Nilimesh Das

Co-transcriptional folding orchestrates sequential multi-effector sensing by a glycine tandem riboswitch - Nature Communications Riboswitches are RNA elements that regulate gene expression through dynamic changes in secondary structure. Here, the authors reveal how the glycine tandem riboswitch integrates sequential signals via...

How does a riboswitch regulate genes?
glycine tandem riboswitch follows a stepwise 5’ to 3’ folding pathway guided by polymerase pausing and stepwise ligand binding, leading to cooperativity through non-equilibrium mechanisms, not classical concerted model.
www.nature.com/articles/s41...

14.02.2026 16:15 — 👍 0    🔁 0    💬 0    📌 0

MYC binding to nascent RNA suppresses innate immune signaling by R-loop-derived RNA-DNA hybrids RNA-binding-mediated multimerization of MYC concentrates RNA-degrading factors around double-stranded RNAs and R-loops. This prevents aberrant RNAs from accumulating and leaking into the cytosol. Thro...

RNA-binding protein MYC binds to nascent, intronic RNA.
It then forms multimers, and suppresses the accumulation of R-loop to prevent innate immune signalling: Cell www.cell.com/cell/fulltex...

14.02.2026 08:19 — 👍 1    🔁 0    💬 0    📌 0

Structural dynamics of mixed-subunit CaMKIIα/β heterododecamers filmed by high-speed AFM Nature Communications - High-speed AFM reveals CaMKIIα/β subunits are mixed within 12-unit rings, with βs frequently neighboring. Activated heterooligomers form stable kinase...

HS-AFM revaealed the architecture of CaMKIIα/β, a protein essential for memory!

Dynamic HS-AFM imaging shows how α and β subunits mix and stabilize the active state.

rdcu.be/e3VCP

14.02.2026 01:31 — 👍 1    🔁 0    💬 0    📌 0

Intrinsically disordered regions facilitate target search to drive promoter selectivity by a yeast transcription factor Nature Communications - The study reveals how intrinsically disordered regions enable a yeast transcription factor to locate and selectively bind its target promoters by promoting DNA association...

Non-specific interaction plays a big role on how selectivity emerges in cells!!
Intrinsically disordered regions power the search facilitating initial non-specific association with DNA to find promoter.
rdcu.be/e0mIF

23.01.2026 07:19 — 👍 1    🔁 0    💬 0    📌 0

Stag2 dependent chromatin remodeling enforces the erythroid-specific Gata1 cistrome The transcription factor GATA1 has pleiotropic hematopoietic functions, particularly in erythroid and megakaryocytic ontogeny. While mechanistic investigations have uncovered many facets of GATA1 biol...

🚨 Excited to share our new preprint: Stag2 dependent chromatin remodeling enforces the erythroid-specific Gata1 cistrome. This work was led by Columbia VP&S MD student Varun Sudunagunta (‼️ Program Directors: Varun is applying to IM residencies this year!) www.biorxiv.org/content/10.1...

22.09.2025 14:29 — 👍 5    🔁 3    💬 2    📌 0

Confocal scanning laser microscopy, fluorescence lifetime imaging & Raman analyses allowed @nhm-london.bsky.social, @slcuplants.bsky.social & @cambridge-ee.bsky.social researchers to resolve plant & fungal structures fossil
Read in @newphyt.bsky.social
doi.org/10.1111/nph....

@dromius.bsky.social

12.11.2025 12:31 — 👍 37    🔁 12    💬 1    📌 2

Unraveling Protein Clumps: Using Fluorescence to Study Aggregation at the Nano Scale This study uses advanced fluorescence techniques to track how proteins like bromelain clump together at extremely low concentrations. The authors compare different methods, highlighting how fluorescen...

Protein aggregation in cells can start at nanomolar levels as tiny clusters that are hard to see with standard methods. This study uses fluorescence correlation spectroscopy to spot and study these invisible early aggregates.

www.growkudos.com/publications...

30.12.2025 08:09 — 👍 1    🔁 0    💬 0    📌 0

Formation of multicompartment structures through aging of protein-RNA condensates Cells can dynamically organize reactions through the formation of biomolecular condensates. These viscoelastic networks exhibit complex material properties and mesoscale architectures, including the a...

In aged condensates, weaker protein–RNA interactions release RNA from the dense phase. Aging plus slow macromolecular diffusion then tarts nucleatiin, producing double-emulsion.

Formation of multi compartment structures through aging of protein-RNA condensates: www.cell.com/biophysj/ful...

28.12.2025 02:02 — 👍 2    🔁 0    💬 0    📌 0

Cryo-EM snapshots of Wadjet show how ATP fuels a 360° dimer rotation to trap DNA and set the stage for loop extrusion

31.10.2025 15:56 — 👍 2    🔁 0    💬 0    📌 0

Ancient amino acid sets enable stable protein folds Early proteins likely arose from a chemically limited set of amino acids available through prebiotic chemistry, raising a central question in molecular evolution: could such primitive compositions yie...

You don't need all 20 amino acids to build proteins! Here, authors showed
a reduced 10-amino-acid alphabet form exceptionally stable and resistant to mutations proteins!!
A key insight into the #OriginOfLife and a new foundation for minimalist #ProteinDesign.

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

31.10.2025 06:53 — 👍 2    🔁 0    💬 0    📌 0

How Water Shapes Protein Behavior in Crowded Spaces This study explores how proteins behave under crowded conditions, mimicking the complex environment inside cells. Using bromelain (a protein found in pineapple) and Ficoll-70 (a sugar-based crowding a...

link.growkudos.com/1b8sjkvls00

12.09.2025 15:40 — 👍 2    🔁 0    💬 0    📌 0

Diagram to represent the interrelated factors involved in the photo-regulatory mechanisms of Arabidopsis CRY complexes. Dual mechanisms of action, including the “Lock-and-Key” and the “Liquid-Liquid Phase Separation (LLPS)” mechanisms, explain, at least partially, the structural diversity of CRY-interacting proteins and the functional diversity of the CRY photoreceptors.

💪 Small but mighty! This JIPB mini-review explores the remarkable dual-action mechanism of #Arabidopsis cryptochromes. PlantScience onlinelibrary.wiley.com/doi/10.1111/...

28.02.2024 13:20 — 👍 5    🔁 3    💬 0    📌 0