Biology subjects

DAS, P.

Publications and source records attributed to DAS, P..

3 recordsLinked to original sources

bioRxiv2024

Computational Exploration of Protein Structure Dynamics and RNA structural Consequences of PKD1 Missense Variants: Implications in ADPKD Pathogenesis

Autosomal dominant polycystic kidney disease (ADPKD), a genetic disorder characterized by the formation of fluid-filled cysts within the kidneys, leading to progressive renal dysfunction, is primarily caused by mutations in PKD1, a gene encoding for the protein polycystin-1 (PC1). Understanding the structural consequences of PKD1 variants is crucial for elucidating disease mechanisms and developing targeted therapies. In this study, we analyzed the effects of nine missense PKD1 variants, including c.6928G>A p.G2310R, c.8809G>A p.E2937K, c.2899T>C p.W967R, c.6284A>G p.D2095G, c.6644G>A p.R2215Q, c.7810G>A p.D2604N, c.11249G>C p.R3750P, c.1001C>T p.T334M, and c.3101A>G p.N1034S on RNA structures, their interactions utilizing computational tools. We also explain the effects of these variants on PC1 protein dynamics, stability, and interactions using molecular dynamics (MD) simulation. These variants are located at crucial domains such as the REJ domain, PKD domains, and cation channel domain, potentially compromising PC1s function and contributing to ADPKD pathogenesis. Findings reveal substantial deviations in RNA structures and their interactions with other proteins or RNAs and also protein structure and dynamics for variants such as c.8809G>A (p.E2937K), c.11249G>C (p.R3750P), c.3101A>G (p.N1034S), c.6928G>A (p.G2310R), c.6644G>A (p.R2215Q) suggesting their potential implications in disease etiology. The study also suggests that although certain variants may have minimal effects on RNA conformations, their observed alterations in MD simulations indicate potential impact on protein structure dynamics highlighting the importance of evaluating the functional consequences of genetic variants by considering both RNA and protein levels. This study offers valuable perspectives of the utility of studying the structure dynamics through computational tools in prioritizing the variants for their functional implications and understanding the molecular mechanisms underlying ADPKD pathogenesis and developing therapeutic interventions. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=173 SRC="FIGDIR/small/586139v1_ufig1.gif" ALT="Figure 1"> View larger version (79K): org.highwire.dtl.DTLVardef@4623f0org.highwire.dtl.DTLVardef@e186a1org.highwire.dtl.DTLVardef@4deffaorg.highwire.dtl.DTLVardef@c60744_HPS_FORMAT_FIGEXP M_FIG C_FIG

genetics↗

bioRxiv2023

Calcimycin mediates apoptosis in Breast and Cervical cancer cells by inducing intracellular calcium levels in a P2RX4-dependent manner

Calcimycin (A23187) is a polyether antibiotic and divalent cation ionophore, extracted from Streptomyces chartrecensis. With wide variety of antimicrobial activities, it also exhibits cytotoxicity of tumor cells. Calcimycin exhibit therapeutic potential against tumor cell growth; however, the molecular mechanism remains to be fully elucidated. Present study explores the mechanism of calcimycin-induced apoptosis cancer cell lines. Calcimycin induces apoptosis accompanied by increased intracellular calcium-level and increased expression of purinergic receptor-P2RX4, a ligand-gated ion channel. The percentage of apoptotic cancer cells in a dose-dependent manner quickly rose as recorded with MTT assays, Phase contrast imaging, wound healing assay, fluorescence imaging by DAPI and AO/EB staining and FACS. Mitochondrial potential was analyzed by TMRM assay as Ca2+ signaling is well known to be influenced and synchronized by mitochondria also. Calcimycin treatment tends to increase the intracellular calcium level, mRNA expression of ATP receptor P2RX4, and phosphorylation of p38. Blocking of either intracellular calcium by BAPTA-AM, P2RX4 expression by antagonist 5-BDBD, and phospho-p38 by SB203580, abrogated the apoptotic activity of calcimycin. Taken together, these results show that calcimycin induces apoptosis in P2RX4 dependent ATP mediated intracellular Ca2+ and p38 MAPK mediated pathway in both the cancer cell lines.

cancer biology↗

bioRxiv2022

An in vitro and computational validation of a novel loss-of-functional mutation in PAX9 associated with non-syndromic tooth agenesis

Congenital tooth agenesis (CTA) is one of the most common craniofacial anomalies. Its frequency varies among different population depending upon the genetic heterogeneity. CTA could be of familial or sporadic and syndromic or non-syndromic. Five major genes are found to be associated with non-syndromic CTA namely, PAX9, MSX1, EDA1, AXIN2 and WNT10A. In this study, an India family with CTA was investigated and a novel c.336C>G variation was identified in the exon 3 of PAX9, leading to substitution of evolutionary conserved Cys with Trp at 112 amino acid position located at the functionally significant DNA binding paired domain region. Functional analysis revealed that p.Cys112Trp mutation did not prevent the nuclear localization although mutant protein had higher cytoplasmic retention. EMSA using e5 probe revealed that mutant protein was unable to bind with the paired-domain binding site. Subsequently, GST pull-down assay revealed lower binding activity of the mutant protein with its known interactor MSX1. Further RNA-sequencing of PAX9 over-expressed HEK293, identified two potential novel targets, WNT4 and WNT7b those are up-regulated by wild-type PAX9 but not by mutant. These in vitro results were consistent with the computational results. The in vitro and computational observations altogether suggest that c.336C>G (p.Cys112Trp) variation leads to loss-of-function of PAX9 leading to CTA in this family.

molecular biology↗