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Dataset results
14 results for “Nucleocapsid protein”
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>
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
Open the record for dataset details and reuse information.
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.
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.
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.
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.
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.
SARS-CoV-2 Nucleocapsid protein attenuates stress granule formation and interacts directly with mRNAs to impair host stress response
GEO Series GSE171010. Homo sapiens. 26 samples. Type: Expression profiling by high throughput sequencing; Other.
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