Biology subjects

Mukhopadhyay, J.

Publications and source records attributed to Mukhopadhyay, J..

3 recordsLinked to original sources

bioRxiv2026

Human prion proteins and mutants through the lens of systems biology

Autocatalytic conformational changes of cellular prion proteins (PrPC) to the {beta}-sheet-enriched scrapie isoform (PrPSC) drive prion diseases, yet the precise molecular mechanisms remain unclear. To address this, we employ a multi-pronged framework integrating network-theoretic analyses, molecular dynamics (MD) simulations, and experimental validation to characterize critical residues governing human PrP (huPrP) structural integrity. Residue Interaction Networks (RINs) of: (A) wild-type (WT) huPrP, and, (B) five disease-associated point mutants (Met166Val, Glu220Lys, Glu200Lys, Asp178Asn, and Ser170Asn) were evaluated using three rigorous network methods: centrality measures, Shortest Path Alteration Fraction (SPAF), and Differential Networks (DN). Across all the diverse point mutations, five residues (Met206, Val209, Val210, Met213, and Cys214) consistently exhibit high centrality scores. SPAF and DN analyses demonstrate that alterations at these positions disrupt connectivity and increase the propensity for misfolding and protease resistance. To validate these topological findings, key residues within the C-terminal domain (121-230) were substituted via site-directed mutagenesis. Thermal denaturation monitored by circular dichroism (CD) spectroscopy reveals that the Met213Ala substitution significantly lowers the melting temperature, Tm, relative to the WT, whereas the Val210Ala variant unfolds with a Tm comparable to the WT. Furthermore, MD simulations of de novo AlphaFold-predicted mutant structures corroborate these findings. Mutants exhibit greater structural flexibility and deviation, with average root Mean Square Deviations rising from 0.18 nm (WT) to 0.32 nm (Cys214Ala), 0.29 nm (Met206Ala), and 0.25 nm (Val210Lys). This integration of theoretical and experimental techniques provides a robust framework for identifying critical determinants of protein stability.

systems biology↗

bioRxiv2026

Nanoscale visualization of ribonucleoprotein condensates with ultrastructure RNA expansion microscopy

Superresolution imaging of RNAs in their native cellular context is crucial for investigating RNA biology. Here, we develop Ultrastructure RNA Expansion (UREx) microscopy, an expansion microscopy approach, that retains cellular RNAs and RNP granule condensates. We demonstrate that UREx retains the highly ordered core-shell architecture of Neat1 RNA in the paraspeckles, confirming RNA ultrastructure preservation. In addition to robust RNA retention, UREx also preserves protein epitopes and overall cellular protein ultrastructure thus enabling context-dependent visualization of RNAs in cells as well as intact tissues. Employing UREx, we visualize RNP condensates in the intact Drosophila germline and resolve diffraction-limited oskar granules into RNP nanoclusters. Together, our findings establish UREx as a broadly applicable and cost-effective resource to interrogate the nanoscale spatial organization of RNAs and proteins within diffraction-limited RNP assemblies.

cell biology↗

bioRxiv2025

Azadiradione regulates Heat Shock Factor 1 function by interacting with its DNA-binding domain independent of the oligomerization domain

Heat shock factor 1 (HSF1) masters cellular proteostasis under stress by upregulating the expression of molecular chaperones that help refold or degrade the misfolded proteins. HSF1 activation involves a monomer-to-oligomer transition and binding to its recognition sequence, the heat shock elements (HSEs) on its target gene promoters. HSF1 activity declines with age as well as in neurodegenerative disorders (NDs) such as Parkinsons disease, highlighting the need for strategies to restore its function. Azadiradione (AZD), a limonoid isolated from Azadirachta indica seeds, directly activates HSF1 in cellular and preclinical ND models, unlike other small-molecule activators reported elsewhere. We investigated the molecular basis of AZD-mediated HSF1 activation using purified variants of this protein including those without its oligomerization and transactivation domain. Fluorescence polarization and dynamic light scattering assays revealed that AZD promotes the oligomerization of monomeric HSF1 to enhance its HSE-binding affinity by engaging with its DNA-binding domain (DBD). The oligomerization domain known to be required for stress-induced activation, appears redundant in AZD-mediated activation. Furthermore, evidence suggests AZD-induced conformational alterations in the HSE facilitate its binding to the HSF1 monomer. Notably, AZD reduces the DNA-binding ability of pre-assembled oligomeric HSF1 by triggering its amyloid-like aggregation. This finding also highlighted a potential anticancer effect of AZD, as cancer cells heavily depend on this HSF1 population for rapid proliferation and survival. Overall, these findings offer novel insights into the functional regulation of HSF1 and suggest a framework for developing small-molecule HSF1 activators with therapeutic potential for protein conformation disorders.

biochemistry↗