Department of Biological Sciences

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Ab initio Folding Simulation of the Trp-cage Mini-protein Approaches NMR Resolution
(Elsiever, 2003-03-28) Chowdhury, Shibasish
Here, we report a 100 ns molecular dynamics simulation of the folding process of a recently designed autonomous-folding mini-protein designated as tc5b with a new AMBER force field parameter set developed based on condensed-phase quantum mechanical calculations and a Generalized Born continuum solvent model. Starting from its fully extended conformation, our simulation has produced a final structure resembling that of NMR native structure to within 1 Å main-chain root mean square deviation. Remarkably, the simulated structure stayed in the native state for most part of the simulation after it reached the state. Of greater significance is that our simulation has not only reached the correct main-chain conformation, but also a very high degree of accuracy in side-chain packing conformation. This feat has traditionally been a challenge for ab initio simulation studies. In addition to characterization of the trajectory, comparison of our results to experimental data is also presented. Analysis of the trajectory suggests that the rate-limiting step of folding of this mini-protein is the packing of the Trp side-chain.
Analysis of seven putative Na+/H+ antiporters of Arthrospira platensis NIES-39 using transcription profiling and in silico studies: an indication towards alkaline pH acclimation
(Springer, 2019-09) Chowdhury, Shibasish; Bhagavatula, Vani
Na+/H+ antiporters mediated pH regulation is one of the known mechanism(s), which advocates a possible role of the antiporters in the alkaline pH tolerance of Arthrospira platensis NIES-39. Seven putative Na+/H+ antiporters have been reported in A. platensis NIES-39. Based upon the in silico analysis, the seven putative antiporters were characterized into two different superfamilies, where A1, Q2, L2, and L6 belonged to the CPA1 family whereas C5, D5 and O6 belonged to CPA2 family. The orientation of functionally important residues in both CPA1 and CPA2 subfamily are conserved in modeled Q2 and C5 antiporters. Conserved domain analysis of the seven putative antiporters indicated the presence of nine different kinds of domains. Out of these nine domains, six domains function as monovalent cation-proton antiporters and two as the universal stress protein (Usp) category. Transcription profile of these seven antiporters was also generated at three different pH (7, 9 and 11) and time frames which showed a significant difference in the mRNA levels along with a temporal pattern of the expression profile. The in silico and the real-time PCR analysis put together, suggest the active participation of these seven putative Na+/H+ antiporters in alkaline pH homeostasis of this cyanobacterial strain where CPA1 subfamily antiporters play a major role.
Analysis of seven putative Na+/H+ antiporters of Arthrospira platensis NIES-39 using transcription profiling and in silico studies: an indication towards alkaline pH acclimation
(Springer, 2019-09) Bhagavatula, Vani; Chowdhury, Shibasish
Na+/H+ antiporters mediated pH regulation is one of the known mechanism(s), which advocates a possible role of the antiporters in the alkaline pH tolerance of Arthrospira platensis NIES-39. Seven putative Na+/H+ antiporters have been reported in A. platensis NIES-39. Based upon the in silico analysis, the seven putative antiporters were characterized into two different superfamilies, where A1, Q2, L2, and L6 belonged to the CPA1 family whereas C5, D5 and O6 belonged to CPA2 family. The orientation of functionally important residues in both CPA1 and CPA2 subfamily are conserved in modeled Q2 and C5 antiporters. Conserved domain analysis of the seven putative antiporters indicated the presence of nine different kinds of domains. Out of these nine domains, six domains function as monovalent cation-proton antiporters and two as the universal stress protein (Usp) category. Transcription profile of these seven antiporters was also generated at three different pH (7, 9 and 11) and time frames which showed a significant difference in the mRNA levels along with a temporal pattern of the expression profile. The in silico and the real-time PCR analysis put together, suggest the active participation of these seven putative Na+/H+ antiporters in alkaline pH homeostasis of this cyanobacterial strain where CPA1 subfamily antiporters play a major role.
Autophagy Regulated by Gain of Function Mutant p53 Enhances Proteasomal Inhibitor-Mediated Cell Death through Induction of ROS and ERK in Lung Cancer Cells
(Hindawi, 2019) Chowdhury, Shibasish; Chowdhury, Rajdeep; Mukherjee, Sudeshna
Mutations in p53, especially gain of function (GOF) mutations, are highly frequent in lung cancers and are known to facilitate tumor aggressiveness. Yet, the links between mutant GOF-p53 and lung cancers are not well established. In the present study, we set to examine how we can better sensitize resistant GOF-p53 lung cancer cells through modulation of cellular protein degradation machineries, proteasome and autophagy. H1299 p53 null lung cancer cells were stably transfected with R273H mutant GOF-p53 or wild-type (wt) p53 or empty vectors. The presence of R273H-P53 conferred the cancer cells with drug resistance not only against the widely used chemotherapeutic agents like cisplatin (CDDP) or 5-flurouracil (5-FU) but also against potent alternative modes of therapy like proteasomal inhibition. Therefore, there is an urgent need for new strategies that can overcome GOF-p53 induced drug resistance and prolong patient survival following failure of standard therapies. We observed that the proteasomal inhibitor, peptide aldehyde N-acetyl-leu-leu-norleucinal (commonly termed as ALLN), caused an activation of cellular homeostatic machinery, autophagy in R273H-P53 cells. Interestingly, inhibition of autophagy by chloroquine (CQ) alone or in combination with ALLN failed to induce enhanced cell death in the R273H-P53 cells; however, in contrast, an activation of autophagy by serum starvation or rapamycin increased sensitivity of cells to ALLN-induced cytotoxicity. An activated autophagy was associated with increased ROS and ERK signaling and an inhibition of either ROS or ERK signaling resulted in reduced cytotoxicity. Furthermore, inhibition of GOF-p53 was found to enhance autophagy resulting in increased cell death. Our findings provide novel insights pertaining to mechanisms by which a GOF-p53 harboring lung cancer cell is better sensitized, which can lead to the development of advanced therapy against resistant lung cancer cells.
Breaking non-native hydrophobic clusters is the rate-limiting step in the folding of an alanine-based peptide
(Wiley, 2002-11-25) Chowdhury, Shibasish
The formation mechanism of an alanine-based peptide has been studied by all-atom molecular dynamics simulations with a recently developed all-atom point-charge force ﬁeld and the Generalize Born continuum solvent model at an effective salt concentration of 0.2M. Thirty-two simulations were conducted. Each simulation was performed for 100 ns. A surprisingly complex folding process was observed. The development of the helical content can be divided into three phases with time constants of 0.06 – 0.08, 1.4 –2.3, and 12–13 ns, respectively. Helices initiate extreme rapidly in the ﬁrst phase similar to that estimated from explicit solvent simulations. Hydrophobic collapse also takes place in this phase. A folding intermediate state develops in the second phase and is unfolded to allow the peptide to reach the transition state in the third phase. The folding intermediate states are characterized by the two-turn short helices and the transition states are helix–turn– helix motifs— both of which are stabilized by hydrophobic clusters. The equilibrium helical content, calculated by both the main-chain ⌽–⌿ torsion angles and the main-chain hydrogen bonds, is 64 – 66%, which is in remarkable agreement with experiments. After corrected for the solvent viscosity effect, an extrapolated folding time of 16 –20 ns is obtained that is in qualitative agreement with experiments. Contrary to the prevailing opinion, neither initiation nor growth of the helix is the rate-limiting step. Instead, the rate-limiting step for this peptide is breaking the non-native hydrophobic clusters in order to reach the transition state. The implication to the folding mechanisms of proteins is also discussed
Characterizing the rate-limiting step of Trp-cage folding by all-atom molecular dynamics simulations
(ACS, 2004) Chowdhury, Shibasish
In this study, the detailed mechanisms of the rapid-folding Trp-cage mini-protein were investigated by extensive all-atom molecular dynamics simulations of both wild-type and mutant proteins using a recently developed point-charge force field within the AMBER simulation package and the generalized Born treatment of solvation. Among the 77 100-ns simulations performed on the wild-type protein, 5 of the simulation trajectories yielded structures with main-chain RMSDs of 1.0−2.0 Å from the native NMR structure. A gradual reduction in the value of the main-chain RMSD distribution was observed during the simulations, which is consistent with the folding funnel theory. The folding time of ∼3 μs based on native tertiary contacts is in reasonable agreement with an experimental value of ∼4 μs. Detailed analysis suggests that packing of the structurally important Trp25 side chain is involved in the rate-limiting step and unfolding of the misfolded states and overcoming the additional entropic barrier also contributed to the rate-limiting steps. This is reinforced by the faster folding rate of the W25F mutant. Two putative folding pathways were observed from the simulations, and their folding rates differed by about 200-fold, leading to a 3.2 kcal/mol folding free energy barrier difference. Of this, approximately 2.2 kcal/mol was due to unfolding of the misfolded states, and about 1.0 kcal/mol was due to overcoming the entropic cost to move Trp25 side chain into the native orientation. Although formation of the main-chain contacts was not the rate-limiting step, we observed a hierarchical process in which the short-range native contacts formed faster than the long-range ones. These observations are consistent with the contact-order theory.
Chloroquine attenuates hypoxia-mediated autophagy to curb thrombosis- an ex vivo and in vivo study
(2024-04) Mukherjee, Sudeshna; Majumder, Syamantak; Chowdhury, Shibasish; Chowdhury, Rajdeep
Hypoxia can trigger the activation of blood platelets, leading to thrombosis. If not addressed clinically, it can cause severe complications and fatal consequences as well. The current treatment regime for thrombosis is often palliative and includes long-term administration of anticoagulants, which has the risk of over-bleeding in injury and other secondary effects as well. This demands a deeper understanding of the process and exploration of an alternative therapeutic avenue. Interestingly, recent studies demonstrate that platelets though atypical and enucleated, possess components of autophagy machinery. This cellular homeostatic process though well-studied in non-platelet cells, is under-explored in platelets.
Chloroquine induces transitory attenuation of proliferation of human lung cancer cells through regulation of mutant P53 and YAP
(Springer, 2022-11) Chowdhury, Shibasish; Chowdhury, Rajdeep; Mukherjee, Sudeshna
Non-small cell lung carcinoma (NSCLC) is the most common cause of cancer-associated deaths worldwide. Though recent development in targeted therapy has improved NSCLC prognosis, yet there is an unmet need to identify novel causative factors and appropriate therapeutic regimen against NSCLCs.
Cisplatin-induced oxidative stress regulates YAP to modulate epigenome promoting survival of osteosarcoma cells
(2025-08) Chowdhury, Rajdeep; Chowdhury, Shibasish; Mukherjee, Sudeshna
The widely used chemotherapeutic drug cisplatin (CDDP) is an integral part of the pre-operative chemotherapy protocol for high-grade osteosarcoma (OS). However, despite an aggressive treatment regimen, drug refractoriness is a major hindrance to successful therapy. We previously identified key transcriptomic alterations essential for the survival of OS cells following CDDP exposure. In the present study, we further demonstrate that CDDP treatment resulted in a ROS-dependent enrichment of the repressive histone mark H3K27me3 at the upstream promoter regions of growth-promoting genes such as CCNA2, and on the promoter of the negative regulator of Yes-Associated Protein (YAP)-LATS1, thereby contributing to their transcriptional repression. This was associated with a growth arrest, and quenching of ROS with N-acetyl cysteine (NAC) reversed it. Importantly, repression of LATS1 led to an increased nuclear localization of YAP, while pharmacological or genetic ablation of YAP reduced CDDP-mediated induction of repressive marks. YAP was further found to co-localize and co-immunoprecipitate with the Polycomb Repressive Complex 2 (PRC2) catalytic member-the histone methyl transferase-EZH2, indicating its putative role in mediating transcriptional repression. In lieu of the above, inhibition of YAP or reversal of the repressive chromatin state using a histone deacetylase (HDAC) inhibitor sensitized OS cells to a low-dose CDDP treatment as well. Overall, the present study demonstrates an interplay between oxidative stress, epigenetics, and YAP in modulating OS cell fate post CDDP exposure.
Common and Unique microRNAs in Multiple Carcinomas Regulate Similar Network of Pathways to Mediate Cancer Progression
(Springer Nature, 2020) Chowdhury, Rajdeep; Chowdhury, Shibasish; Majumder, Syamantak; Majumder, Syamantak
Cancer is a complex disease with a fatal outcome. Early detection of cancer, by monitoring appropriate molecular markers is very important for its therapeutic management. In this regard, the short non-coding RNA molecules, microRNAs (miRNAs) have shown great promise due to their availability in circulating fluids facilitating non-invasive detection of cancer. In this study, an in silico comparative analysis was performed to identify specific signature miRNAs dysregulated across multiple carcinomas and simultaneously identify unique miRNAs for each cancer type as well. The miRNA-seq data of cancer patient was obtained from GDC portal and their differential expressions along with the pathways regulated by both common and unique miRNAs were analyzed. Our studies show twelve miRNAs commonly dysregulated across seven different cancer types. Interestingly, four of those miRNAs (hsa-mir-210, hsa-mir-19a, hsa-mir-7 and hsa-mir-3662) are already reported as circulatory miRNAs (circRNAs); while, the miR-183 cluster along with hsa-mir-93 have been found to be incorporated in exosomes signifying the importance of the identified miRNAs for their use as prospective, non-invasive biomarkers. Further, the target mRNAs and pathways regulated by both common and unique miRNAs were analyzed, which interestingly had significant commonality. This suggests that miRNAs that are commonly de-regulated and specifically altered in multiple cancers might regulate similar pathways to promote cancer. Our data is of significance because we not only identify a set of common and unique miRNAs for multiple cancers but also highlight the pathways regulated by them, which might facilitate the development of future non-invasive biomarkers conducive for early detection of cancers.
Cyanobacterial Stresses: An Ecophysiological, Biotechnological and Bioinformatic Approach
(LAMBERT Academic Publishing, 2014-02-26) Chowdhury, Shibasish
From time immemorial cyanobacteria have been acquiring an inquisitive field of burgeoning research owing to their ecological adaptivity, ubiquitous presence and efficient source of compounds of biotechnological significance. Cyanobacteria are supposed to have evolved during the Precambrian era and believed to be the first one to introduce oxygen into the initially reducing atmosphere by oxygenic photosynthesis. Reactive oxygen species (ROS) in cyanobacteria are commonly generated during normal growth and development. However abiotic and biotic stresses enhance the level of ROS which in turn pose the danger of oxidative stress. Ability to perceive ROS and to rapidly initiate antioxidant defenses is crucial for their survival. Therefore cyanobacteria evolved four lines of defense mechanisms with enzymatic and non-enzymatic antioxidants as an arsenal to cope with multiple stresses. Moreover bioinformatical methods and tools provide an insight to the in silico structure prediction of the antioxidative proteins of cyanobacterial origin.
Denatured-state ensemble and the early-stage folding of the G29A mutant of the B-domain of protein A
(ACS, 2005-04) Chowdhury, Shibasish
The folding mechanism of the G29A mutant of the B-domain of protein A (BdpA) has been studied by all-atom molecular dynamics simulation using AMBER force field (ff03) and generalized Born continuum solvent model. Started from the extended chain conformation, a total of 16 simulations (400 ns each) at 300 K captured some early folding events of the G29A mutant of BdpA. In one of the 16 trajectories, the G29A mutant folded within 2.8 Å (root mean square) of the wild-type NMR structure. We observed that the fast burial of hydrophobic residues was the driving force to bring the distant residues into close proximity. The initiation of the helix I and III occurred during the stage of hydrophobic collapse. The initiation and growth of the helix II was slow. Both the secondary structure formation and the development of the native tertiary contacts suggested a multistage folding process. Clustering analysis indicated that two helix species (helices I and III) could be intermediates. Further analysis revealed that the hydrophobic residues of partially folded helix II formed nativelike hydrophobic contacts with helices I and III that stabilized a nativelike state and delayed the completion of folding of the entire protein. The details of the early folding process were compared with other theoretical and experimental studies. It was found that a nativelike hydrophobic cluster was formed by residues including F30, I31, L34, L44, L45, and A48 that prevented further development of the native structures, and breaking the hydrophobic cluster like this one contributed to the rate-limiting step. This was in complete agreement with the recent kinetic measurements in which mutations of these residues to Gly and Ala substantially increased the folding rates by as much as 60 times. Apparently, destabilization of nonnative states dramatically enhanced the folding rates.
Differential response of photosynthetic apparatus towards alkaline pH treatment in NIES-39 and PCC 7345 strains of Arthrospira platensis
(Springer, 2021-05) Chowdhury, Shibasish; Bhagavatula, Vani
Alkaline stress is one of the severe abiotic stresses, which is not well studied so far, especially among cyanobacteria. To affirm the characteristics of alkaline stress and the subsequent adaptive responses in Arthrospira platensis NIES-39 and Arthrospira platensis PCC 7345, photosynthetic pigments, spectral properties of thylakoids, PSII and PSI activities, and pigment-protein profiles of thylakoids under different pH regimes were examined. The accessory pigments showed a pH-mediated sensitivity. The pigment-protein complexes of thylakoids are also affected, resulting in the altered fluorescence emission profile. At pH 11, a possible shift of the PBsome antenna complex from PSII to PSI is observed. PSII reaction center is found to be more susceptible to alkaline stress in comparison to the PSI. In Arthrospira platensis NIES-39 at pH 11, a drop of 68% in the oxygen evolution with a significant increase of PSI activity by 114% is recorded within 24 h of pH treatment. Alterations in the cellular ultrastructure of Arthrospira platensis NIES-39 at pH 11 were observed, along with the increased number of plastoglobules attached with the thylakoid membranes. Arthrospira platensis NIES-39 is more adaptable to pH variation than Arthrospira platensis PCC 7345.
DRP1-mediated mitochondrial dynamics orchestrate EMT in glioblastoma cells
(2025-12) Chowdhury, Shibasish; Chowdhury, Rajdeep; Mukherjee, Sudeshna
Epithelial to mesenchymal transition (EMT), a differentiation process, frequently imparts invasive properties in Glioblastoma Multiforme (GBM), which leads to a poor prognosis. Cells lose apical-basal polarity, cell-cell connections, and/or chemo-resistance during EMT, which can result in the spread of cancer and the acquisition of additional stem cell-like traits. It is unclear how organelle dynamics influence EMT in this respect. The interaction between cytoskeletal and mitochondrial regulators governing GBM cell EMT is explored in this article.
Drug Tolerant Cells: An Emerging Target With Unique Transcriptomic Features
(Sage, 2019) Chowdhury, Rajdeep; Majumder, Syamantak; Chowdhury, Shibasish
Long-term outcome of cancer therapy is often severely perturbed by the acquisition of drug resistance. Recent evidence point toward the survival of a subpopulation of tumor cells under acute drug stress that over time can re-populate the tumor. These transiently existing, weakly proliferative, drug-tolerant cells facilitate tumor cell survival until more stable resistance mechanisms are acquired. From a therapeutic perspective, understanding the molecular features of the tolerant cells is critical to attenuation of resistance. In this article, we discuss the transcriptomic features of drug-tolerant osteosarcoma cells that survive a high dose of cisplatin shock. We present the unique transcriptome of the minimally dividing tolerant cells in comparison with the proliferative persisters or resistant cells derived from the tolerant cells. Targeting the tolerant cells can represent an efficient therapeutic strategy impeding tumor recurrence.
Dynamic alterations of H3K4me3 and H3K27me3 at ADAM17 and Jagged-1 gene promoters cause an inflammatory switch of endothelial cells
(Wiley, 2021-09-14) Chowdhury, Shibasish; Majumder, Syamantak; Kuncharam, Bhanu Vardhan Reddy
Histone protein modifications control the inflammatory state of many immune cells. However, how dynamic alteration in histone methylation causes endothelial inflammation and apoptosis is not clearly understood. To examine this, we explored two contrasting histone methylations; an activating histone H3 lysine 4 trimethy- lation (H3K4me3) and a repressive histone H3 lysine 27 trimethylation (H3K27me3) in endothelial cells (EC) undergoing inflammation. Through computeraided reconstruction and 3D printing of the human coronary artery, we developed a unique model where EC were exposed to a pattern of oscillatory/disturbed flow as similar to in vivo conditions. Upon induction of endothelial inflammation, we detected a significant rise in H3K4me3 caused by an increase in the expression of SET1/ COMPASS family of H3K4 methyltransferases, including MLL1, MLL2, and SET1B. In contrast, EC undergoing inflammation exhibited truncated H3K27me3 level engendered by EZH2 cytosolic translocation through threonine 367 phosphorylation and an increase in the expression of histone demethylating enzyme JMJD3 and UTX. Additionally, many SET1/COMPASS family of proteins, including MLL1 (C), MLL2, and WDR5, were associated with either UTX or JMJD3 or both and such association was elevated in EC upon exposure to inflammatory stimuli. Dynamic enrichment of H3K4me3 and loss of H3K27me3 at Notchassociated gene promoters caused ADAM17 and Jagged1 derepression and abrupt Notch activation. Conversely, either reducing H3K4me3 or increasing H3K27me3 in EC undergoing inflammation atte- nuated Notch activation, endothelial inflammation, and apoptosis. Together, these findings indicate that dynamic chromatin modifications may cause an inflammatory and apoptotic switch of EC and that epigenetic reprogramming can potentially im- prove outcomes in endothelial inflammationassociated cardiovascular diseases.
Dysregulated expression but redundant function of the long non-coding RNA HOTAIR in diabetic kidney disease
(Springer, 2019-08-09) Chowdhury, Shibasish; Majumder, Syamantak
Long non-coding RNAs (lncRNAs) are garnering increasing attention for their putative roles in the pathogenesis of chronic diseases, including diabetic kidney disease (DKD). However, much about in vivo lncRNA functionality in the adult organism remains unclear. To better understand lncRNA regulation and function in DKD, we explored the effects of the modular scaffold lncRNA HOTAIR (HOX antisense intergenic RNA), which approximates chromatin modifying complexes to their target sites on the genome. Methods Experiments were performed in human kidney tissue, in mice with streptozotocin-induced diabetes, the db/db mouse model of type 2 diabetes, podocyte-specific Hotair knockout mice and conditionally immortalised mouse podocytes. Results HOTAIR was observed to be expressed by several kidney cell-types, including glomerular podocytes, in both human and mouse kidneys.However, knockout ofHotair frompodocytes had almost no effect on kidney structure, function or ultrastructure. Glomerular HOTAIR expression was found to be increased in human DKD, in the kidneys of mice with streptozotocin-induced diabetes and in the kidneys of db/db mice. Likewise, exposure of cultured mouse podocytes to high glucose caused upregulation of Hotair expression, which occurred in a p65-dependent manner. Although HOTAIR expression was upregulated in DKD and in high glucose-exposed podocytes, its knockout did not alter the development of kidney damage in diabetic mice. Rather, in a bioinformatic analysis of human kidney tissue, HOTAIR expression closely paralleled the expression of its genic neighbour, HOXC11, which is important to developmental patterning but which has an uncertain role in the adult kidney . Conclusions/interpretation Many lncRNAs have been found to bind to the same chromatin modifying complexes. Thus, there is likely to exist sufficient redundancy in the system that the biological effects of dysregulated lncRNAs in kidney disease may often be inconsequential. The example of the archetypal scaffold lncRNA, HOTAIR, illustrates how lncRNA dysregulation may be a bystander in DKD without necessarily contributing to the pathogenesis of the condition. In the absence of in vivo validation, caution should be taken before ascribing major functional roles to single lncRNAs in the pathogenesis of chronic diseases.
Effect of coordinated ions on structure and flexiblity of parallel G-quandruplexes: a molecular dynamics study
(Taylor & Francis, 2012-05-15) Chowdhury, Shibasish
Single tract guanine residues can associate to form stable parallel quadruplex structures in the presence of certain cations. Nanosecond scale molecular dynamics simulations have been performed on fully solvated fibre model of parallel d(G7) quadruplex structures with Na+ or K+ ions coordinated in the cavity formed by the O6 atoms of the guanine bases. The AMBER 4.1 force field and Particle Mesh Ewald technique for electrostatic interactions have been used in all simulations. These quadruplex structures are stable during the simulation, with the middle four base tetrads showing root mean square deviation values between 0.5 to 0.8 Å from the initial structure as well the high resolution crystal structure. Even in the absence of any coordinated ion in the initial structure, the G-quadruplex structure remains intact throughout the simulation. During the 1.1 ns MD simulation, one Na+ counter ion from the solvent as well as several water molecules enter the central cavity to occupy the empty coordination sites within the parallel quadruplex and help stabilize the structure. Hydrogen bonding pattern depends on the nature of the coordinated ion, with the G-tetrad undergoing local structural variation to accommodate cations of different sizes. In the absence of any coordinated ion, due to strong mutual repulsion, O6 atoms within G-tetrad are forced farther apart from each other, which leads to a considerably different hydrogen bonding scheme within the G-tetrads and very favourable interaction energy between the guanine bases constituting a G-tetrad. However, a coordinated ion between G-tetrads provides extra stacking energy for the G-tetrads and makes the quadruplex structure more rigid. Na+ ions, within the quadruplex cavity, are more mobile than coordinated K+ ions. A number of hydrogen bonded water molecules are observed within the grooves of all quadruplex structures.
Epigenetic adaptations in drug-tolerant tumor cells
(Elsevier, 2023) Chowdhury, Rajdeep; Chowdhury, Shibasish; Mukherjee, Sudeshna
Traditional chemotherapy against cancer is often severely hampered by acquired resistance to the drug. Epigenetic alterations and other mechanisms like drug efflux, drug metabolism, and engagement of survival pathways are crucial in evading drug pressure. Herein, growing evidence suggests that a subpopulation of tumor cells can often tolerate drug onslaught by entering a “persister” state with minimal proliferation. The molecular features of these persister cells are gradually unraveling. Notably, the “persisters” act as a cache of cells that can eventually re-populate the tumor post-withdrawal drug pressure and contribute to acquiring stable drug-resistant features. This underlines the clinical significance of the tolerant cells. Accumulating evidence highlights the importance of modulation of the epigenome as a critical adaptive strategy for evading drug pressure. Chromatin remodeling, altered DNA methylation, and de-regulation of non-coding RNA expression and function contribute significantly to this persister state. No wonder targeting adaptive epigenetic modifications is increasingly recognized as an appropriate therapeutic strategy to sensitize them and restore drug sensitivity. Furthermore, manipulating the tumor microenvironment and “drug holiday” is also explored to maneuver the epigenome. However, heterogeneity in adaptive strategies and lack of targeted therapies have significantly hindered the translation of epigenetic therapy to the clinics. In this review, we comprehensively analyze the epigenetic alterations adapted by the drug-tolerant cells, the therapeutic strategies employed to date, and their limitations and future prospects.
Evolution of endonuclease IV protein family: an in silico analysis
(Springer, 2019-04-06) Chowdhury, Shibasish
DNA repair is one of the key cellular events which balances between evolvability and integrity of the genome. Endonuclease IV enzymes are class II AP endonucleases under base excision repair pathway which act on abasic site and break the phosphodiester bond at the 5′ side. The role and activity of endonuclease IV proteins vary among different organisms; even it is absent in higher eukaryotes. The evolution of this protein family was studied by analyzing all homologs of the endonuclease IV protein family through different in silico techniques including phylogenetic tree generation and model building. The sequence analysis revealed four consensus sequence motifs within the AP2EC domain which are functionally important and conserved throughout the evolution process. It was also observed that the species and endonuclease IV gene evolution shape up differently in most of the organisms. Presence of the mitochondria-targeted signal peptides in fungal species Saccharomyces and Coccidioides suggest a possible endosymbiotic transfer of endonuclease IV genes to lower eukaryotes. Evolutionary changes among various clades in the protein-based phylogenetic tree have been investigated by comparison of homology models which suggests the conservation of overall fold of endonuclease IV proteins except for few alterations in loop orientation in few clades.