Biology subjects

Chaudhuri, B.

Publications and source records attributed to Chaudhuri, B..

8 recordsLinked to original sources

bioRxiv2026

A Structure-Based hERG Pose Selection Workflow Integrating Induced-Fit Docking, Shape Similarity, Interaction Fingerprints, and Molecular Dynamics

The recent availability of several ligand-bound hERG/Kv11.1 cryo-EM structures creates an opportunity for prospective structure-based modeling, but it also introduces a practical problem: a new ligand may be compatible with only a subset of the available receptor conformations, and docking may generate several plausible poses within each template. We therefore evaluated a template-aware pose-selection framework using the astemizole-, pimozide-, and E4031-bound hERG structures as experimental reference environments, with apo 8ZYN included as a receptor-state control. The ligand set separated into two study-defined chemical regions: a low-polarity, highly lipophilic Group I represented by astemizole and pimozide, and a more polar Group II represented by E4031. Induced-fit docking (IFD) improved self-docking relative to rigid Glide, whereas apo 8ZYN did not reproduce ligand-bound behavior during short molecular dynamics (MD) assessment. Across the retrospective ligand-bound analyses, six of seven group-matched systems met the dual MD-quality criterion, whereas none of eight group-mismatched systems did. Highest static shape similarity was the most consistent pose-selection criterion for Group I, while an interaction-fingerprint (IFP)-favored 30:70 shape:IFP composite was retained provisionally for the single retrospective Group II reference. Application to dofetilide, ibutilide, and terfenadine produced binding hypotheses with residue-contact patterns consistent with independent hERG literature. Together, these results support using ligand-bound hERG structures as chemically selective reference environments for pose prioritization rather than as interchangeable receptor templates.

pharmacology and toxicology↗

bioRxiv2026

Hydroxychloroquine alters the cytoskeleton to impair cell migration

Hydroxychloroquine (HCQ), a clinically relevant quinoline derivative, impairs both collective and individual cell migration by disrupting actin and vimentin cytoskeletal dynamics during wound healing. In scratch assays with HeLa cells, HCQ treatment significantly reduces wound closure rates and inhibits bursts of coordinated migration, as well as single-cell motility. Quantitative imaging reveals that HCQ diminishes actin filament density at the wound edge and induces reorganization of the vimentin network, resulting in smaller nuclei and compromised structural connectivity. Particle tracking micro-rheology demonstrates that HCQ softens the cytoplasm and decreases cellular mechanical heterogeneity. In vitro spectroscopic studies show that HCQ binds cooperatively to actin with micromolar affinity, perturbing its secondary structure, reducing filament polymerisation rates, and impairs interactions between actin and actin binding proteins (ABPs). HCQ also significantly suppresses lamellipodial protrusive activity, indicating a link between cytoskeletal remodelling and impaired cell migration. Collectively, these findings establish that HCQ disrupts essential mechanisms for directed migration by modulating the cytoskeleton and cell mechanics. This multifaceted impairment may underlie therapeutic potential of HCQ as an anticancer agent by restricting cellular invasive capacity and remodelling required for tumour progression.

cell biology↗

bioRxiv2025

A conformationally heterogeneous bending pivot enables bent-to-straight transition in the central helix of mycobacterial FtsZ

Conformational changes in the central helix at the inter-domain cleft of bacterial treadmilling motor protein FtsZ are coupled to polymerization. Central helix of mycobacterial FtsZ interconverts between a bent and a straight form, with an unknown mechanism. We probed the mechanism of this conformational switching in the central helix of mycobacterial FtsZ using multi-temperature synchrotron crystallography at 20 {o}C, 30 {o}C, 37 {o}C and -173 {o}C temperatures. A comparison of the resultant crystal structures of FtsZ revealed altered conformations at the bending pivot of the bent central helix inside the inter-domain cleft. Further, ensemble modeling of FtsZ structure shows that this bending pivot is labile at near-physiological temperatures. Conformational fluctuations in this pivot region resulted in breakage of regular alpha helical hydrogen bonds that likely made the central helix easily bendable. These fluctuations are largely arrested in the straightened form of the central helix in comparison to the bent form. To summarize, multi-temperature crystallography combined with ensemble modeling suggest that conformational heterogeneity and associated perturbations of helix-forming interactions in the bending pivot can trigger bent-to-straight conformational transition in the central helix of mycobacterial FtsZ. This work demonstrates the effectiveness of multi-temperature crystallography in delineating the mechanisms of conformational changes in protein machines.

biophysics↗

bioRxiv2024

Tubules, rods and spirals: diverse modes of SepF-FtsZ assembling

Z-ring formation by FtsZ, the master assembler of divisome, is a key step in bacterial cell division. Both formation and membrane anchoring of the Z-ring requires assistance of a number of Z-ring binding proteins, such as FtsA, EzrA, SepF, SepH and ZipA. SepF participates in bundling and membrane anchoring of FtsZ in gram-positive bacteria. We report in vitro biophysical studies of the interactions between FtsZ and cytoplasmic component of cognate SepF from three different bacteria: Mycobacterium tuberculosis, Staphylococcus aureus and Enterococcus gallinarum. While the cytosolic domain of SepF from M. tuberculosis is a dimer, those from S. aureus and E. gallinarum polymerize to form ring-like structures. Mycobacterial SepF helps in bundling of FtsZ filaments to form thick filaments and large spirals. On the other hand, ring-forming SepF from the Firmicutes bundle FtsZ into tubules.

biophysics↗

bioRxiv2024

Combining in-line chromatography coupled SAXS and AIpredicted structures to dissect the mechanism of ParB1parS1 partition assembly formation

Coupling of solution SAXS and AI-predicted structures can be a powerful strategy for delineating subtle conformational changes and self-association in protein switches. ParB, which is a condensate-forming DNA clamp that aids in bacterial chromosomal origin segregation, undergoes CTP-induced conformational switching to enable DNA sliding. The nature of parS DNA-induced conformational change in full-length ParB, and the structural features that govern self-association of ParB for partition assembly condensate formation, remains sparsely understood. We combined chromatography-coupled SAXS, rigid domains obtained from Alphafold model of ParB1 from Vibrio cholerae, and synthetic SAXS data describing known domain interfaces, to build integrative models of conformational states of full-length ParB1. These integrative models revealed how parS1 DNA loading primed ParB1 for clamping and sliding. The CTPase domains in ParB1 were moved nearer upon DNA loading to facilitate clamping, and a lumen lined with a weak DNA binding site was formed below parS1 binding site for capturing the sliding DNA. Furthermore, we showed that an N-terminal segment of ParB1 undergoes concentration-dependent oligomerization. An intrinsically disordered linker joining this oligomerization-prone N-terminal segment and the C-terminal domain curbs self-association of full-length ParB1, which is likely relevant for ParB1-mediated higher order partition assembly formation. To summarize, SAXS and Alphafold were effectively combined to provide unique insights into context-specific domain rearrangements and self-association in ParB1 for the mechanistic understanding of partition assembly formation.

biophysics↗

bioRxiv2020

Robust integrated intracellular organization of the human iPS cell: where, how much, and how variable?

Despite the intimate link between cell organization and function, the principles underlying intracellular organization and the relation between organization, gene expression and phenotype are not well understood. We address this by creating a benchmark for mean cell organization and the natural range of cell-to-cell variation. This benchmark can be used for comparison to other normal or abnormal cell states. To do this, we developed a reproducible microscope imaging pipeline to generate a high-quality dataset of 3D, high-resolution images of over 200,000 live cells from 25 isogenic human induced pluripotent stem cell (hiPSC) lines from the Allen Cell Collection. Each line contains one fluorescently tagged protein, created via endogenous CRISPR/Cas9 gene editing, representing a key cellular structure or organelle. We used these images to develop a new multi-part and generalizable analysis approach of the locations, amounts, and variation of these 25 cellular structures. Taking an integrated approach, we found that both the extent to which a structures individual location varied ("stereotypy") and the extent to which the structure localized relative to all the other cellular structures ("concordance") were robust to a wide range of cell shape variation, from flatter to taller, smaller to larger, or less to more polarized cells. We also found that these cellular structures varied greatly in how their volumes scaled with cell and nuclear size. These analyses create a data-driven set of quantitative rules for the locations, amounts, and variation of 25 cellular structures within the hiPSC as a normal baseline for cell organization.

cell biology↗

bioRxiv2019

Crystal structure of the membrane anchoring domain of mycobacterial Wag31: a dimer-of-dimer suggests how a Wag31 filament might self-assemble

Wag31, or DivIVA, is an essential protein and a drug target in human pathogen Mycobacterium tuberculosis that self-assembles at the negatively curved membrane surface to form a higher-order structural scaffold, maintains rod-shaped cellular morphology, and localizes key cell-wall synthesizing proteins at the pole for exclusive polar growth. We determined the crystal structure of N-terminal membrane anchoring domain of mycobacterial Wag31 at 2.3 [A] resolution using molecular replacement method. Crystal packing analysis revealed a previously unseen dimer-of-dimer assembly state of N-terminal Wag31 with C2 point group symmetry, which is formed by antiparallel stacking of two coiled coil dimers. Size-exclusion column chromatography-coupled small angle solution X-ray scattering data showed a tetrameric form as a major assembly state of N-terminal Wag31 in solution, further supporting the crystal structure. Plausible models of linear self-assembling, and branching, of Wag31 filaments consistent with available data are suggested.

biophysics↗

bioRxiv2018

Higher order assembling of the mycobacterial essential polar growth factor DivIVA/Wag31

How proteins localize at the pole remains an enigma. DivIVA/Wag31, which is an essential pole organizing protein in mycobacteria, can assemble at the negatively curved side of the membrane at the growing pole to form a higher order structural scaffold for maintaining cellular morphology and localizing various target proteins for cell-wall biogenesis. A single-site phosphorylation in Wag31 is linked to the regulation of peptidoglycan biosynthesis for optimal mycobacterial growth. The structural organization of polar scaffold formed by coiled-coil rich Wag31, which is a target for anti-tubercular agent amino-pyrimidine sulfonamide, remains to be determined. Here, we report biophysical characterizations of a phospho-mimetic (T73E) and a phospho-ablative (T73A) form of mycobacterial Wag31 using circular dichroism, small angle solution X-ray scattering and atomic force microscopy. While data obtained from both variants of Wag31 in solution states suggested formation of alpha-helical, large, elongated particles, their structural organizations were different. Atomic force microscopic images of Wag31 indicate polymer formation, with occasional curving, sharp bending and branching. Observed structural features in this first view of the polymeric forms of Wag31 suggest a basis for higher order network scaffold formation for polar protein localization.

biophysics↗