Biology subjects

Deb, I.

Publications and source records attributed to Deb, I..

7 recordsLinked to original sources

bioRxiv2024

Structural and dynamic consequences of inosine, 2'-O-methylation, and N6-methyladenosine modifications in RNA G-quadruplex: A molecular dynamics study

RNA G-quadruplexes (rG4) are stable non-canonical structures, often found to regulate important biological processes such as transcription, translation, splicing, RNA localization, and other steps in gene expression. rG4 structures can also influence DNA-related processes e.g. DNA replication, telomere elongation and homeostasis, and recombination. Due to the involvement of rG4s in such important processes, these structures are potential therapeutic targets against different diseases e.g., viral infection and cancer. Hence, a better understanding of the structure and stability of rG4s and their role in various therapeutically important cellular processes can help in the design of effective therapeutic strategies for targeting such structures. In the present study, we present our findings on the structural and dynamic effect of RNA modifications (inosine; 2'-O-methylation, and m6A-methylation) on RNA G-quadruplex structure from molecular dynamics simulations. Additionally, we also report the dynamic and energetic aspects of inter-quadruplex interactions and the influence of non-G purine tetrads neighboring the inter-quadruplex junction on the interactions.

biophysics↗

bioRxiv2023

Exuberant de novo dendritic spine growth in mature neurons

Dendritic spines are structural correlates of excitatory synapses maintaining stable synaptic communications. However, this strong spine-synapse relationship was mainly characterized in excitatory pyramidal neurons (PyNs), raising a possibility that inferring synaptic density from dendritic spine number may not be universally applied to all neuronal types. Here we found that the ectopic expression of H-Ras increased dendritic spine numbers regardless of cortical cell types such as layer 2/3 pyramidal neurons (PyNs), parvalbumin (PV)- and vasoactive intestinal peptide (VIP)-positive interneurons (INs) in the primary motor cortex (M1). The probability of detecting dendritic spines was positively correlated with the magnitude of H-Ras activity, suggesting elevated local H-Ras activity is involved in the process of dendritic spine formation. H-Ras overexpression caused high spine turnover rate via adding more spines rather than eliminating them. Two-photon photolysis of glutamate triggered de novo dendritic spine formation in mature neurons, suggesting H-Ras induced spine formation is not restricted to the early development. In PyNs and PV-INs, but not VIP-INs, we observed a shift in average spine neck length towards longer filopodia-like phenotypes. The portion of dendritic spines lacking key excitatory synaptic proteins were significantly increased in H-Ras transfected neurons, suggesting that these increased spines have other distinct functions. High spine density caused by H-Ras did not result in change in the frequency or the amplitude of miniature excitatory postsynaptic currents (mEPSCs). Thus, our results propose that dendritic spines possess more multifaceted functions beyond the morphological proxy of excitatory synapse.

neuroscience↗

bioRxiv2023

Genetic Variations and Altered Blood mRNA Level of Circadian Genes and BDNF as Risk Factors of Post-Stroke Cognitive Impairment among Eastern Indians

BackgroundPost-stroke cognitive impairment (PSCI) is a clinical outcome in around 30% of post-stroke survivors. BDNF is a major gene in this regard. It regulates and being regulated by circadian rhythm. The circadian genes are correlated with stroke timings at molecular level. However, studies suggesting the role of these on susceptibility to PSCI is limited. AimWe aim here to determine a) genetic risk variants in circadian clock genes, BDNF and b) dysregulation in expression level of CLOCK, BMAL1 and BDNF, that may be associated with PSCI. MethodsBDNF (rs6265G/A, rs56164415C/T), CLOCK (rs1801260T/C, rs4580704G/C) and CRY2 (rs2292912C/G) genes variants were genotyped among 119 post-stroke survivors and 292 controls from Eastern part of India. In addition, we analysed their gene expression in PBMC from 15 PSCI cases and 12 controls. The mRNA data for BDNF was further validated by its plasma level through ELISA. ResultsAmong the studied variants, only rs4580704/CLOCK showed an overall association with PSCI (P = 0.001) and lower BMSE score. Its C allele showed a correlation with attention deficiency. The language and memory impairments showed association with rs6265/BDNF while the CC genotype of rs2292912/CRY2 negatively influenced language and executive function. A significant decrease in gene expression for CLOCK and BDNF in PBMC (influenced by specific genotypes) of PSCI patients was observed than controls. Unlike, Pro-BDNF, plasma level mBDNF was also lower in them. ConclusionsOur results suggest that the circadian genes and BDNF play a role in PSCI on both genetic and transcript level.

neuroscience↗

bioRxiv2023

Structural and thermodynamic consequences of base pairs containing pseudouridine and N1-methylpseudouridine in RNA duplexes

Pseudouridine ({Psi}) is one of the most common post-transcriptional modifications in RNA and has been known to play significant roles in several crucial biological processes. The N1-methyl derivative of pseudouridine i.e N1-methylpseudouridine has also been reported to be important for the stability and function of RNA. Several studies suggest the importance of pseudouridine and N1-methylpseudouridine in mRNA therapeutics. The critical contribution of pseudouridine, especially that of its N1-methyl derivative in the efficiency of the COVID-19 mRNA vaccines, suggests the requirement to better understand the role of these modifications in the structure, stability and function of RNA. In the present study, we have investigated the consequences of the presence of these modifications in the stability of RNA duplex structures by analyzing different structural properties, hydration characteristics and energetics of these duplexes. We have previously studied the structural and thermodynamic properties of RNA duplexes with an internal {Psi}-A pair and reported the stabilizing effect of {Psi} over U (Deb, I. et al. Sci Rep 9, 16278 (2019)). Here, we have extended our work to understand the properties of RNA duplexes with an internal m1{Psi}-A pair and also theoretically demonstrate the effect of substituting internal U-G, U-U and U-C mismatches with the {Psi}-G, {Psi}-U and {Psi}-C mismatches and also with the m1{Psi}-G, m1{Psi}-U and m1{Psi}-C mismatches respectively, within dsRNA. Our results indicate the context-dependent stabilization of base stacking interactions by N1-methylpseudouridine compared to uridine and pseudouridine, presumably resulting from the increased molecular polarizability due to the presence of the methyl group.

biophysics↗

bioRxiv2022

Comparative Analysis of RNA Secondary Structure Accuracy on Predicted RNA 3D Models

RNA structure is conformationally dynamic, and accurate all-atom tertiary (3D) structure modeling of RNA remains challenging with the prevailing tools. Secondary structure (2D) information is the standard prerequisite for most RNA 3D modeling. Despite several 2D and 3D structure prediction tools proposed in recent years, one of the challenges is to choose the best combination for accurate RNA 3D structure prediction. Here, we benchmarked seven small RNA PDB structures (40 to 90 nucleotides) with different topologies to understand the effects of different 2D structure predictions on the accuracy of 3D modeling. The current study explores the blind challenge of 2D to 3D conversions and highlights the performances of de novo RNA 3D modeling from their predicted 2D structure constraints. Our results show that conformational sampling-based methods such as SimRNA and IsRNA1 depend less on 2D accuracy, whereas motif-based methods account for 2D evidence. Our observations illustrate the disparities in available 3D and 2D prediction methods and may further offer insights into developing topology-specific or family-specific RNA structure prediction pipelines.

bioinformatics↗

bioRxiv2022

N1-Methylpseudouridine and pseudouridine modifications modulate mRNA decoding during translation

The ribosome relies on hydrogen bonding interactions between mRNA codons and incoming aminoacyl-tRNAs to ensure rapid and accurate protein production. The inclusion of chemically modified bases into mRNAs has the potential to alter the strength and pattern of hydrogen bonding between mRNAs and aminoacyl-tRNAs to alter protein synthesis. We investigated how the Nl-methylpseudouridine (m1{Psi}) modification, commonly incorporated into therapeutic and vaccine mRNA sequences, influences the ability of codons to react with cognate and near-cognate tRNAs and release factors. We find that the presence of a single m1{Psi} does not substantially change the rate constants for amino acid addition by cognate tRNAs or termination by release factors. However, insertion of m1{Psi} can affect the selection of near-cognate tRNAs both in vitro and in human cells. Our observations demonstrate that m1{Psi}, and the related naturally occurring pseudouridine ({Psi}) modification, exhibit the ability to both increase and decrease the extent of amino acid misincorporation in a codon-position and tRNA dependent manner. To ascertain the chemical logic for our biochemical and cellular observations, we computationally modeled tRNAIle(GAU) bound to unmodified and m1{Psi}- or {Psi}-modified phenylalanine codons (UUU). Our modeling suggests that changes in the energetics of mRNA:tRNA interactions largely correlate with the context specificity of Ile-miscoding events we observe on {Psi} and m1{Psi} containing Phe codons. These studies reveal that the sequence context of a given modification within an mRNA plays a large role in determining how (and if) the modification impacts the number and distribution of proteoforms synthesized by the ribosome.

biochemistry↗

bioRxiv2019

Accelerating Dissociative Events in Molecular Dynamics Simulations by Selective Potential Scaling

Molecular dynamics (or MD) simulations can be a powerful tool for modeling complex dissociative processes such as ligand unbinding. However, many biologically relevant dissociative processes occur on timescales that far exceed the timescales of typical MD simulations. Here, we implement and apply an enhanced sampling method in which specific energy terms in the potential energy function are selectively "scaled" to accelerate dissociative events during simulations. Using ligand unbinding as an example of a complex dissociative process, we selectively scaled-up ligand-water interactions in an attempt to increase the rate of ligand unbinding. By applying our selectively scaled MD (or ssMD) approach to three cyclin-dependent kinase 2 (CDK2)-inhibitor complexes, we were able to significantly accelerate ligand unbinding thereby allowing, in some cases, unbinding events to occur within as little as 2 ns. Moreover, we found that we could make realistic estimates of the unbinding [Formula] as well as the binding free energies ({triangleup}Gsim) of the three inhibitors from our ssMD simulation data. To accomplish this, we employed a previously described Kramers-based rate extrapolation (KRE) method and a newly described free energy extrapolation (FEE) method. Because our ssMD approach is general, it should find utility as an easy-to-deploy, enhanced sampling method for modeling other dissociative processes.

biophysics↗