Aniruddha Das
@aniruddhad.bsky.social
Postdoctoral Fellow at University of Texas, Ph.D. in Biochemistry | Interested in Proteostasis Network, Ubiquitin-Proteasome System, Protein Quality Control Pathways, Proteasome Complex
Very interesting work by Hoppe group. Leucine inhibits degradation of outer mitochondrial membrane proteins to adapt mitochondrial respiration | Nature Cell Biology share.google/0GpbVUCmqJ8Q...
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...
share.google
November 1, 2025 at 4:26 AM
Very interesting work by Hoppe group. Leucine inhibits degradation of outer mitochondrial membrane proteins to adapt mitochondrial respiration | Nature Cell Biology share.google/0GpbVUCmqJ8Q...
Reposted by Aniruddha Das
New online: Structure of the TXNL1-bound proteasome
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.
go.nature.com
August 6, 2025 at 11:29 AM
New online: Structure of the TXNL1-bound proteasome
Reposted by Aniruddha Das
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/...
June 27, 2025 at 8:10 PM
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/...
Reposted by Aniruddha Das
Inhibition of peroxisomal protein PRX-11 promotes longevity in Caenorhabditis elegans via enhancements to mitochondria www.biorxiv.org/content/10.1...
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...
www.biorxiv.org
May 31, 2025 at 7:27 AM
Inhibition of peroxisomal protein PRX-11 promotes longevity in Caenorhabditis elegans via enhancements to mitochondria www.biorxiv.org/content/10.1...
Reposted by Aniruddha Das
Identified in the 1970s, the precise molecular function of the alternative initiation factor eIF2A has remained unclear. Here, we map its interactome and uncover a surprising role in ribosome-associated quality control (RQC) upon ribosome stalling. 1/x
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
The alternative initiation factor eIF2A regulates 40S subunit turnover in ribosome-associated quality control
The noncanonical translation initiation factor eIF2A plays critical roles in diverse cellular processes, including the integrated stress response, neurodegeneration and tumorigenesis. However, the pre...
www.biorxiv.org
May 26, 2025 at 9:35 PM
Identified in the 1970s, the precise molecular function of the alternative initiation factor eIF2A has remained unclear. Here, we map its interactome and uncover a surprising role in ribosome-associated quality control (RQC) upon ribosome stalling. 1/x
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Aniruddha Das
1/
New preprint!
How do transcription factors (TFs) use intrinsically disordered regions (IDRs) to find their target sites?
www.biorxiv.org/content/10.1...
#TranscriptionFactors #IDPs #SingleMolecule #Biophysics
New preprint!
How do transcription factors (TFs) use intrinsically disordered regions (IDRs) to find their target sites?
www.biorxiv.org/content/10.1...
#TranscriptionFactors #IDPs #SingleMolecule #Biophysics
Intrinsically disordered regions facilitate Msn2 target search to drive promoter selectivity
Transcription factors (TFs) regulate gene expression by binding specific DNA motifs, yet only a fraction of putative sites is occupied in vivo. Intrinsically disordered regions (IDRs) have emerged as ...
www.biorxiv.org
May 27, 2025 at 10:11 PM
1/
New preprint!
How do transcription factors (TFs) use intrinsically disordered regions (IDRs) to find their target sites?
www.biorxiv.org/content/10.1...
#TranscriptionFactors #IDPs #SingleMolecule #Biophysics
New preprint!
How do transcription factors (TFs) use intrinsically disordered regions (IDRs) to find their target sites?
www.biorxiv.org/content/10.1...
#TranscriptionFactors #IDPs #SingleMolecule #Biophysics
Reposted by Aniruddha Das
Excited to share our latest study on how K29/K48-branched #ubiquitin chains are forged by the #E3 ligase TRIP12, and how this suggests a consensus mechanism for chain formation by HECT E3s!
@natsmb.nature.com
1/7
www.nature.com/articles/s41...
@natsmb.nature.com
1/7
www.nature.com/articles/s41...
TRIP12 structures reveal HECT E3 formation of K29 linkages and branched ubiquitin chains - Nature Structural & Molecular Biology
Using biochemistry, chemical biology, and cryo-EM, Maiwald et al. elucidate how TRIP12 forms K29 linkages and K29/K48-linked branched ubiquitin chains, revealing a mechanism for polyubiquitylation sha...
www.nature.com
May 26, 2025 at 9:37 AM
Excited to share our latest study on how K29/K48-branched #ubiquitin chains are forged by the #E3 ligase TRIP12, and how this suggests a consensus mechanism for chain formation by HECT E3s!
@natsmb.nature.com
1/7
www.nature.com/articles/s41...
@natsmb.nature.com
1/7
www.nature.com/articles/s41...
Reposted by Aniruddha Das
Our new study of chromatin ubiquitylation by variant PRC1 on the single-molecule scale: We visualize directly how vPRC1 ubiquitylates neighboring nucleosomes during a single binding event, showing a potential mechanism how H2Aub domains are established.
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Single-molecule analysis reveals the mechanism of chromatin ubiquitylation by variant PRC1 complexes
Single-molecule experiments show that active conformation formation controls chromatin ubiquitylation kinetics by variant PRC1.
www.science.org
May 21, 2025 at 6:59 PM
Our new study of chromatin ubiquitylation by variant PRC1 on the single-molecule scale: We visualize directly how vPRC1 ubiquitylates neighboring nucleosomes during a single binding event, showing a potential mechanism how H2Aub domains are established.
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Reposted by Aniruddha Das
Excited that our work revealing the structure and function of the monster stress response silencing factor, the E3 ligase SIFI, is now out! Congratulations to the most amazing team of Zhi Yang, Diane Haakonsen, Michael Heider and Sam Witus!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Molecular basis of SIFI activity in the integrated stress response - Nature
Nature - Molecular basis of SIFI activity in the integrated stress response
www.nature.com
May 7, 2025 at 10:27 AM
Excited that our work revealing the structure and function of the monster stress response silencing factor, the E3 ligase SIFI, is now out! Congratulations to the most amazing team of Zhi Yang, Diane Haakonsen, Michael Heider and Sam Witus!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Aniruddha Das
Amazing chemical biology/structural biology work on K29/K48 branching E3 Ufd4/TRIP12 www.nature.com/articles/s41...
Structural visualization of HECT-type E3 ligase Ufd4 accepting and transferring ubiquitin to form K29/K48-branched polyubiquitination - Nature Communications
The K29/K48 hetero-polyubiquitin signal has been reported to be an enhanced degradation signal, but the enzymatic mechanism of this ubiquitin chain formation is unclear. Here, the authors reveal how t...
www.nature.com
May 10, 2025 at 12:05 PM
Amazing chemical biology/structural biology work on K29/K48 branching E3 Ufd4/TRIP12 www.nature.com/articles/s41...
Reposted by Aniruddha Das
Kinome screening identifies integrated stress response kinase EIF2AK1/HRI as a negative regulator of PINK1 mitophagy signaling
pmc.ncbi.nlm.nih.gov/articles/PMC...
pmc.ncbi.nlm.nih.gov/articles/PMC...
Kinome screening identifies integrated stress response kinase EIF2AK1/HRI as a negative regulator of PINK1 mitophagy signaling
Loss-of-function mutations in the PINK1 kinase lead to early-onset Parkinson’s disease (PD). PINK1 is activated by mitochondrial damage to phosphorylate ubiquitin and Parkin, triggering mitophagy. PIN...
pmc.ncbi.nlm.nih.gov
May 11, 2025 at 11:48 AM
Kinome screening identifies integrated stress response kinase EIF2AK1/HRI as a negative regulator of PINK1 mitophagy signaling
pmc.ncbi.nlm.nih.gov/articles/PMC...
pmc.ncbi.nlm.nih.gov/articles/PMC...
Reposted by Aniruddha Das
You want to start tomography? Solve structures inside cells? Reach Nyquist 😳 ? @phaips.vd.st and I have a website for you! tomoguide.github.io
You'll find a tutorial on how to reconstruct tomograms, pick particles and do subtomogram averaging, using different software!
Hope it will be useful !
You'll find a tutorial on how to reconstruct tomograms, pick particles and do subtomogram averaging, using different software!
Hope it will be useful !
May 6, 2025 at 4:42 PM
You want to start tomography? Solve structures inside cells? Reach Nyquist 😳 ? @phaips.vd.st and I have a website for you! tomoguide.github.io
You'll find a tutorial on how to reconstruct tomograms, pick particles and do subtomogram averaging, using different software!
Hope it will be useful !
You'll find a tutorial on how to reconstruct tomograms, pick particles and do subtomogram averaging, using different software!
Hope it will be useful !
Reposted by Aniruddha Das
New preprint out from the lab of Cheryl Arrowsmith and colleagues at University of Toronto and the SGC comes ProtacID, a BioID approach to understand both the productive and non-productive interactors of degraders.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Characterization of PROTAC specificity and endogenous protein interactomes using ProtacID
Here we describe ProtacID, a flexible BioID (proximity-dependent biotinylation)-based approach to identify PROTAC-proximal proteins in living cells. ProtacID analysis of VHL- and CRBN-recruiting PROTA...
www.biorxiv.org
May 5, 2025 at 1:01 AM
New preprint out from the lab of Cheryl Arrowsmith and colleagues at University of Toronto and the SGC comes ProtacID, a BioID approach to understand both the productive and non-productive interactors of degraders.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Aniruddha Das
New review from authors Annabel Cardno, Bryony Kennedy, and Catherine Lindon from University of Cambridge comes a review of the important aspects to consider for obtaining optimal degrader activity. From localization to activity of ligase to target accessibility!
www.nature.com/articles/s42...
www.nature.com/articles/s42...
Cellular parameters shaping pathways of targeted protein degradation - Communications Biology
This review discusses the cellular pathways mediating Targeted Protein Degradation approaches and points to some gaps in our understanding of the biology of novel therapeutic tools such as PROTACs.
www.nature.com
May 5, 2025 at 1:20 AM
New review from authors Annabel Cardno, Bryony Kennedy, and Catherine Lindon from University of Cambridge comes a review of the important aspects to consider for obtaining optimal degrader activity. From localization to activity of ligase to target accessibility!
www.nature.com/articles/s42...
www.nature.com/articles/s42...
Reposted by Aniruddha Das
Super happy to share that our work on the specific inhibition of USP30 - a clinical stage Parkinson's drug target - is now online at NSMB www.nature.com/articles/s41... Have a read if you fancy chimeric protein engineering or a framework for DUB ligandability. Huge congratulations to Nafizul & team!
Chimeric deubiquitinase engineering reveals structural basis for specific inhibition of the mitophagy regulator USP30 - Nature Structural & Molecular Biology
Kazi et al. report the crystal structure of the mitochondrial deubiquitinase USP, a clinical stage Parkinson’s disease drug target, in complex with a specific inhibitor. The authors delineate a framew...
www.nature.com
May 5, 2025 at 11:02 AM
Super happy to share that our work on the specific inhibition of USP30 - a clinical stage Parkinson's drug target - is now online at NSMB www.nature.com/articles/s41... Have a read if you fancy chimeric protein engineering or a framework for DUB ligandability. Huge congratulations to Nafizul & team!
Reposted by Aniruddha Das
Reposted by Aniruddha Das
Happy to see our review out in ChemBioChem @chemistryeurope.bsky.social in which we describe the tools and strategies for deciphering linkage type-specific #ubiquitin signalling: doi.org/10.1002/cbic.... Thanks to Julian for spearheading this, and to Camilla and Dominik for important contributions.
April 22, 2025 at 11:31 AM
Happy to see our review out in ChemBioChem @chemistryeurope.bsky.social in which we describe the tools and strategies for deciphering linkage type-specific #ubiquitin signalling: doi.org/10.1002/cbic.... Thanks to Julian for spearheading this, and to Camilla and Dominik for important contributions.
Reposted by Aniruddha Das
Excited to share our latest paper in Science Advances! We finally dissected a new pathway for mitochondrial quality control upon mtDNA replication stress! Let’s start a short thread! 🧵
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Retromer promotes the lysosomal turnover of mtDNA
Lysosomal uptake of mtDNA controls mitochondrial quality.
www.science.org
April 4, 2025 at 6:42 PM
Excited to share our latest paper in Science Advances! We finally dissected a new pathway for mitochondrial quality control upon mtDNA replication stress! Let’s start a short thread! 🧵
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Reposted by Aniruddha Das
Super excited to share our latest work on deciphering the #Ubiquitin Code
“𝗨𝗯𝗶𝗥𝗘𝗔𝗗 𝗱𝗲𝗰𝗶𝗽𝗵𝗲𝗿𝘀 𝗽𝗿𝗼𝘁𝗲𝗮𝘀𝗼𝗺𝗮𝗹 𝗱𝗲𝗴𝗿𝗮𝗱𝗮𝘁𝗶𝗼𝗻 𝗰𝗼𝗱𝗲 𝗼𝗳 𝗵𝗼𝗺𝗼𝘁𝘆𝗽𝗶𝗰 𝗮𝗻𝗱 𝗯𝗿𝗮𝗻𝗰𝗵𝗲𝗱 𝗞48 𝗮𝗻𝗱 𝗞63 𝘂𝗯𝗶𝗾𝘂𝗶𝘁𝗶𝗻 𝗰𝗵𝗮𝗶𝗻𝘀”
@cp-molcell.bsky.social
1/8
www.cell.com/molecular-ce...
“𝗨𝗯𝗶𝗥𝗘𝗔𝗗 𝗱𝗲𝗰𝗶𝗽𝗵𝗲𝗿𝘀 𝗽𝗿𝗼𝘁𝗲𝗮𝘀𝗼𝗺𝗮𝗹 𝗱𝗲𝗴𝗿𝗮𝗱𝗮𝘁𝗶𝗼𝗻 𝗰𝗼𝗱𝗲 𝗼𝗳 𝗵𝗼𝗺𝗼𝘁𝘆𝗽𝗶𝗰 𝗮𝗻𝗱 𝗯𝗿𝗮𝗻𝗰𝗵𝗲𝗱 𝗞48 𝗮𝗻𝗱 𝗞63 𝘂𝗯𝗶𝗾𝘂𝗶𝘁𝗶𝗻 𝗰𝗵𝗮𝗶𝗻𝘀”
@cp-molcell.bsky.social
1/8
www.cell.com/molecular-ce...
UbiREAD deciphers proteasomal degradation code of homotypic and branched K48 and K63 ubiquitin chains
Ubiquitin chains determine the fates of their modified proteins, including proteasomal
degradation. Kiss et al. present UbiREAD, a technology to monitor cellular degradation
and deubiquitination at hi...
www.cell.com
March 24, 2025 at 2:54 PM
Super excited to share our latest work on deciphering the #Ubiquitin Code
“𝗨𝗯𝗶𝗥𝗘𝗔𝗗 𝗱𝗲𝗰𝗶𝗽𝗵𝗲𝗿𝘀 𝗽𝗿𝗼𝘁𝗲𝗮𝘀𝗼𝗺𝗮𝗹 𝗱𝗲𝗴𝗿𝗮𝗱𝗮𝘁𝗶𝗼𝗻 𝗰𝗼𝗱𝗲 𝗼𝗳 𝗵𝗼𝗺𝗼𝘁𝘆𝗽𝗶𝗰 𝗮𝗻𝗱 𝗯𝗿𝗮𝗻𝗰𝗵𝗲𝗱 𝗞48 𝗮𝗻𝗱 𝗞63 𝘂𝗯𝗶𝗾𝘂𝗶𝘁𝗶𝗻 𝗰𝗵𝗮𝗶𝗻𝘀”
@cp-molcell.bsky.social
1/8
www.cell.com/molecular-ce...
“𝗨𝗯𝗶𝗥𝗘𝗔𝗗 𝗱𝗲𝗰𝗶𝗽𝗵𝗲𝗿𝘀 𝗽𝗿𝗼𝘁𝗲𝗮𝘀𝗼𝗺𝗮𝗹 𝗱𝗲𝗴𝗿𝗮𝗱𝗮𝘁𝗶𝗼𝗻 𝗰𝗼𝗱𝗲 𝗼𝗳 𝗵𝗼𝗺𝗼𝘁𝘆𝗽𝗶𝗰 𝗮𝗻𝗱 𝗯𝗿𝗮𝗻𝗰𝗵𝗲𝗱 𝗞48 𝗮𝗻𝗱 𝗞63 𝘂𝗯𝗶𝗾𝘂𝗶𝘁𝗶𝗻 𝗰𝗵𝗮𝗶𝗻𝘀”
@cp-molcell.bsky.social
1/8
www.cell.com/molecular-ce...
Reposted by Aniruddha Das
#preprint Postdoc Nirbhik Acharya used NMR to find three transient helices within intrinsically-disordered regions of shuttle protein Dsk2 -- these interact with STI1. The STI1 is important for phase separation and proteasome condensates in yeast. Comments welcome!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
STI1 domain dynamically engages transient helices in disordered regions to drive self-association and phase separation of yeast ubiquilin Dsk2
Ubiquitin-binding shuttle proteins are important components of stress-induced biomolecular condensates in cells. Yeast Dsk2 scaffolds proteasome-containing condensates via multivalent interactions wit...
www.biorxiv.org
March 18, 2025 at 12:40 AM
#preprint Postdoc Nirbhik Acharya used NMR to find three transient helices within intrinsically-disordered regions of shuttle protein Dsk2 -- these interact with STI1. The STI1 is important for phase separation and proteasome condensates in yeast. Comments welcome!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Aniruddha Das
Fantastic article from Linda Hendershot—an incredible scientist and one of the most supportive and inspiring researchers I've had the pleasure of meeting.
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
A BiP-centric view of endoplasmic reticulum functions and of my career
After completing my post-doctoral training at the University of Alabama, Birmingham and a brief period on the faculty there, I joined the Department o…
www.sciencedirect.com
March 9, 2025 at 6:43 PM
Fantastic article from Linda Hendershot—an incredible scientist and one of the most supportive and inspiring researchers I've had the pleasure of meeting.
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
Reposted by Aniruddha Das
Happy to share this new #glycotime work with collaborator Tony Wyss-Coray, led by grad student Sophia Shi, mucin loss at the BBB is associated with aging and cognitive decline, can be reversed by restoration with with gene therapy. Aging is a mucinopathy!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Glycocalyx dysregulation impairs blood–brain barrier in ageing and disease - Nature
Disruption of mucin-domain glycoprotein expression and function in the endothelial glycocalyx are associated with ageing and Alzheimer’s disease, leading to dysregulated blood–brain barrier function.
www.nature.com
February 26, 2025 at 9:58 PM
Happy to share this new #glycotime work with collaborator Tony Wyss-Coray, led by grad student Sophia Shi, mucin loss at the BBB is associated with aging and cognitive decline, can be reversed by restoration with with gene therapy. Aging is a mucinopathy!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Aniruddha Das
I'm super excited to share our study in collaboration with @jnpruneda.bsky.social, published today in @embojournal.org! We show that PARPs are modified with a non-canonical ester-linked mono-ADP-ribosylated ubiquitin species for the first time in cells: www.embopress.org/doi/full/10....
Ubiquitin is directly linked via an ester to protein-conjugated mono-ADP-ribose | The EMBO Journal
imageimageCertain E3 ligases have been found to ubiquitylate hydroxyl groups on free NAD+ and
ADP-ribose in vitro, but the in vivo occurrence of this dual post-translational modification
has remained ...
www.embopress.org
February 25, 2025 at 5:52 PM
I'm super excited to share our study in collaboration with @jnpruneda.bsky.social, published today in @embojournal.org! We show that PARPs are modified with a non-canonical ester-linked mono-ADP-ribosylated ubiquitin species for the first time in cells: www.embopress.org/doi/full/10....
Reposted by Aniruddha Das
Check out these insights into (and the importance of) delivering ubiquitin-independent proteasomal substrates for degradation in the nucleus!
Thrilled to share our collaborative work on the structural basis and myeloma disease link of the midnolin-proteasome pathway with Chris Nardone from the Elledge lab, Jingjing Gao from the Shao lab @sshaolab.bsky.social and all the co-authors who put in the hard work! www.biorxiv.org/content/10.1...
Structural basis for the midnolin-proteasome pathway and its role in suppressing myeloma
The midnolin-proteasome pathway degrades many nuclear proteins without ubiquitination, but how it operates mechanistically remains unclear. Here, we present structures of the midnolin-proteasome compl...
www.biorxiv.org
February 24, 2025 at 9:35 PM
Check out these insights into (and the importance of) delivering ubiquitin-independent proteasomal substrates for degradation in the nucleus!
Reposted by Aniruddha Das
Amazing work by @sijiewang.bsky.social and our collaborators is out in JACS today. Interested in covalent inhibitors of protein-protein interactions? Check it out. pubs.acs.org/doi/10.1021/...
Identification of Covalent Cyclic Peptide Inhibitors Targeting Protein–Protein Interactions Using Phage Display
Peptide macrocycles are promising therapeutics for a variety of disease indications due to their overall metabolic stability and potential to make highly selective binding interactions with targets. R...
pubs.acs.org
February 25, 2025 at 2:51 AM
Amazing work by @sijiewang.bsky.social and our collaborators is out in JACS today. Interested in covalent inhibitors of protein-protein interactions? Check it out. pubs.acs.org/doi/10.1021/...