Biology subjects

Mondal, D.

Publications and source records attributed to Mondal, D..

14 recordsLinked to original sources

bioRxiv2026

Conformational Switching between ON and OFF States Proceeds through Multiple Pathways in the SAM-III Translational Riboswitch

Gene regulation by translational riboswitches relies on repeated and reversible conformational switching between ON (apo) and OFF (holo) states. The switching mechanism often involves significant structural rearrangement, and the role of the metal ions in this mechanism is unclear. Using molecular dynamics simulations, we studied the switching transition of a translational riboswitch that regulates the concentration of S-adenosyl methionine (SAM), the `universal methyl donor'. We show that Mg2+ ions are essential for stabilizing the ON-state, and the three-way junction exhibits a `breathing-like' dynamic interconversion between open and closed modes. The riboswitch has a low population of a holo-like READY (R) state with a partially organized SAM-binding pocket prior to ligand binding. Multiple intermediates are observed in the switching landscape, contributing to the gradual stepwise structural transition between the ON and R states, and proceeding through multiple competing pathways. Interestingly, Mg2+ ions influence the dominant pathway for the ON to R state transition, whereas the reverse transition shows a weak dependence. These results provide broad insights into the function of translational riboswitches, which repeatedly and rapidly respond to changes in metabolite concentrations, in contrast to transcriptional riboswitches.

biophysics↗

bioRxiv2026

Effect of Glycosylation on the Free Energy Landscape of the Catalytic Domain of Human Carbonic Anhydrase IX

N-linked glycosylation is known to modulate the catalytic function of human carbonic anhydrase (HCA) IX, yet its influence on the underlying free-energy landscape remains largely unexplored. In the present work, we combine extensive all-atom molecular dynamics simulations with kinetic transition network analysis to investigate the effect of glycosylation on the conformational organization of the catalytic domain of HCA IX in both monomeric and dimeric forms. The multidimensional conformational space is discretized into distinct free energy minima using the distribution of reciprocal interatomic distances (DRID), and the effective barriers separating them are estimated using the max flow-min cut formalism. The corresponding free energy landscapes are visualized in terms of disconnectivity graphs, which provide a faithful representation of underlying kinetics. Minimum free energy paths, mean first passage times, as well as frustration metrics are computed to further quantify the effect of glycosylation on landscape topography. Unglycosylated systems are found to exhibit predominantly funnel-like landscapes, with a limited number of metastable states in the vicinity of the native protein fold. In contrast, glycosylation enhances landscape complexity, resulting in a wide array of relaxation timescales. Strikingly, the two glycan chains affect the landscape topography in distinct ways, despite having closely matching sequences. Dimerization couples the glycan chain dynamics, with transitions between key metastable states involving coordinated motions of both the chains. Our work illustrates that interpretation in terms of disconnectivity graphs and transition networks could reveal important insights into the organization of glycoprotein energy landscapes.

biophysics↗

bioRxiv2026

Mg2+-Dependent Multistep Folding and Stabilization of the GAAA Tetraloop-Receptor Interaction in a Group I Intron

Group I Introns are non-coding regions of pre-mRNA that catalyze their splicing from the RNA sequence by folding to a specific structure. We used computer simulations to study the folding mechanism of the P4-P6 domain in the Tetrahymena thermophila group I intron, focusing on the GAAA tetraloop-receptor (TL-R) interaction, which is a ubiquitous tertiary interaction in RNA structures. We show that the intron folds via a multistep pathway, populating seven states with distinct tertiary contacts. Under physiological Mg2+ concentrations ([Mg2+]), the loop-bulge-P4 tertiary interaction is essential to stabilize the docked TL-R complex, whereas in high [Mg2+], the TL-R complex is stable by itself. The solvated Mg2+ ions modulate the TL-R docking-undocking dynamics and stabilize non-native intermediate states. The condensation of Mg2+ in the major grooves of the TL and R helices is critical for them to attain specific stiffness essential for their facile docking. The results highlight the critical role of Mg2+ ions in facilitating TL-R interaction formation, which stabilizes long-range tertiary contacts in RNA structures. For Table of Contents Use Only O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/700762v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@142852org.highwire.dtl.DTLVardef@1632ad1org.highwire.dtl.DTLVardef@190021aorg.highwire.dtl.DTLVardef@17a1261_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2025

Dimerization Mechanism of HIV-1 RNA Hairpins to Extended Duplex Structures

Genomic RNA (gRNA) dimerization is essential for retroviral replication. In the gRNA of human immunodeficiency virus (HIV-1), the hairpin-like dimerization initiation sequence (DIS) forms a kissing-complex (KC) with the DIS sequence in another gRNA, which later converts into a stable extended-duplex (ED). Using coarse-grained simulations, we mapped the transition of HIV-1 DIS RNA hairpins (HPs) to ED and identified multiple intermediates beyond the KC. The KC has an anionic pocket stabilized through the condensation of Mg2+ ions. Hence, when only K+ ions are present at physiological levels, the HPs to ED transitions occur through a different dominant pathway devoid of the KC. We also observed purine base flipping near KC hydrogen bonds, revealing the population of a sub-ensemble of intermediates. The proposed dimerization mechanism of HPs to ED, along with the sub-ensemble of KC conformations and its anionic pocket, provides a strategic framework for designing specific retroviral drugs targeting this pathway. For Table of Contents Use Only O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/683870v1_ufig1.gif" ALT="Figure 1"> View larger version (94K): org.highwire.dtl.DTLVardef@2cb0f5org.highwire.dtl.DTLVardef@15c8d1org.highwire.dtl.DTLVardef@3321cborg.highwire.dtl.DTLVardef@efd30d_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2025

Transition Metal Binding Drives Folding of a Metalloregulatory Riboswitch by Modulating Conformational Flexibility at Helical Junctions

Transition metal ions are crucial for bacterias survival. Bacteria employ metalloregulatory riboswitches to respond to varying metal ion concentrations. The czcD (NiCo) transcription riboswitch specifically senses Co2+, Ni2+, and Fe2+ ions at micromolar concentrations amid millimolar Mg2+. We used computer simulations with multi-resolution RNA models to understand how global conformational changes in the NiCo riboswitch are coupled to the remarkable specific binding of Co2+. We show that the riboswitch folds through an intermediate state, where a partially folded four-way junction (4WJ) creates an anionic pocket large enough to accommodate the binding of solvated divalent ions. The binding of Co2+ is coupled to the stability of the weak non-canonical G{middle dot}A base pairs at the helical junction that drive the formation of native-like coaxial stacking of four helices. The Co2+ binding further twists the 4WJ, which locks the ions in the bound state. Electronic structure calculations show that enhanced orbital interactions between conserved guanines in the 4WJ and Co2+ are responsible for the high specificity of the riboswitch in binding to Co2+ over Mg2+. We provide a framework for understanding and engineering tunable RNA-based biosensors and developing antimicrobials, as metal intoxication is an evolutionary strategy to inhibit bacterial growth.

biophysics↗

bioRxiv2025

Conformational Pathways of Translational T-box Riboswitch Governing tRNA Recognition for Gene Regulation

The availability of various amino acids is essential for the synthesis of proteins during translation. In bacteria, T-box riboswitches play a critical role in regulating the concentrations of amino acids by sensing and decoding the aminoacylation status of tRNAs for precise control of amino acid biosynthesis and transport pathways. We used computer simulations to probe the mechanism of tRNA recognition by a translational T-box riboswitch using the iles T-box riboswitch as a model system. We show that the T-box aptamer populates three distinct thermodynamic states - undocked, predocked, and docked - depending on the relative orientation between its three stems (stem I, II, and IIA/B). The relative population of the three states is strongly dependent on the Mg2+ concentration. In the undocked and predocked states, the freely moving stem I catches the tRNA from the solution using the fly-casting mechanism. Subsequently, the tRNA-bound stem I docks to stem II in a specific orientation with the help of noncanonical intra- and inter-backbone hydrogen bonds, which facilitate tRNA interaction with the discriminator domain to detect the aminoacylation state of tRNA and regulate the gene. Since T-box riboswitches are prime targets in designing antibiotics, our proposed mechanism of tRNA recognition by T-box reveals multiple critical sites in the riboswitch that can be targeted for developing new antibiotics. Interestingly, molecules acting as antibiotics exist targeting one of the proposed sites. These results also have broad implications for understanding the role of specific RNA-RNA interactions in various cellular processes.

biophysics↗

bioRxiv2024

Recognizing amino acid sidechains in a medium resolution cryo-electron density map

Building an accurate atomic structure model of a protein into a cryo-electron microscopy (cryo-EM) map at worse than 3 [A] resolution is difficult. To facilitate this task, we devised a method for assigning the amino acid residue sequence to the backbone fragments traced in an input cryo-EM map (EMSequenceFinder). EMSequenceFinder relies on a Bayesian scoring function for ranking 20 standard amino acid residue types at a given backbone position, based on the fit to a density map, map resolution, and secondary structure propensity. The fit to a density is quantified by a convolutional neural network that was trained on [~]5.56 million amino acid residue densities extracted from cryo-EM maps at 3-10 [A] resolution and corresponding atomic structure models deposited in the Electron Microscopy Data Bank (EMDB). We benchmarked EMSequenceFinder by predicting the sequences of 58,044 distinct L-helix and {beta}-strand fragments, given the fragment backbone coordinates fitted in their density maps. EMSequenceFinder identifies the correct sequence as the best-scoring sequence in 77.8% of these cases. We also assessed EMSequenceFinder on separate datasets of cryo-EM maps at resolutions from 4 to 6 L. The accuracy of EMSequenceFinder (63.5%) was better than that of three tested state-of-the-art methods, including findMysequence (45%), ModelAngelo (27%), and sequence_from_map in Phenix (12.9%). We further illustrate EMSequenceFinder by threading the SARS-CoV-2 NSP2 sequence into eight cryo-EM maps at resolutions from 3.7 to 7.0 [A]. EMSequenceFinder is implemented in our open-source Integrative Modeling Platform (IMP) program. Thus, it is expected to be helpful for integrative structure modeling based on a cryo-EM map and other information, such as models of protein complex components and chemical crosslinks between them. EMSequenceFinder is available as part of our open source IMP distribution at https://integrativemodeling.org/.

biophysics↗

bioRxiv2024

T-follicular helper cells are epigenetically poised to transdifferentiate into T-regulatory type-1 cells

Chronic antigenic stimulation can trigger the formation of IL-10-producing T-regulatory type 1 (TR1) cells in vivo. We have recently shown that T follicular helper (TFH) cells are precursors of TR1 cells and that the TFH-to-TR1 cell transdifferentiation process is characterized by the progressive loss and acquisition of opposing transcription factor gene expression programs that evolve through at least one transitional cell stage. Here, we use a broad range of bulk and single-cell transcriptional and epigenetic tools to investigate the epigenetic underpinnings of this process. At the single cell level, the TFH-to-TR1 cell transition is accompanied by both, downregulation of TFH cell-specific gene expression due to loss of chromatin accessibility, and upregulation of TR1 cell-specific genes linked to chromatin regions that remain accessible throughout the transdifferentiation process, with minimal generation of new open chromatin regions. By interrogating the epigenetic status of accessible TR1 genes on purified TFH and conventional T cells, we find that most of these genes, including Il10, are already poised for expression at the TFH cell stage. Whereas these genes are closed and hypermethylated in Tconv cells, they are accessible, hypomethylated and enriched for H3K27ac-marked and hypomethylated active enhancers in TFH cells. These enhancers are enriched for binding sites for the TFH and TR1-associated transcription factors TOX-2, IRF4 and c-MAF. Together, these data suggest that the TR1 gene expression program is genetically imprinted at the TFH cell stage.

immunology↗

bioRxiv2023

Cortical F-actin filament organization corrals E-cadherin/HMR-1 during cytokinetic furrow ingression in C. elegans embryos

In metazoan cells, the delicate equilibrium between proliferative cell division and inter-cellular adhesion is crucial for achieving growth while maintaining tissue integrity and homeostasis. The transmembrane adhesion receptor, E-cadherin, not only facilitates cell-cell adhesion but modulates cytokinesis by impeding cortical F-actin flow and inhibiting actomyosin contractility. In the C. elegans zygote, newly established cell-cell interfaces following cytokinesis lack E-cadherin/HMR-1 (Padmanabhan et al., 2017b). The mechanisms responsible for the spatial exclusion of HMR-1, however remain elusive. Here, we show that HMR-1 is actively prevented from entering the cytokinetic furrow zone during early embryonic divisions in C. elegans. The compact alignment of unbranched F-actin filaments polymerized by the formin/CYK-1 restricts HMR-1 from entering the ingressing furrow. This corralling phenomenon depends on the physical association between HMR-1 and F-actin mediated via the {beta}- and - catenins, HMP-2 and HMP-1, respectively. Our findings reveal a previously unknown reciprocal regulatory relationship between cell adhesion and cell division machineries, ensuring the precise orchestration of the cytokinesis during embryonic development.

cell biology↗

bioRxiv2023

Nanostructured Hydrotropes Caged Cytochrome c with Boosted Stability in Harsh Environments: A Molecular Insights

Green and nano-structured catalytic media are vital for bio-catalysis to attenuate the denaturation tendency of biocata-lysts under severe reaction conditions. Hydrotropes with multi-faceted physiochemical properties represent promising systems for sustainable protein packaging. Herein, the suitability of adenosine-5-triphosphate (ATP) and cholinium sa-licylate ([Cho][Sal]) ionic liquid (IL) to form nano-structures and to nano-confine Cytochrome c (Cyt c) were demonstrat-ed to enhance the stability and activity under multiple stressors. Experimental and computational analyses were under-taken to explain the nano-structured phenomenon of ATP and IL, structural organizations of nano-confined Cyt c, and site-specific interactions that stabilize the protein structure. Both ATP and IL form nano-structures in aqueous media and could cage Cyt c via multiple nonspecific soft interactions. Remarkably, the engineered molecular nano-cages of ATP (5-10 mM), IL (300 mg/mL), and ATP+IL surrounding Cyt c resulted in 9-to-72-fold higher peroxidase activity than native Cyt c with exceptionally high thermal tolerance (110oC). The polar interactions with the cardiolipin binding site of Cyt c, mediated by hydrotropes, were well correlated with the increased peroxidase activity. Furthermore, higher activity trends were observed in the presence of urea, GuHCl, and trypsin without any protein degradation. Specific binding of hy-drotropes in highly mobile regions of Cyt c ({Omega} 40-54 residues) and enhanced H-bonding with Lys and Arg offered excel-lent stability under extreme conditions. Additionally, ATP effectively counteracted reactive oxygen species (ROS)-induced denaturation of Cyt c, which was enhanced by the [Sal] counterpart of IL. Overall, this study explored the robustness of nano-structured hydrotropes to have a higher potential for protein packaging with improved stability and activity under extreme conditions. Thus, the present work highlights a novel strategy for real-time industrial bio-catalysis to protect mitochondrial cells from ROS-instigated apoptosis. SummarySuitability of ATP and [Cho][Sal] ionic liquid to form nanostructured hydrotropes and their utility in protein packaging in extreme conditions are discussed. Both ATP and IL form nanostructures in aqueous media and could cage Cyt c via multiple nonspecific soft interactions. The engineered molecular nanocages surrounding Cyt c resulted in 9-to-72-fold higher peroxidase activity than native Cyt c with exceptionally high thermal tolerance (110{degrees}C) and stability in the presence of urea, GuHCl, and trypsin without any protein degradation. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=133 SRC="FIGDIR/small/527166v3_ufig1.gif" ALT="Figure 1"> View larger version (55K): org.highwire.dtl.DTLVardef@167eb39org.highwire.dtl.DTLVardef@183fa44org.highwire.dtl.DTLVardef@1a38f57org.highwire.dtl.DTLVardef@117d203_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2021

Saturated Proteostasis and Nuclear Injuries Defeat Homeostatic Potentials of α-Synuclein Filaments

Biogenesis of inclusion bodies (IBs) facilitates protein quality control (PQC). Canonical aggresomes execute degradation of misfolded proteins while non-degradable amyloids quarantine into Insoluble Protein Deposits. Lewy Bodies (LBs) are well-known neurodegenerative IBs of -Synuclein associated diseases like Dementia with Lewy bodies (DLB) and Parkinsons disease. Intriguingly, the PQC benefits and drawbacks associated with LBs remain underexplored. Here, we report that the crosstalk between LBs and aggresome-like IBs of -Synuclein (Syn-aggresomes) buffers amyloidogenic -Synuclein load in primary neurons and mitotic cell models. Using cellular biochemistry, genetic knockdown, and microscopy tools we find that LBs possess unorthodox PQC-capacities of self-quarantining the Syn-amyloids, and being degradable upon receding fresh amyloidogenesis. Syn-aggresomes equilibrate biogenesis of LBs by facilitating spontaneous and opportunistic turnover of soluble -Synuclein and Syn-amyloids, respectively. However, LBs overgrow at the perinucleus once amyloidogenesis sets in and are misidentified by cytosolic BICD2 as cargos for motor-protein dynein. Simultaneously, microtubules surrounding the perinuclear LBs are distorted, misbalancing the dynein motor-force on nucleoskeleton leading to lamina injuries. Like typical Laminopathies, nucleocytoplasmic mixing, DNA-damage, and deregulated transcription of stress chaperones defeat the proteostatic purposes of LBs. We confirmed the lamina disintegrities in brain sections of Parkinsons disease patients. Together, our study provides insights into the intricate complexities of proteostatic possibilities associated with -Synuclein inclusions and offers understanding on the proteostasis-sensitivity of LB-containing aging neurons via lamina-injuries. Significance statementAmyloid inclusions of -Synuclein called Lewy Bodies (LBs) are hallmark of multiple neurodegenerative diseases like Dementia with Lewy Bodies and Parkinsons disease. A significant reason for the degeneration of LB-containing aging neurons in these diseases is their sensitivity to proteostasis stresses. We find two distinct inclusions of -Synuclein in the same neurons/cells. First, the Syn-aggresomes titrate the biogenesis of the other i.e., the LBs, by facilitating degradation of soluble -Synuclein. Syn-amyloids deposited in LBs remain degradable but LBs overgrow at the perinucleus once the kinetics of amyloid-biogenesis exceeds aggresome-assisted degradation of -Synuclein. Perinuclear LBs destabilize local tubulin-meshwork and are misidentified as cargo for cytosolic motor dynein. Aberrant cytoskeleton-nucleoskeleton tension disintegrates lamina, deregulates stress-responsive transcription, and triggers proteostasis-sensitivity in LB-containing neurons.

cell biology↗

bioRxiv2020

An extensive computational approach to inhibit MSP-1 of P.vivax elucidates further horizon in the establishment next generation therapeutics against malaria

Malaria represents a life-threatening disease caused by the obligate intra-erythrocytic protozoa of the Plasmodium genus, exerting a sinister global health burden and accounting for approximately 660,000 deaths annually. Additionally, 219 million new cases are reported each year, most of which result from the growing issue of artemisinin resistance shown by the Plasmodium parasite. Much of the research done for the purpose of development of therapeutics against malaria has traditionally been focused on Plasmodium falciparum, which is responsible for majority of the cases of mortality due to malaria, Plasmodium vivax is also known to contribute greatly towards the malaria relate morbidities particularly in vivax endemic areas. In this study, we have used two different computational approaches aimed at establishing newer concepts towards the development of advanced therapeutics against vivax malaria by targeting the surface antigen, merozoite surface protein-1 (MSP-1). In-silico approach involving computational siRNA designing against MSP-1 resulted in a total of four candidate siRNAs being rationally validated following corroboration with a plethora of algorithms. Additionally, molecular docking analysis unraveled a total of three anti-parasitic peptides. These peptides namely: AP02283, AP02285 and AP00101 were found to exhibit considerable binding affinity with MSP-1 of P.vivax, thus providing an apparent indication of their anti-malarial property and affirming their potency to be used as novel molecules for development of next generation anti-malarials. However, irrespective of the prospective magnitude of these in-silico findings, the results require extensive validation by further rigorous laboratory experiments involving both in-vitro and in-vivo approaches.

bioinformatics↗

bioRxiv2020

The covariance shift (C-SHIFT) algorithm for normalizing biological data

Omics technologies are powerful tools for analyzing patterns in gene expression data for thousands of genes. Due to a number of systematic variations in experiments, the raw gene expression data is often obfuscated by undesirable technical noises. Various normalization techniques were designed in an attempt to remove these non-biological errors prior to any statistical analysis. One of the reasons for normalizing data is the need for recovering the covariance matrix used in gene network analysis. In this paper, we introduce a novel normalization technique, called the covariance shift (C-SHIFT) method. This normalization algorithm uses optimization techniques together with the blessing of dimensionality philosophy and energy minimization hypothesis for covariance matrix recovery under additive noise (in biology, known as the bias). Thus, it is perfectly suited for the analysis of logarithmic gene expression data. Numerical experiments on synthetic data demonstrate the methods advantage over the classical normalization techniques. Namely, the comparison is made with rank, quantile, cyclic LOESS (locally estimated scatterplot smoothing), and MAD (median absolute deviation) normalization methods.

bioinformatics↗

bioRxiv2020

Improved Supra-Organization Is A Conformational And Functional Adaptation Of Respiratory Complexes

Multiple surveillance mechanisms accelerate proteasome mediated degradation of misfolded proteins to prevent protein aggregation inside and outside mitochondria. But how cells safeguard mitochondrial function despite increased protein aggregation during proteasome inactivation? Here, using two-dimensional complexome profiling, we extensively characterize the dynamic states of respiratory complexes (RCs) in proteasome-inhibited cells. We report that RC-subunits are increasingly integrated into supra-organizations to optimize catalytic activity simultaneous to their aggregation inside mitochondria. Complex-II (CII) and CV are incorporated into oligomers. CI, CIII, and CIV subcomplexes are associated into holocomplexes followed by integration into supercomplexes. Time-course experiments reveal that the core (CI+CIII2) stoichiometry of supercomplex (I+III2+IV) is preserved during early-stress while CIV composition varies. Simultaneously, increased CI-activity suggests conformational optimization of supercomplexes for better function. Re-establishment of steady-state stoichiometry and relative increase in supercomplex-quantity consolidates functional adaptation during prolonged proteasome-inhibition. Together, we name this pre-emptive adaptive mechanism as improved Supra-organization of Respiratory Complexes (iSRC). We find that iSRC is active in multiple protein-unfolding stresses, in multiple cell-types that differ in proteostatic and metabolic demands, and reversible upon stress-withdrawal.

biochemistry↗