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Dataset results
23 results for “Nucleocapsid”
SIRAH-CoV2 initiative: RNA binding domain of nucleocapsid phosphoprotein (PDB id:6VYO)
<p>This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of SARS-CoV2 RNA binding domain of the nucleocapsid phosphoprotein in its APO form with Zn ions bound (PDB id:6VYO, Bioassembly 1). Simulations were performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported in <a href="https://pubs.acs.org/doi/10.1021/acs.jctc.9b00006">Machado et al. JCTC 2019</a>, adding 150 mM NaCl according to <a href="https://pubs.acs.org/doi/10.1021/acs.jctc.9b00953">Machado & Pantano JCTC 2020</a>. Zinc ions were parameterized as reported in <a href="https://pubs.acs.org/doi/10.1021/acs.jcim.0c00160">Klein et al. 2020</a>.</p> <p>The file 6VYO_SIRAHcg_rawdata.tar contains all the raw information required to visualize (on VMD), analyze, backmap, and eventually continue the simulations using Amber18 or higher. Step-By-Step tutorials for running, visualizing, and analyzing CG trajectories using <a href="https://academic.oup.com/bioinformatics/article/32/10/1568/1743152">SirahTools</a> can be found at www.sirahff.com. Additionally, the file 6VYO_SIRAHcg_10us_prot.tar contains only the protein coordinates, while 6VYO_SIRAHcg_10us_prot_skip10ns.tar contains one frame every 10ns.</p> <p>To take a quick look at the trajectory:</p> <p>1- Untar the file 6VYO_SIRAHcg_10us_prot_skip10ns.tar</p> <p>2- Open the trajectory on VMD using the command line:</p> <p>vmd 6VYO_SIRAHcg_prot_10us_skip10ns.prmtop 6VYO_SIRAHcg_prot_10us_skip10ns.ncrst 6VYO_SIRAHcg_prot_10us_skip10ns.nc -e sirah_vmdtk.tcl</p> <p>Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc. </p> <p>This dataset is part of the SIRAH-CoV2 initiative.</p> <p>For further details, please contact Florencia Klein (fklein@pasteur.edu.uy) or Sergio Pantano (spantano@pasteur.edu.uy).</p>
SIRAH-CoV2 initiative: Nucleocapsid protein N-terminal RNA binding domain (PDB id:6M3M)
<p>This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of SARS-CoV2 Nucleocapsid protein N-terminal RNA binding domain (PDB id:6M3M). Simulations have been performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported in <a href="https://pubs.acs.org/doi/10.1021/acs.jctc.9b00006">Machado et al. JCTC 2019</a>, adding 150 mM NaCl according to <a href="https://pubs.acs.org/doi/10.1021/acs.jctc.9b00953">Machado & Pantano JCTC 2020</a>. </p> <p>The files 6M3M_SIRAHcg_rawdata.tar contains all the raw information required to visualize (on VMD), analyze, backmap, and eventually continue the simulations using Amber18 or higher. Step-By-Step tutorials for running, visualizing, and analyzing CG trajectories using <a href="https://academic.oup.com/bioinformatics/article/32/10/1568/1743152">SirahTools</a> can be found at www.sirahff.com.</p> <p>Additionally, the file 6M3M_SIRAHcg_10us_prot.tar contains only the protein coordinates, while 6M3M_SIRAHcg_10us_prot_skip10ns.tar contains one frame every 10ns.</p> <p>To take a quick look at the trajectory:</p> <p>1- Untar the file 6M3M_SIRAHcg_10us_prot_skip10ns.tar</p> <p>2- Open the trajectory on VMD using the command line:</p> <p>vmd 6W4B_SIRAHcg_prot.prmtop 6W4B_SIRAHcg_prot.ncrst 6W4B_SIRAHcg_prot_10us_skip10ns.nc -e sirah_vmdtk.tcl</p> <p>Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc. </p> <p>This dataset is part of the SIRAH-CoV2 initiative.</p> <p>For further details, please contact Florencia Klein (fklein@pasteur.edu.uy) or Sergio Pantano (spantano@pasteur.edu.uy).</p>
Structural dynamics of SARS-CoV-2 nucleocapsid protein induced by RNA binding
<p>This dataset contains files of the molecular dynamics simulations performed in "Structural dynamics of SARS-CoV-2 nucleocapsid protein induced by RNA binding" study. Further information in presented in README.md file and the abstract of the study is presented below:</p> <p>"The nucleocapsid (N) protein of the SARS-CoV-2 virus, the causal agent of COVID-19, is a multifunction phosphoprotein that plays critical roles in the virus life cycle, including transcription and packaging of the viral RNA. To play such diverse roles, the N protein has two globular RNA-binding modules, the N- (NTD) and C-terminal (CTD) domains, which are connected by an intrinsically disordered region. Despite the wealth of structural data available for the isolated NTD and CTD, how these domains are arranged in the full-length protein and how the oligomerization of N influences its RNA-binding activity remains largely unclear. Herein, using experimental data from electron microscopy and biochemical/biophysical techniques combined with molecular modeling and molecular dynamics simulations, we showed that, in the absence of RNA, the N protein formed structurally dynamic dimers, with the NTD and CTD arranged in extended conformations. However, in the presence of RNA, the N protein assumed a more compact conformation where the NTD and CTD are packed together. We also provided an octameric model for the full-length N bound to RNA that was consistent with electron microscopy images of the N protein in the presence of RNA. Together, our results shed new light on the dynamics and higher-order oligomeric structure of this versatile protein."</p>
SARS-CoV-2 nucleocapsid and RT-PCR results
<p><span>We collected blood samples from patients admitted to the hospital during a period with RT-PCR based-screening of patients for Severe Acute Respiratory Syndrome Cornavirus-2 (SARS-CoV-2). Retrospectively the SARS-CoV-2 nucleocapsid protein (NP) plasma concentrations were measured with an ELISA method and used for an initial time course study to find the optimal time-point for sampling blood. Next, we estimated the diagnostic accuracy i.e. the clinical sensitivity and specificity at different plasma NP cut-off concentrations.</span></p> <p><span>The time course study revealed profiles with rapid or more slow declines in NP titers after the RT-PCR result. Nevertheless, in the time interval 0 – 7 days after the RT-PCR result, the NP concentration was always above the level of detection at 1.66 pg/ml suggesting that the diagnosis could be established in the time interval of 0 - 7 days.</span></p> <p><span>The median time gap between the plasma NP and RT-PCR results was 0.0 days (n = 1957, interval: -26 to + 21 days). Reducing the time gap to seven days, the clinical sensitivity was 90.0% (n= 60, 95% CI, 82.4% to 97.6%) at a specificity of 95.9% (n=1876, 95% CI, 95.0% to 96.8%). Curve analysis by receiver operation characteristics identified a cut-off concentration of 1.87 pg/mL NP as optimal resulting in a positive predictive value of 41.2%, a negative predictive value of 99.7% and a prevalence of 3.1%.</span></p> <p><span>In conclusion, the NP method is acceptable for making the laboratory diagnosis of SARS-CoV-2, and an intended use of plasma NP as a prospective nosocomial screening method is considered feasible.</span></p>
A hybrid structure determination approach to investigate the druggability of the nucleocapsid protein of SARS-CoV-2
<p><span>The ongoing pandemic caused by SARS-CoV-2 has called for concerted efforts to generate new insights into the biology of betacoronaviruses to inform drug screening and development. Here, we establish a workflow to determine the RNA recognition and druggability of the nucleocapsid N-protein of SARS-CoV-2, a highly abundant protein crucial for the viral life cycle. We use a synergistic method that combines NMR spectroscopy and protein-RNA cross-linking coupled to mass spectrometry to quickly determine the RNA binding of two RNA recognition domains of the N-protein. Finally, we explore the druggability of these domains by performing an NMR fragment screening. This workflow identified small molecule chemotypes that bind to RNA binding interfaces and that have promising properties for further drug development.</span></p> <p><span>This deposition contains the NMR data acquired to determine the structural features of RBDs- RNA recognition as well as selected relevant data regarding the characterization of promising molecular fragments to disrupt protein-RNA interaction.</span></p> <p><span>Furthermore, we included the molecular docking files used to obtain the reported structural model.</span></p>
Phase separation of SARS-CoV-2 nucleocapsid protein with TDP-43 is dependant on C-terminus domains
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LAMMPS trajectories for "The disordered N-terminal tail of SARS CoV-2 Nucleocapsid protein forms a dynamic complex with RNA"
<p><strong>LAMMPS trajectory data for:</strong><br> <strong>The disordered N-terminal tail of SARS CoV-2 Nucleocapsid protein forms a dynamic complex with RNA</strong><br> Jasmine Cubuk<sup>1,2</sup>, Jhullian J. Alston<sup>1,2</sup>, J. Jeremías Incicco<sup>1,2</sup>, Alex S. Holehouse<sup>1,2</sup>, Kathleen B Hall<sup>1</sup>, Melissa D. Stuchell-Brereton<sup>1,2</sup>, Andrea Soranno<sup>1,2,*</sup></p> <p><sup>1</sup>Department of Biochemistry and Molecular Biophysics, Washington University in St Louis, 660 St Euclid Ave, 63110, Saint Louis, MO, USA</p> <p><sup>2</sup>Center for Biomolecular Condensates, Washington University in St Louis, 1 Brookings Drive, 63130, Saint Louis, MO, USA</p> <p><strong>Corresponding author: </strong>Andrea Soranno (soranno@wustl.edu)<br> <strong>Questions about simulations: </strong>Alex Holehouse (alex.holehouse@wustl.edu)</p> <p><strong>Preprint link: </strong><a href="https://doi.org/10.1101/2023.02.10.527914">https://doi.org/10.1101/2023.02.10.527914</a></p> <p><strong>GitHub link to simulation info:</strong> <a href="https://github.com/holehouse-lab/supportingdata/tree/master/2023/cubuk_2023">https://github.com/holehouse-lab/supportingdata/tree/master/2023/cubuk_2023</a></p> <p><strong>Funding: </strong>This research was supported by the NIH National Institute on Allergic and Infectious Diseases with R01AI163142 (to A.S., A.S.H.) and by the NIH National Cancer Institute F99CA264413 (to J.J.A.).</p> <p> </p>
A Study Assessing the Safety, Tolerability, Immunogenicity of COVID-19 Vaccine Candidate PRIME-2-CoV_Beta, Orf Virus Expressing SARS-CoV_2 Spike and Nucleocapsid Proteins
ClinicalTrials.gov study NCT05367843. IPD Sharing: Not stated. Countries: 2. Publications: 1.
SARS-CoV-2 nucleocapsid and RT-PCR results
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A hybrid structure determination approach to investigate the druggability of the nucleocapsid protein of SARS-CoV-2
Open the record for dataset details and reuse information.
SARS-CoV-2 Nucleocapsid protein attenuates stress granule formation and interacts directly with mRNAs to impair host stress response (RNA-Seq)
GEO Series GSE171009. Homo sapiens. 8 samples. Type: Expression profiling by high throughput sequencing.
Characterization of nucleocapsid-RNA interactions in Rift Valley fever virus infected cells
GEO Series GSE186067. Homo sapiens. 9 samples. Type: Expression profiling by high throughput sequencing.
Genomic RNA elements drive phase separation of the SARS-CoV-2 nucleocapsid
GEO Series GSE162569. Severe acute respiratory syndrome coronavirus 2. 27 samples. Type: Other.
Microarray Profile of Measles Virus Nucleocapsid Protein (MVNP) Regulated Gene Expression in RANKL and M-CSF stimulated normal human bone marrow derived non-adherent cells.
GEO Series GSE29106. Homo sapiens. 2 samples. Type: Expression profiling by array.
SARS-CoV-2 infection establishes an enhanced, stable, and age-independent CD8+ T cell response against a dominant nucleocapsid epitope using highly restricted TCRs
GEO Series GSE227971. Homo sapiens. 1 samples. Type: Expression profiling by high throughput sequencing.
Neuro-PASC is characterized by enhanced CD4+ and diminished CD8+ T cell responses to SARS-CoV-2 Nucleocapsid protein
GEO Series GSE225942. Homo sapiens. 38 samples. Type: Other.
SARS-CoV-2 Nucleocapsid protein attenuates stress granule formation and interacts directly with mRNAs to impair host stress response (iCLIP-Seq)
GEO Series GSE171008. Homo sapiens. 18 samples. Type: Other.
The role of SARS-CoV-2 nucleocapsid protein in effecting immune cells and insights on its molecular mechanisms
GEO Series GSE236800. Mus musculus. 9 samples. Type: Expression profiling by high throughput sequencing.
Predicting COVID-19 Severity with a Specific Nucleocapsid Antibody plus Disease Risk Factor Score
GEO Series GSE172471. Human parainfluenza virus 4b; Influenza B virus; Human respirovirus 1; human metapneumovirus; Human respiratory syncytial virus B; Human adenovirus sp.; Human coronavirus OC43; Human coronavirus HKU1; Severe acute respiratory syndrome coronavirus 2; Homo sapiens; Human respiratory syncytial virus A; Dromedary camel coronavirus; Human orthorubulavirus 2; Human coronavirus 229E; Human respirovirus 3; Influenza A virus; Human coronavirus NL63; Severe acute respiratory syndrome-related coronavirus. 90 samples. Type: Protein profiling by protein array.
The highly conserved RNA-binding specificity of nucleocapsid protein facilitates the identification of drugs with broad anti-coronavirus activity.
GEO Series GSE209797. Escherichia coli. 72 samples. Type: Other.
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International Brain Laboratory public data
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