Biology subjects

Kumar, K.

Publications and source records attributed to Kumar, K..

At least 55 records · Page 3Linked to original sources

bioRxiv2023

Comparative transcriptome analysis in contrasting finger millet (Eleusine coracana (L.) Gaertn) genotypes for heat stress

Eleusine coracana (L.) Gaertn is a crucial C4 species renowned for its stress robustness and nutritional significance. Because of its adaptability traits, finger millet (ragi) is a storehouse of critical genomic resources for crop improvement. However, more knowledge about this crops molecular responses to heat stress must be gained. Hence, in the present study, we generated RNA seq data from the leaf tissue of the finger millet to observe the physiological changes and gene expression study in heat-sensitive (KJNS-46) and heat-tolerant (PES-110) genotypes of Ragi in response to high temperatures. On average, each sample generated about 24 million reads. Nearly 684 transcripts were differentially expressed (DEGs) between the heat-stressed samples of both genotypes. Pathway analysis and functional annotation analysis revealed the activation of various genes involved in response to stress, precisely heat, oxidation-reduction process, water deprivation, heat shock protein and transcription factors, calcium, and kinase signaling. The basal regulatory genes, such as bZIP, were involved in response to heat stress, indicating that heat stress activates genes related to basal regulatory processes or housekeeping. A substantial percentage of the DEGs belonged to proteins of unknown functions (PUFs), i.e., uncharacterized. The expression pattern of a few selected DEGs genes was analyzed in both genotypes by quantitative RT-PCR. The present study found some candidate genes and pathways that may confer tolerance to heat stress in ragi. These results will provide valuable information to improve heat tolerance in heat-susceptible agronomically important varieties of ragi and other crop plants.

plant biology↗

bioRxiv2022

Computational investigations in inhibition of alcohol/aldehyde dehydrogenase in lignocellulosic hydrolysates

Second generation alcoholic biofuels synthesis from lignocellulosic biomass (LB) consists three steps viz., pre-treatment, detoxification, and fermentation. This dilute acid pre-treatment process generates several compounds like acids, aldehydes, ketones, oxides and their phenolic derivatives that are potential inhibitors of some of the crucial enzymes in the metabolic pathway of ABE fermentation. With application of hybrid quantum mechanics/ molecular mechanics (QM/MM) approach, our aim is to discern the molecular mechanism of inhibition of key AADs across solventogenic species. The objectives of present study are: (1) identification and homology modelling of key AADs; (2) validation, quality assessment and physiochemical characterization of the modelled enzymes; (3) identification, construction and optimization of chemical structure of potent microbial inhibitors in LH; and (4) applications of hybrid QM/MM simulations to profile the molecular interactions between microbial inhibitors and key AADs. Our computational investigation has revealed various important facets of inhibition of the AAD enzymes, which could guide structural biologist in designing efficient and robust enzymes. Moreover, our methodology also provides a general framework which could applied for deciphering the molecular mechanism of inhibition behaviour of other enzymes. HighlightsO_LIHomology modelling of 7 alcohol/aldehyde dehydrogenase (AAD) in solventogenic Clostridia C_LIO_LIIdentification and structural optimization of potent microbial inhibitors in lignocellulosic hydrolysates C_LIO_LIQM/MM simulations to profile the molecular interactions between 10 inhibitors and 7 AADs C_LIO_LIDiscernment of the molecular mechanism of inhibition of key alcohol/aldehyde dehydrogenase C_LIO_LIA methodological framework for deciphering the molecular mechanism of enzyme inhibition C_LI

bioinformatics↗

bioRxiv2022

Graph Regularized Probabilistic MatrixFactorization for Drug-Drug Interactions Prediction

Co-administration of two or more drugs simultaneously can result in adverse drug reactions. Identifying drug-drug interactions (DDIs) is necessary, especially for drug development and for repurposing old drugs. DDI prediction can be viewed as a matrix completion task, for which matrix factorization (MF) appears as a suitable solution. This paper presents a novel Graph Regularized Probabilistic Matrix Factorization (GRPMF) method, which incorporates expert knowledge through a novel graph-based regularization strategy within an MF framework. An efficient and sounded optimization algorithm is proposed to solve the resulting non-convex problem in an alternating fashion. The performance of the proposed method is evaluated through the DrugBank dataset, and comparisons are provided against state-of-the-art techniques. The results demonstrate the superior performance of GRPMF when compared to its counterparts.

bioinformatics↗

bioRxiv2022

Single session of rTMS enhances brain metastability and intrinsic ignition

BackgroundEmerging evidence support the view that brain stimulation might improve essential tremor (ET) by altering brain networks and facilitating plasticity. Yet, we are still missing a mechanistic explanation of the whole brain dynamics underlying these plasticity defining changes. MethodIn this study, we explored the effect of low-frequency repetitive transcranial magnetic stimulation (rTMS) over left primary motor cortex (L-M1) on functional connectivity dynamics (FCD) in patients with ET. Resting-state fMRI (RsfMRI) was acquired before and after a single session of rTMS in 30 patients with ET and compared with RsfMRI of 20 age and gender matched healthy controls (HCs). We have measured the effect of brain stimulation using network topological re-organization through whole brain integration and segregation, brain stability and capacity of neural propagation through metastability and intrinsic ignition. ResultsPatients with ET had altered FCD measures compared to controls. After a single session rTMS, the brain connectivity measures approached normality and patients with ET revealed significantly higher integration, lower segregation with higher metastability and increased intrinsic ignition. ConclusionBrain metastability and intrinsic ignition measures could be valuable tools in appreciating mechanisms of brain stimulation in ET and other neurological diseases.

neuroscience↗

bioRxiv2022

Rare CNVs and phenome-wide profiling: a tale of brain-structural divergence and phenotypical convergence

Copy number variations (CNVs) are rare genomic deletions and duplications that can exert profound effects on brain and behavior. Previous reports of pleiotropy in CNVs imply that they converge on shared mechanisms at some level of pathway cascades, from genes to large-scale neural circuits to the phenome. However, studies to date have primarily examined single CNV loci in small clinical cohorts. It remains unknown how distinct CNVs escalate the risk for the same developmental and psychiatric disorders. Here, we quantitatively dissect the impact on brain organization and behavioral differentiation across eight key CNVs. In 534 clinical CNV carriers from multiple sites, we explored CNV-specific brain morphology patterns. We extensively annotated these CNV-associated patterns with deep phenotyping assays through the UK Biobank resource. Although the eight CNVs cause disparate brain changes, they are tied to similar phenotypic profiles across [~]1000 lifestyle indicators. Our population-level investigation established brain structural divergences and phenotypical convergences of CNVs, with direct relevance to major brain disorders.

genetics↗

bioRxiv2022

Transcriptome analysis reveals robust transcriptional reprogramming during early stages of Cicer-Ascochyta interaction

Ascochyta blight (AB) caused by a filamentous fungus Ascochyta rabiei is a major threat to global chickpea production. The mechanisms underlying chickpea response to A. rabiei remain elusive. Here, we investigated the comparative transcriptional dynamics of AB-resistant and susceptible chickpea genotypes upon A. rabiei infection to understand the early host defence response. Our findings revealed that AB-resistant plants underwent rapid and extensive transcriptional reprogramming compared to susceptible host. At early stage (24-hpi), mainly cell wall remodeling and secondary metabolite pathways were highly activated, while DEGs related with signaling components viz. protein kinases, transcription factors, and hormonal pathways show remarkable upsurge at 72-hpi, especially in resistant genotype. Notably, our data suggests imperative role of JA, ET, and ABA signaling in providing immunity against A. rabiei. Furthermore, gene co-expression networks and modules corroborated the importance of cell wall remodeling, signal transduction and phytohormone pathways. The hub genes such as MYB14, PRE6 and MADS-SOC1 discovered in these modules might be the master regulators governing chickpea immunity. Overall, we not only provide novel insights for comprehensive understanding of immune signaling components mediating AB resistance/susceptibility at early Cicer-Ascochyta interactions, but also offer a valuable resource for developing AB-resistant chickpea. HighlightsComparative transcriptomic and co-expression analysis of AB-resistant and susceptible chickpea genotypes reveals high-amplitude transcriptional dynamics in resistant plants, and also identifies TFs, PKs and phytohormone-crosstalk as core regulators for AB-resistance.

plant biology↗

bioRxiv2021

Local activation of focal adhesion kinase orchestrates the positioning of presynaptic scaffold proteins and Ca2+ channel function to control glucose dependent insulin secretion.

A developing understanding suggests that spatial compartmentalisation of components the glucose stimulus-secretion pathway in pancreatic {beta} cells are critical in controlling insulin secretion. To investigate the mechanisms, we have developed live-cell sub-cellular imaging methods using the organotypic pancreatic slice. We demonstrate that the organotypic pancreatic slice, when compared with isolated islets, preserves intact {beta} cell structure, and enhances glucose dependent Ca2+ responses and insulin secretion. Using the slice technique, we have discovered the essential role of local activation of integrins and the downstream component, focal adhesion kinase, in regulating {beta} cells. Integrins and focal adhesion kinase are exclusively activated at the {beta} cell capillary interface and using in situ and in vitro models we show their activation both positions presynaptic scaffold proteins, like ELKS and liprin, and regulates glucose dependent Ca2+ responses and insulin secretion. We conclude that focal adhesion kinase orchestrates the final steps of glucose dependent insulin secretion within the restricted domain where {beta} cells contact the islet capillaries.

cell biology↗

bioRxiv2021

Probing neuropeptide volume transmission in vivo by a novel all-optical approach

Neuropeptides are essential signaling molecules in the nervous system involved in modulating neural circuits and behavior. Although hypothesized to signal via volume transmission through G-protein coupled receptors (GPCR), remarkably little is known about their extrasynaptic diffusion. Here, we developed an all-optical approach to probe neuropeptide volume transmission in mouse neocortex. To control neuropeptide release, we engineered photosensitive nanovesicles with somatostatin-14 (SST) that is released with near-infrared light stimulation. To detect SST, we created a new cell-based neurotransmitter fluorescent engineered reporter (CNiFER) using the SST2 GPCR. Under two-photon imaging, we determined the time to activate SST2R at defined distances as well as the maximal distance and loss rate for SST volume transmission in neocortex. Importantly, we determined that SST transmission is significantly faster in neocortex with a chemically degraded extracellular matrix, a diseased condition indicated in neuroinflammation and Parkinsons disease. These new neurotechnologies can reveal important biological signaling processes previously not possible, and provide new opportunities to investigate volume transmission in the brain.

neuroscience↗

bioRxiv2021

The nuclear effector ArPEC25 from the necrotrophic fungus Ascochyta rabiei targets the chickpea transcription factor CaβLIM1a and negatively modulates lignin biosynthesis for host susceptibility

Fungal pathogens deploy a barrage of secreted effectors to subvert host immunity, often by evading, disrupting, or altering key components of transcription, defense signaling, and metabolic pathways. However, the underlying mechanisms of effectors and their host targets are largely unexplored in necrotrophic fungal pathogens. Here, we describe the effector protein ArPEC25, which is secreted by the necrotroph Ascochyta rabiei, the causal agent of Ascochyta blight disease in chickpea (Cicer arietinum), and is indispensable for virulence. After entering host cells, ArPEC25 localizes to the nucleus and targets the host LIM transcription factor Ca{beta}LIM1a. Ca{beta}LIM1a is a transcriptional regulator of CaPAL1, which encodes phenylalanine ammonia lyase, the regulatory, gatekeeping enzyme of the phenylpropanoid pathway. ArPEC25 inhibits the transactivation of Ca{beta}LIM1a by interfering with its DNA binding ability. This results in negative regulation of the phenylpropanoid pathway and decreased levels of intermediates of lignin biosynthesis, thereby suppressing lignin production. Our findings illustrate the role of fungal effectors in enhancing virulence by targeting a key defense pathway that leads to the biosynthesis of various secondary metabolites and antifungal compounds. This study provides a template for the study of less explored necrotrophic effectors and their host target functions. One-sentence summaryThe Ascochyta rabiei effector ArPEC25 enters the host nucleus and targets the transcription factor Ca{beta}LIM1a to manipulate phenylpropanoid pathway for negative modulation of chickpea lignin biosynthesis.

plant biology↗

bioRxiv2021

Identification and validation of E3 ubiquitin ligase XIAP as a novel substrate of deubiquitinase USP7 (HAUSP) - Implication towards oncogenesis

The induction of apoptosis upon USP7 (HAUSP) inhibition is established in cancers that contain a wild-type p53 (p53Wt) through the USP7-Mdm2-p53 axis, but no clear explanation has yet been reported for the same to occur in cancers containing mutant 53 (p53Mut) or even p53 null (p53Null) systems. Instead of this USP7-Mdm2-p53 axis USP7 also works through an alternative new pathway identified in this study. Here in this study, we observed that the magnitude of apoptosis induction in response to USP7 inhibition was remarkably similar between cancer cells showing p53Null or p53Mut and those with p53Wt. Through a proteomics-based approach, we were able to identify XIAP as a novel interacting partner for USP7. XIAP is a potent and well-characterized member of the inhibitor of apoptosis proteins (IAPs), which function through caspase inhibition. We successfully identified USP7 as a positive regulator of XIAP at post-translational but not at its transcriptional level. Using molecular modelling coupled with domain deletion studies, we show that the first three Ubl domains in association with the catalytic domain of USP7 interact with the BIR2 and the linker region between BIR2 and BIR3 domains of XIAP. Modulation of expression and catalytic activity of USP7 in multiple type of cancer cell lines showed that USP7 stabilizes XIAP through its deubiquitinase activity. We have also observed that USP7 sensitizes cells against chemotherapeutic drugs through stabilization of XIAP. Thus, USP7 promotes tumorigenesis in multiple cancers, via stabilization of XIAP that results in apoptosis inhibition in caspase dependent pathway. Moreover, we observed that combinatorial inhibition of USP7 and XIAP can induce cellular apoptosis in a higher magnitude than their individual inhibition. Additionally, our results indicates that nanoformulated P5091 and P22077 showed higher potency for killing C6 cells in comparison to normal drugs. To the best of our knowledge, this is the first report on identification and validation of XIAP, a crucial E3 ubiquitin ligase, as a novel substrate of the deubiquitinase USP7 and they together involve in empowerment of the tumorigenic potential of cancer cells.

cancer biology↗

bioRxiv2021

Fine-tuning the transcriptional regulatory model of adaptation response to phosphate stress in maize (Zea mays L.)

The post green revolution agriculture is based on generous application of fertilizers and high-yielding genotypes that are suited for such high input regimes. Cereals, like maize (Zea mays L.) are capable of utilizing less than 20% of the applied inorganic phosphate (Pi) - a non-renewable fertilizer resource. A greater understanding of the molecular mechanisms underlying the acquisition, transportation and utilization of Pi may lead to strategies to enhance phosphorus use efficiency (PUE) in field crops. In this study, we selected 12 Pi responsive genes in maize and carried out their comparative transcriptional expression in root and leaf tissues of a hydroponically grown Pi stress tolerant maize inbred line HKI-163, under sufficient and deficient Pi conditions. Pi starvation led to significant increase in root length; marked proliferation of root hairs and lesser number of crown roots. Eleven genes were significantly up or down regulated in Pi deficient condition. The putative acid phosphatase, ZmACP5, expression was up regulated by 162.81 and 74.40 fold in root and leaf tissues, respectively. The RNase, ZmRNS1 showed 115 fold up regulation in roots under Pi deprivation. Among the two putative high affinity Pi transporters ZmPht1;4 was found specific to root, whereas ZmPht2 was found to be up regulated in both root and leaf tissues. The genes involved in Pi homeostasis pathway (ZmSIZ1, SPX1 and Pho2) were up regulated in root and leaf. In light of the expression profiling of selected regulatory genes, an updated model of transcriptional regulation under Pi starvation in maize has been proposed.

plant biology↗

bioRxiv2020

Optimal Adaptive Electrode Selection to Maximize Simultaneously Recorded Neuron Yield

Neural-Matrix style, high-density electrode arrays for brain-machine interfaces (BMIs) and neuroscientific research require the use of multiplexing: Each recording channel can be routed to one of several electrode sites on the array. This capability allows the user to flexibly distribute recording channels to the locations where the most desirable neural signals can be resolved. For example, in the Neuropixel probe, 960 electrodes can be addressed by 384 recording channels. However, currently no adaptive methods exist to use recorded neural data to optimize/customize the electrode selections per recording context. Here, we present an algorithm called classification-based selection (CBS) that optimizes the joint electrode selections for all recording channels so as to maximize isolation quality of detected neurons. We show, in experiments using Neuropixels in non-human primates, that this algorithm yields a similar number of isolated neurons as would be obtained if all electrodes were recorded simultaneously. Neuron counts were 41-85% improved over previously published electrode selection strategies. The neurons isolated from electrodes selected by CBS were a 73% match, by spike timing, to the complete set of recordable neurons around the probe. The electrodes selected by CBS exhibited higher average per-recording-channel signal-to-noise ratio. CBS, and selection optimization in general, could play an important role in development of neurotechnologies for BMI, as signal bandwidth becomes an increasingly limiting factor. Code and experimental data have been made available1.

neuroscience↗

bioRxiv2020

Modulation of fungal virulence through CRZ1 regulated F-BAR-dependent actin remodeling and endocytosis in chickpea infecting phytopathogen Ascochyta rabiei

Polarized hyphal growth of filamentous pathogenic fungi is an essential event for host penetration and colonization. The long-range early endosomal trafficking during the hyphal growth is crucial for nutrient uptake, sensing of host-specific cues, and regulation of effector production. Bin1/Amphiphysin/Rvs167 (BAR) domain-containing proteins mediate fundamental cellular processes, including membrane remodeling and endocytosis. Here, we identified an F-BAR domain protein (ArF-BAR) in the necrotrophic fungus Ascochyta rabiei and demonstrate its involvement in endosome-dependent fungal virulence on the host plant, Cicer arietinum. We show that ArF-BAR regulates endocytosis at the hyphal tip, localizes to the early endosomes, and is involved in actin dynamics. Functional studies involving gene knockout and complementation experiments reveal that ArF-BAR is essential for virulence. The loss-of-function of ArF-BAR results in delayed formation of first septa from the hyphal tip, crucial for host penetration and proliferation. ArF-BAR was induced in response to oxidative stress and infection and localized to endocytic vesicles within the fungal hyphae. We also show that ArF-BAR is able to tubulate synthetic liposomes, suggesting the functional role of F-BAR domain in membrane tubule formation in vivo. Further, our studies identified a stress-induced transcription factor, ArCRZ1 (Calcineurin-responsive zinc finger 1) as key regulator for transcriptional reprogramming of ArF-BAR. We propose a model in which ArCRZ1 functions upstream of ArF-BAR to regulate fungal pathogenesis through a mechanism that involves membrane remodeling and actin cytoskeleton regulation. Author summaryBAR-domain superfamily is known to mold amorphous lipid bilayer into defined tubular shapes and critical for endosome formation and trafficking. Although these processes are studied earlier in the context of their structural and biochemical properties, there is limited evidence on the direct role of F-BAR domain proteins in the pathophysiological development of other economically important fungi. Our study assumes functional significance for plant infection as we identified an F-BAR domain-containing protein that is regulated by a distinct transcriptional network. We characterized F-BAR in a necrotrophic fungal pathogen, Ascochyta rabiei that causes the Ascochyta blight (AB) disease in chickpea plants. Additionally, we have also identified a calcium-regulated CRZ1 transcription factor that regulates the transcription of ArF-BAR. Our study will help to understand the complex interplay underlying the endosome formation required for fungal virulence.

plant biology↗

bioRxiv2020

Transcriptomic dysregulations associated with SARS-CoV-2 infection in human nasopharyngeal and peripheral blood mononuclear cells

IntroductionOver 24 million people have been infected globally with the novel coronavirus, SARS-CoV-2, with more than 820,000 succumbing to the resulting COVID-19 disease as of the end of August 2020. The molecular mechanisms underlying the pathogenesis of the disease are not completely elucidated. Thus, we aim to understand host response to SARS-CoV-2 infection by comparing samples collected from two distinct compartments (infection site and blood), obtained from COVID-19 subjects and healthy controls. MethodsWe used two publicly available gene expression datasets generated via RNA sequencing in two different samples; nasopharyngeal swabs and peripheral blood mononuclear cells (PBMCs). We performed a differential gene expression analysis between COVID-19 subjects and healthy controls in the two datasets and then functionally profiled their differentially expressed genes (DEGs). The genes involved in innate immunity were also determined. ResultsWe found a clear difference in the host response to SARS-CoV-2 infection between the two sample groups. In COVID-19 subjects, the nasopharyngeal sample group indicated upregulation of genes involved in cytokine activity and interferon signalling pathway, as well as downregulation of genes involved in oxidative phosphorylation and viral transcription. Host response in COVID-19 subjects for the PBMC group, involved upregulation of genes involved in the complement system and immunoglobulin mediated immune response. CXCL13, GABRE, IFITM3 were upregulated and HSPA1B was downregulated in COVID-19 subjects in both sample groups. ConclusionOur results indicate the host response to SARS-CoV-2 is compartmentalized and suggests potential biomarkers of response to SARS-CoV-2 infection. HighlightsO_LITranscriptomic profiling from publicly available RNA-seq count data revealed a site-specific immune response in COVID-19. C_LIO_LIHost response was found cellular-mediated in nasopharyngeal samples and humoral-mediated in PBMCs samples. C_LIO_LICXCL13, GABRE and IFITM3 commonly upregulated and HSPA1B downregulated in both sample groups highlights the potential of these molecules as markers of response to SARS-CoV-2 infection. C_LI

immunology↗

bioRxiv2020

Nest records, Nest Site selection of Gyps bengalensis White-rumped Vulture and the role of Feeding Station in Kangra, Himachal Pradesh

Active nests of Gyps bengalensis White-rumped Vulture depends on elevation and aspects for nest site selection, while feeding station plays a significant role for determining the position of the nesting sites.This study attempted to record nest count for the breeding period 2018, identify key variables for the nest site selection and understand the role of feeding station in the nest site selection. Nest counts were conducted during the breeding period, each nest was categorized into active and inactive nest based on assesment of different components. Simultaneously, different variables (tree height, tree species, elevation and aspect) were recorded for each nest. Aerial distance was used to determine the role of feeding station for selecting the nesting sites. From the 24 nesting sites, 352 active nests were recorded, and a significant Pearsons correlation for elevation and aspect were drawn. We found, vulture prefer single tree species for nesting. We also found that, 71% (n = 17) nesting sites located within radial distance of 20 km of the feeding station. High congregration of active nests within short radial distance from feeding station, signify the positive impact of management of feeding station by the wildlife wing of Forest department since 2008, for the ex-situ conservation of critically endangered Gyps bengalensis White-rumped Vulture

ecology↗

bioRxiv2020

The Harmine and Exendin-4 Combination Markedly Expands Human Beta Cell Mass In Vivo: Quantification and Visualization By iDISCO+ 3D Imaging

463 million people globally suffer from diabetes. The majority are deficient in insulin-producing pancreatic beta cells, although beta cells remain in most people with diabetes. Unfortunately, although many diabetes drugs exist, none is able to increase adult human beta cell numbers. Recently, small molecules that inhibit the kinase, DYRK1A, have been suggested to induce human beta cell replication in vitro and in vivo as assessed using proliferation markers, and this is enhanced by drugs that stimulate the GLP1 receptor (GLP1R) on beta cells. DYRK1A inhibitors also enhance human beta cell differentiation and function. However, it is unknown whether any drug can actually increase human beta cell mass in vivo, reflecting: 1) the intrinsic resistance of human beta cells to regeneration; and, 2) the current technical inability to accurately assess human beta cell mass in vivo. Here, we demonstrate for the first time that combining a DYRK1A inhibitor with a GLP1R agonist increases actual human beta cell numbers and overall mass in vivo by 400-700% in diabetic and non-diabetic mice over three months. We further describe a novel application of tissue-clearing and 3D imaging for quantification of human beta cell mass. These findings should be transformative for diabetes treatment.

cell biology↗

bioRxiv2020

Different Perspective of Machine LearningTechnique to Better Predict Breast Cancer Survival

Machine learning (ML) plays a key job in the guide of cancer diagnosis and identification. The researcher has implemented different algorithms of ML for the prediction of breast cancer. Some researchers recommend their algorithms are more accurate, faster, and easier than others. My study relies on recently developed machine learning algorithms like genetic algorithms and deep belief nets. Im interested to build a framework to precisely separate among benign and malignant tumors. Weve optimized the training algorithm. During this unique circumstance, we applied the genetic algorithm procedure to settle on the main genuine highlights and perfect boundary estimations of the AI classifiers. The examinations rely upon affectability, cross-validation, precision, and ROC curve. Among all the varying kinds of classifiers used in this paper genetic programming is the premier viable model for highlight determination and classifier.

bioinformatics↗

bioRxiv2020

Investigation of the effect of temperature on the structure of SARS-Cov-2 Spike Protein by Molecular Dynamics Simulations

Statistical and epidemiological data imply temperature sensitivity of the SARS-CoV-2 coronavirus. However, the molecular level understanding of the virus structure at different temperature is still not clear. Spike protein is the outermost structural protein of the SARS-CoV-2 virus which interacts with the Angiotensin Converting Enzyme 2 (ACE2), a human receptor, and enters the respiratory system. In this study, we performed an all atom molecular dynamics simulation to study the effect of temperature on the structure of the Spike protein. After 200ns of simulation at different temperatures, we came across some interesting phenomena exhibited by the protein. We found that the solvent exposed domain of Spike protein, namely S1, is more mobile than the transmembrane domain, S2. Structural studies implied the presence of several charged residues on the surface of N-terminal Domain of S1 which are optimally oriented at 10-30 {degrees}C. Bioinformatics analyses indicated that it is capable of binding to other human receptors and should not be disregarded. Additionally, we found that receptor binding motif (RBM), present on the receptor binding domain (RBD) of S1, begins to close around temperature of 40 {degrees}C and attains a completely closed conformation at 50 {degrees}C. The closed conformation disables its ability to bind to ACE2, due to the burying of its receptor binding residues. Our results clearly show that there are active and inactive states of the protein at different temperatures. This would not only prove beneficial for understanding the fundamental nature of the virus, but would be also useful in the development of vaccines and therapeutics. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=89 SRC="FIGDIR/small/145086v2_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@1e631eeorg.highwire.dtl.DTLVardef@1d83278org.highwire.dtl.DTLVardef@d98d3borg.highwire.dtl.DTLVardef@c75b7f_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIStatistical and epidemiological evidence show that external climatic conditions influence the SARS-CoV infectivity, but we still lack a molecular level understanding of the same. C_LIO_LIHere, we study the influence of temperature on the structure of the Spike glycoprotein, the outermost structural protein, of the virus which binds to the human receptor ACE2. C_LIO_LIResults show that the Spikes S1 domain is very sensitive to external atmospheric conditions compared to the S2 transmembrane domain. C_LIO_LIThe N-terminal domain comprises of several solvent exposed charged residues that are capable of binding to human proteins. The region is specifically stable at temperatures ranging around 10-30{degrees} C. C_LIO_LIThe Receptor Binding Motif adopts a closed conformation at 40{degrees}C and completely closes at higher temperatures making it unsuitable of binding to human receptors C_LI

biophysics↗