BITS Faculty Publications
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Item Mapping allosteric rewiring in viral RNA: sequence-encoded control of protein binding mechanisms(2025) Chakraborty, AmritaRNA recognition by proteins is governed not only by static structure but also by allostery encoded within non-local dynamic motifs. In this study, we systematically identify allosteric communication hubs in RNA and map multiple residue-connected pathways, revealing how these networks are rewired upon mutation and protein binding. To capture these effects under physiological salt conditions, we performed tens of microseconds of atomistic and steered molecular dynamics simulations and computed binding free energies for Tat–TAR complexes across three immunodeficiency virus variants, BIV, HIV-1, and HIV-2. Allosterically coupled sites were identified using contact-based principal component analysis, and communication pathways were traced through an extended graph-network algorithm—the first such application to RNA systems. Two distant motifs—the bulge and the apical loop—emerge as allosteric switches and information hubs: the bulge engages Tat, while the loop interacts with another protein partner, CycT1, both essential for transcriptional activation and antiviral targeting. We find that HIV-2 TAR, with strong loop–bulge coupling and high self-integrity, favour conformational selection and exhibits lower Tat-binding affinity. In contrast, a single C24 insertion in HIV-1 TAR reconfigures communication pathways, enabling an induced-fit mechanism with enhanced affinity. The study not only elucidates an allosteric rewiring between the loop and bulge but also highlights how this communication is dynamically reconfigured upon protein binding. Tat association at the bulge reorganizes and reorients loop residues, thereby promoting the subsequent recruitment of CycT1. This work overall underscores how sequence (even a single mutation) encoded RNA allostery can modulate not only a protein’s binding mechanism and affinity but also influence downstream molecular events within transcriptional signalling cascades.Item Unusual RNA binding of FUS RRM studied by molecular dynamics simulation and enhanced sampling method(Elsevier, 2021-05) Basu, SushmitaAmyotrophic lateral sclerosis (ALS) and frontotemporal lobe degeneration (FTLD) are two inter-related intractable diseases of motor neuron degeneration. Fused in sarcoma (FUS) is found in cytoplasmic accumulation of ALS and FTLD patients, which readily link the protein with the diseases. The RNA recognition motif (RRM) of FUS has the canonical a-b folds along with an unusual lysine-rich loop (KK-loop) between a1 and b2. This KK-loop is highly conserved among FET family proteins. Another contrasting feature of FUS RRM is the absence of critical binding residues, which are otherwise highly conserved in canonical RRMs. These residues in FUS RRM are Thr286, Glu336, Thr338, and Ser367, which are substitutions of lysine, phenylalanine, phenylalanine, and lysine, respectively, in other RRMs. Considering the importance of FUS in RNA regulation and metabolism, and its implication in ALS and FTLD, it is important to elucidate the underlying molecular mechanism of RNA recognition. In this study, we have performed molecular dynamics simulation with enhanced sampling to understand the conformational dynamics of noncanonical FUS RRM and its binding with RNA. We studied two sets of mutations: one with alanine mutation of KK-loop and another with KK-loop mutations along with critical binding residues mutated back to their canonical form. We find that concerted movement of KK-loop and loop between b2 and b3 facilitates the folding of the partner RNA, indicating an induced-fit mechanism of RNA binding. Flexibility of the RRM is highly restricted upon mutating the lysine residues of the KK-loop, resulting in weaker binding with the RNA. Our results also suggest that absence of the canonical residues in FUS RRM along with the KK-loop is equally important in regulating its binding dynamics. This study provides a significant structural insight into the binding of FUS RRM with its cognate RNA, which may further help in designing potential drugs targeting noncanonical RNA recognition.Item Cyclodextrin interaction with specific channel CymA from K. Oxytoca(Cell Press, 2015-01) Prajapati, Jigneshkumar DahyabhaiThe outer membrane acts as a selective uptake barrier in Gram negative bacteria. It contains protein channels (porins) which provide an entry pathway for hydrophilic molecules like small nutrient molecules and β-lactam antibiotics. However the CymA channel is known to take up cyclodextrin molecules giving bacteria the ability to survive on cyclodextrins. Hence understanding uptake of these molecules via porins is vital to comprehend the transport mechanism across the cell membrane. Electrophysiology forms a promising approach to study the permeation of molecules across outer membrane and thereby understanding molecular interactions with the channel. Here we present cyclodextrin interaction studies of CymA from K. oxytoca using single channel electrophysiology. Detailed single channel analysis revealed inherent asymmetric gating characteristics of the channel. Analysis of the ion current reduction through CymA in presence of cyclodextrin led revealed kinetic parameters of substrate binding. To further elucidate the affinity sites of substrate to the channel, mutation of certain channel residues has been performed. An altered channel gating behaviour is observed. To obtain an atomistic view we complement our studies with all-atom molecular dynamics simulation to study the various conductance states of the channel in the absence of cyclodextrin and to get molecular insight into the uptake of cyclodextrins as well.Item Role of electroosmosis in the permeation of neutral molecules: CymA and cyclodextrin as an example(Cell Press, 2016-02) Prajapati, Jigneshkumar DahyabhaiTo quantify the flow of small uncharged molecules into and across nanopores, one often uses ion currents. The respective ion-current fluctuations caused by the presence of the analyte make it possible to draw some conclusions about the direction and magnitude of the analyte flow. However, often this flow appears to be asymmetric with respect to the applied voltage. As a possible reason for this asymmetry, we identified the electroosmotic flow (EOF), which is the water transport associated with ions driven by the external transmembrane voltage. As an example, we quantify the contribution of the EOF through a nanopore by investigating the permeation of a-cyclodextrin through CymA, a cyclodextrin-specific channel from Klebsiella oxytoca. To understand the results from electrophysiology on a molecular level, all-atom molecular dynamics simulations are used to detail the effect of the EOF on substrate entry to and exit from a CymA channel in which the N-terminus has been deleted. The combined experimental and computational results strongly suggest that one needs to account for the significant contribution of the EOF when analyzing the penetration of cyclodextrins through the CymA pore. This example study at the same time points to the more general finding that the EOF needs to be considered in translocation studies of neutral molecules and, at least in many cases, should be able to help in discriminating between translocation and binding events.Item Electro-osmotic driven kinetics of cyclodextrin through the cyma channel(Cell Press, 2016-02) Prajapati, Jigneshkumar DahyabhaiTrans membrane voltage is applied to understand the permeation of uncharged molecules into and across nano pores in Electrophysiology. The permeating molecule blocks the ion flow causing ion current fluctuations. However the fluctuation density is dependent on the magnitude and direction of the applied voltage. This dependency may be assumed due to electro-osmotic (EOF) flow, electrically driven ion – associated water flow. Here we investigate the contribution of the electro-osmotic flow (EOF) as a potential cause for an external voltage driven substrate permeation. As an example, we quantified the permeation of α-cyclodextrin through the cyclodextrin-specific channel-forming porin CymA from the Gram-negative bacterium Klebsiella oxytoca. To further elucidate these effects, substrate interaction studies were performed at various external voltages in presence of three different electrolyte solutions: KCl, NaCl and MgCl2. To demonstrate the significance of the EOF at an atomistic level, the net water flux was calculated and its effect on the binding affinity of substrates was studied by employing extensive molecular dynamics simulations.Item Computational modeling of ion transport in bulk and through a nanopore using the drude polarizable force field(ACS, 2020-06) Prajapati, Jigneshkumar DahyabhaiIn the past two decades, molecular dynamics simulations have become the method of choice for elucidating the transport mechanisms of ions through various membrane channels. Often, these simulations heavily rely on classical nonpolarizable force fields (FFs), which lack electronic polarizability in the treatment of the electrostatics. The recent advancements in the Drude polarizable FF lead to a complete set of parameters for water, ions, protein, and lipids, allowing for a more realistic modeling of membrane proteins. However, the quality of these Drude FFs remains untested for such systems. Here, we examine the quality of this FF set in two ways, i.e., (i) in simple ionic aqueous solution simulations and (ii) in more complex membrane channel simulations. First, the aqueous solutions of KCl, NaCl, MgCl2, and CaCl2 salts are simulated using the polarizable Drude and the nonpolarizable CHARMM36 FFs. The bulk conductivity has been estimated for both FF sets using applied-field simulations for several concentrations and temperatures in the case of all investigated salts and compared to experimental findings. An excellent improvement in the ability of the Drude FF to reproduce the experimental bulk conductivities for KCl, NaCl, and MgCl2 solutions can be observed but not in the case of CaCl2. Moreover, the outer membrane channel OmpC from the bacterium Escherichia coli has been employed to examine the ability of the polarizable and nonpolarizable FFs to reproduce ion transport-related quantities known from experiment. Unbiased and applied-field simulations have been performed in the presence of KCl using both FF sets. Unlike for the bulk systems of aqueous salt solutions, it has been found that the Drude FF is not accurate in modeling KCl transport properties across the OmpC porin.Item Synthesis, molecular modelling and biological evaluation of novel benzyloxy substituted indolyl oxoacetamides as potent pancreatic lipase inhibitors(Springer, 2025-08) Paul, Atish TulshiramA series of 21 indolyl oxoacetamide analogues with benzyloxy-substituents were designed, synthesized and characterized using 1H NMR (Nuclear Magnetic Resonance), 13C NMR, and HRMS (High Resolution Mass Spectrometry) analysis. All the analogues were tested for inhibitory activity against pancreatic lipase. Two analogues, 9f and 10f, exhibited significant activity (IC50 of 2.89 and 2.50 µM, respectively), comparable to the standard drug, orlistat (IC50 = 0.99 µM). The potent analogues 10f and 9f exhibited significant binding affinity for pancreatic lipase (-170.222 kcal mol− 1 and − 153.547 kcal mol− 1). Additionally, both the potent analogues exhibited crucial interaction with Ser 152 and His 263 residues in the PL active site via hydrogen bonding. Molecular dynamics (MD) simulation was performed on the ligand-receptor complex of potent analogue (10f) for 200 ns. The molecule was stabilized by extending the π-π interactions with Phe 77 and Phe 215 of the active site lid domain due to benzyloxy substitution. Toxicity profile prediction indicated that all the analogues were non-hepatotoxic, unlike orlistat.Item Study of side burr formation in steady-state nano-polishing of Si-wafer using molecular dynamics simulation(Sage, 2024-02) Roy, TribeniWith advancements in the semiconductor industry, it is required to have angstrom level surface finish on silicon wafers which is achieved by nano-polishing. However, side burr is formed due to material pile-up from material removal due to abrasive which becomes detrimental to achieving the high surface finish. This study employs molecular dynamics simulations to explore the mechanism underlying side burr formation during nano-polishing of mono-crystalline silicon (Si)-wafer. The study utilizes a diamond nano-abrasive grit to scratch the surface of the Si-wafer and investigates the formation of pile-ups during the steady-state process. It was observed that increasing the depth of cut by four times led to a 6.3-fold increase in the number of amorphous atoms, indicating greater bond breakage in the direction of scratching. As a result, the cutting force exceeds the thrust force at larger depths of the cut. The correlation between the side burr height and the depth of cut is also studied. Results show that the side burr height ratio increases with the depth of cut, indicating a higher sensitivity of side burr height to the depth of cut. The study suggests that to achieve a ductile mode of material removal and minimize the height of the side burr during nano-polishing of Si-wafers, it is crucial to maintain the depth of cut at or below half (≤0.5) of the abrasive radius and ensure an average friction coefficient below 0.6. The outcome of this study can be useful for the actual manufacturing of miniaturized sensors, actuators, and microsystems for microelectromechanical system devices where a high surface finish is crucial.Item Mechanism of surface modification on monocrystalline silicon during diamond polishing at nanometric scale(Sage, 2023-11) Sharma, Anuj; Roy, TribeniThe demand for polished silicon wafers has increased significantly in recent years to cater to the development of the semiconductor industry. For example, polished silicon wafer has direct applications in integrated circuits, radio frequency amplifiers, micro-processors, micro-electromechanical systems, etc. To carry out mechanical polishing, lapping, grinding, or single-point diamond turning of silicon, diamond abrasives were extensively used before the implementation of chemo-mechanical polishing. During the diamond-based polishing, a few problems have already been identified, such as the formation of an amorphous phase, heat-affected zones, low material removal, etc. Some research work has also reported that nano-structured abrasives lead to a thin layer of the amorphous phase and a better material removal rate. In the same direction, a molecular dynamics simulation is carried out in this paper to investigate the mechanism of material removal from monocrystalline silicon during the diamond-abrasive-based polishing process. The present work is mainly focused on the dynamics of material removal phenomena near the abrasive particles at the nanometric scale by considering stress, lattice, cohesive energy, etc. This reveals that a higher value of indentation force results in surface buckling, which creates a zone of both compressive and tensile stresses, which increases the coordination number and forms β-silicon just ahead of the abrasive particle. This mechanism happens by developing a β-silicon phase on the surface with a thickness beyond a certain value of indentation force on the zone of compression. Buckling on this phase happens due to stress localisation in compression, as the flow stress of this phase is less than that of diamond cubic lattices. To avoid the mechanism of surface buckling and process silicon material on the surface, the indentation force needs to be maintained below a critical value. In the present case, it was found that the indentation force of less than or equal to 190 nN for the abrasive size of ϕ8 nm does the material removal by surface processing only without surface buckling. It was also found that surface processing helps to reduce the depth of the amorphous layer significantly without compromising the material removal rate or the generation of a wavy surface. Thus, the present mechanism will help in the polishing of silicon with minimum defects and reduce processing time for the final stage of polishing towards manufacturing ultra-smooth and planer surfaces.Item Strain induced electrochemical behaviors of ionic liquid electrolytes in an electrochemical double layer capacitor: Insights from molecular dynamics simulations(AIP, 2023-12) Roy, TribeniElectrochemical Double Layer Capacitors (EDLCs) with ionic liquid electrolytes outperform conventional ones using aqueous and organic electrolytes in energy density and safety. However, understanding the electrochemical behaviors of ionic liquid electrolytes under compressive/tensile strain is essential for the design of flexible EDLCs as well as normal EDLCs, which are subject to external forces during assembly. Despite many experimental studies, the compression/stretching effects on the performance of ionic liquid EDLCs remain inconclusive and controversial. In addition, there is hardly any evidence of prior theoretical work done in this area, which makes the literature on this topic scarce. Herein, for the first time, we developed an atomistic model to study the processes underlying the electrochemical behaviors of ionic liquids in an EDLC under strain. Constant potential non-equilibrium molecular dynamics simulations are conducted for EMIM BF4 placed between two graphene walls as electrodes. Compared to zero strain, low compression of the EDLC resulted in compromised performance as the electrode charge density dropped by 29%, and the performance reduction deteriorated significantly with a further increase in compression. In contrast, stretching is found to enhance the performance by increasing the charge storage in the electrodes by 7%. The performance changes with compression and stretching are due to changes in the double-layer structure. In addition, an increase in the value of the applied potential during the application of strain leads to capacity retention with compression revealed by the newly performed simulations.