bsky.social
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Wojciech Pokrzywa @wpokrzywa.bsky.social · 12/03/2026
New Review in Trends in Cell Biology with @lumirare.com. First integrative catalogue of 267 cullin-RING substrate receptors (93 linked to germline disorders) + programmatic-friendly Excel resource for the community. www.cell.com/trends/cell-...
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Reposted by Aniruddha Das
Dawafuti Sherpa @dawafutisherpa.bsky.social · 11/03/2026
Excited to announce that FASEB Ignite Career Forum 2026 (preceding FASEB Ubiquitin Mechanisms, Functions, and Therapeutics & Protein Folding in the Cell) is open for registration! Abstract deadline - April 6, 2026 For more details - events.faseb.org/event/Protei... events.faseb.org/event/Ubiqui...
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Reposted by Aniruddha Das
Plaschka lab @plaschkalab.bsky.social · 12/03/2026
Automatic screening of cryo-EM grids using EPU is fast and efficient, but reviewing the generated data & picking the best areas for data collection can be slow and cumbersome. We made a little tool that makes this process more streamlined and enjoyable: github.com/mvorlander/E... 1/4
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Aniruddha Das @aniruddhad.bsky.social · 09/03/2026
How does the cell tune p97/Cdc48 activity for different substrates? Study suggests different adaptor combinations function as molecular accelerators of protein clearance. www.science.org/doi/10.1126/...
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Reposted by Aniruddha Das
Mathieu M.J.E. Rebeaud @chercheurjuteux.com · 08/03/2026
Structural remodeling of the mitochondrial protein biogenesis machinery under proteostatic stress www.science.org/doi/10.1126/...
science.org
Structural remodeling of the mitochondrial protein biogenesis machinery under proteostatic stress
Cryo–electron tomography reveals how mitochondria reorganize their translation and folding systems under proteostatic stress.
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Reposted by Aniruddha Das
Rune Busk Damgaard @rbdamgaard.bsky.social · 07/03/2026
More evidence that LUBAC has functions beyond inflammation: Our study shows that LUBAC regulates AMPK signalling to control metabolic adaptation, autophagy, and cell death. This might explain the metabolic problems observed in LUBAC deficiency and ORAS patients. www.nature.com/articles/s41...
nature.com
M1-linked ubiquitination by LUBAC regulates AMPK signalling and the response to energetic stress - Cell Death & Differentiation
Cell Death & Differentiation - M1-linked ubiquitination by LUBAC regulates AMPK signalling and the response to energetic stress
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Reposted by Aniruddha Das
Craig M. Crews @craigmcrews.bsky.social · 02/03/2026
www.nature.com/articles/s41...
nature.com
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-...
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Reposted by Aniruddha Das
bioRxiv Biochemistry @biorxiv-biochem.bsky.social · 26/02/2026
FAF1 and FAF2 enhance human p97-UFD1-NPL4 complex unfoldase activity enabling rational design of p97 activators www.biorxiv.org/content/10.64898/20…
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Rune Busk Damgaard @rbdamgaard.bsky.social · 24/02/2026
This project started with confusion 🤔 www.nature.com/articles/s41... Loss of LUBAC or OTULIN causes severe inflammatory disease. But patients also show clear metabolic defects. Neither LUBAC nor OTULIN had been linked to metabolic regulation. So where do these metabolic manifestations come from?
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Rune Busk Damgaard @rbdamgaard.bsky.social · 16/02/2026
🧐 What if metabolic defects are not just a consequence of inflammatory disease - but actively contribute to it? Inflammation and metabolism are deeply intertwined, but the molecular links remain unclear. Our new paper in Cell Death & Differentiation uncovers one. 🧵👇 nature.com/articles/s41...
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Haselbach Lab @haselbachlab.bsky.social · 12/02/2026
This is a video summarizing our recent paper (www.nature.com/articles/s41...) youtu.be/eNY2CRlYTRo
nature.com
A multivalent adaptor mechanism drives the nuclear import of proteasomes - Nature Communications
Nuclear protein homeostasis relies on proteasome import into the nucleus. Here the authors identify how assembled human proteasomes are transported across the nuclear pore complex and reveal a mechani...
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Reposted by Aniruddha Das
David Vilchez @thevilchezlab.bsky.social · 05/02/2026
Our new review on proteostasis of organelles in aging & disease is now online in The FEBS Journal! We discuss recent insights on how #proteostasis safeguards organelle integrity and function across the cell in #aging and disease doi.org/10.1111/febs...
doi.org
FEBS Press
Cells rely on regulated proteostasis mechanisms to keep their internal compartments functioning properly. When these mechanisms fail, damaged proteins accumulate, disrupting organelles, such as the n....
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Wyoming Wormboy @wyomingwormboy.bsky.social · 02/01/2026
Greetings! I decided to make a YouTube video of my AlphaFold workshop that I've given a few times in the past year. Caveats aside, people seem to find this useful for thinking about how to model protein interactions and how to interpret various AF outputs 1/2 www.youtube.com/watch?v=u63o...
youtube.com
David's AlphaFold WorkShop 2026
YouTube video by David Fay
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BioMassSpec @realbiomassspec.bsky.social · 25/12/2025
MoSAIC: An Integrated and Modular Workflow for Confident Analysis of Protein Post-Translational Modification Landscapes #MCP www.mcponline.org/article/S153...
mcponline.org
MoSAIC: An Integrated and Modular Workflow for Confident Analysis of Protein Post-Translational Modification Landscapes
Investigating multiple protein post-translational modifications (PTMs) is critical for unraveling the complexities of protein regulation and the dynamic interplay among PTMs, a growing focus in proteo...
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Allegretti Lab @matteoall.bsky.social · 19/12/2025
We are thrilled to share our new pre-print on the molecular anatomy of nuclear proteasome in human sperm cells! #In-cellcryo-ET + #SPA + #LM! @piotrkolata.bsky.social @a-dsantos.bsky.social, @tomdendooven.bsky.social!! doi.org/10.64898/202...
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Elliott Lab @elliottlab.bsky.social · 09/12/2025
Excited to share our work into ubiquitin E1-E2 specificity mechanisms. CryoEM visualising #ubiquitin transfer,biochemistry,evolution @labhofmann.bsky.social & tissue expression analyses @psarkies.bsky.social Big thanks to the team,reviewers & handling editor @dimitristypas.bsky.social rdcu.be/eTRdR
rdcu.be
UBA6 specificity for ubiquitin E2 conjugating enzymes reveals a priority mechanism of BIRC6
Nature Structural & Molecular Biology - Riechmann et al. uncover structural features governing ubiquitin transfer from ubiquitin-activating E1 enzymes UBA1 and UBA6 to specific E2...
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Keith Hornberger @krhornberger.bsky.social · 08/12/2025
Induced ubiquitination of the partially disordered Estrogen Receptor alpha protein via a 14-3-3-directed molecular glue-based PROTAC design
biorxiv.org
Induced ubiquitination of the partially disordered Estrogen Receptor alpha protein via a 14-3-3-directed molecular glue-based PROTAC design
Proteins lacking defined ligandable pockets remain challenging drug targets. Here, we develop a molecular glue-based PROTAC (MGPROTACs) approach that chemically conjugates a molecular glue stabilizer ...
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Aniruddha Das @aniruddhad.bsky.social · 06/12/2025
Cytoplasmic ribosomes on mitochondria alter the local membrane environment for protein import. rupress.org/jcb/article/...
rupress.org
Cytoplasmic ribosomes on mitochondria alter the local membrane environment for protein import | Journal of Cell Biology | Rockefeller University Press
Chang et al. present a membrane-guided approach for identifying a subset of cytoplasmic ribosomes oriented for protein import on the mitochondrial surface
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Reposted by Aniruddha Das
James Olzmann @olzmannlab.bsky.social · 01/12/2025
New preprint out! We show that PROTAC-induced ubiquitination can bypass canonical ERAD to degrade ER membrane proteins. Wonderful collaboration w/ @dannomura.bsky.social and huge credit to grad student superstar Sydney Tomlinson! www.biorxiv.org/content/10.1...
biorxiv.org
Induced ubiquitination bypasses canonical ERAD to drive ER protein degradation
Heterobifunctional proteolysis-targeting chimeras (PROTACs) have emerged as a powerful strategy to degrade disease-relevant proteins, enabling targeting of previously "undruggable" proteins. Current d...
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Reposted by Aniruddha Das
Peter Mabbitt @petermabbitt.bsky.social · 29/11/2025
We’ve made some new tools to manipulate N-recognins. Check them out in our preprint. www.biorxiv.org/content/10.1...
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Green Lab JHMI @greenlab.bsky.social · 24/11/2025
Check out our latest work on how collided ribosomes activate the MAP3K ZAK! 💫 www.nature.com/articles/s41... A fun collaboration with @beckmannlab.bsky.social @doubleshuang.bsky.social
nature.com
ZAK activation at the collided ribosome - Nature
The kinase ZAK is activated at collided ribosomes to mediate the ribotoxic stress response.
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Nature Chemical Biology @natchembio.nature.com · 14/11/2025
A new Review discusses how degrons of different types, with an emphasis on high-order structural ones, regulate substrate-E3 interactions and how their dysregulation is linked to human diseases www.nature.com/articles/s41...
nature.com
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-...
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Janine Brunner @janinebrunner.bsky.social · 14/11/2025
MISO: microfluidic protein isolation enables single-particle cryo-EM structure determination from a single cell colony. Or from a single dish of HEK cell culture in the case of two membrane proteins. Out in Nature Methods now! lnkd.in/gpyBSceg Wonderful collaboration with the Efremov lab.
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Aniruddha Das @aniruddhad.bsky.social · 01/11/2025
Very interesting work by Hoppe group. Leucine inhibits degradation of outer mitochondrial membrane proteins to adapt mitochondrial respiration | Nature Cell Biology share.google/0GpbVUCmqJ8Q...
share.google
Leucine inhibits degradation of outer mitochondrial membrane proteins to adapt mitochondrial respiration - Nature Cell Biology
Li et al. uncover a connection between metabolic cues and mitochondrial protein degradation, showing that specifically leucine stabilizes outer mitochondrial membrane proteins by inhibiting ubiquityla...
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Nature Structural & Molecular Biology @natsmb.nature.com · 06/08/2025
New online: Structure of the TXNL1-bound proteasome
go.nature.com
Structure of the TXNL1-bound proteasome
Nature Structural & Molecular Biology, Published online: 06 August 2025; doi:10.1038/s41594-025-01639-wGao, Nardone et al. report the cryo-EM structure of human TXNL1 bound to the proteasome and reveal interactions required for the stress-induced degradation of TXNL1, an abundant protein that may regulate proteasomal activity.
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Journal of Cell Biology @jcb.org · 27/06/2025
The E3 ligase Parkin ubiquitinates many proteins. Koszela, Walden (@hw1o9.bsky.social) et al. @uofglasgow.bsky.social‬ identify and biochemically validate a direct Parkin interaction with a substrate, Miro1. rupress.org/jcb/article/...
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Pablo Ranea-Robles @pranea.bsky.social · 31/05/2025
Inhibition of peroxisomal protein PRX-11 promotes longevity in Caenorhabditis elegans via enhancements to mitochondria www.biorxiv.org/content/10.1...
biorxiv.org
Inhibition of peroxisomal protein PRX-11 promotes longevity in Caenorhabditis elegans via enhancements to mitochondria
Peroxisomes execute essential functions in cells, including detoxification and lipid oxidation. Despite their centrality to cell biology, the relevance of peroxisomes to aging remains understudied. We...
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