Docking and molecular dynamics studies of human ezrin protein with a modelled SARS-CoV-2 endodomain and their interaction with potential invasion inhibitors
Selvaa Kumar Chellasamy, Eleanor Watson
Journal of King Saud University - Science, doi:10.1016/j.jksus.2022.102277
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Conflicts of Interest: The authors declare no competing or conflicting interests.
References
Bairoch, Apweiler, The Swiss-Prot protein sequence database: its relevance to human molecular medical research, J. Mol. Med
Berendsen, GROMACS: A message-passing parallel molecular dynamics implementation, Comp. Phys. Comm
Berman, Westbrook, Feng, Gilliland, Bhat et al., The protein data bank, Nucleic Acids Res
Biovia, Systèmes, None
Bretscher, Edwards, Fehon, ERM proteins and merlin: integrators at the cell cortex, Nat. Rev. Mol. Cell Biol
Bulut, Hong, Chen, Beauchamp, Rahim et al., Small molecule inhibitors of ezrin inhibit the invasive phenotype of osteosarcoma cells, Oncogene Jan,
doi:10.1038/onc.2011.245Chen, Sawaya, Phillips, Reisler, Quinlan, Multiple Forms of Spire-Actin Complexes and their Functional Consequences, J. Biol. Chem
Ehsani, COVID-19 and iron dysregulation: distant sequence similarity between hepcidin and the novel coronavirus spike glycoprotein, Biol Direct,
doi:10.1186/s13062-020-00275-2Fehon, Mcclatchey, Bretscher, Organizing the cell cortex: the role of
Fehr, Perlman, Coronaviruses: an overview of their replication and 15. pathogenesis, Methods Mol. Biol
Fievet, Louvard, Arpin, ERM proteins in epithelial cell organization and 13. functions, Biochim Biophys Acta
Gautreau, Poullet, Louvard, Arpin, Ezrin, a plasma membrane-microfilament linker, signals cell survival through the phosphatidylinositol 3-kinase/Akt pathway
Jorgensen, Chandrasekhar, Madura, Impey, Klein, Comparison of simple potential functions for simulating liquid water, J. Chem. Phys
Kim, Thiessen, Bolton, Chen, Fu et al., PubChem Substance and Compound databases, Nucleic Acids Res
Kumar, Kumar, Wei, Comparative docking studies to understand the binding affinity of nicotine with soluble ACE2 (sACE2)-SARS-CoV-2 complex over sACE2, Toxicology Reports
Laskowski, Macarthur, Moss, Thornton, PROCHECK -a program to check the stereochemical quality of protein structures, J. App. Cryst
Li, Li, Farzan, Harrison, Structure of SARS coronavirus spike receptor binding domain complexed with receptor, Science
Lu, Hu, Wang, Qi, Gao et al., Molecular basis of binding between novel human coronavirus MERS-CoV and its receptor. CD26, Nature
Lu, Zhao, Li, Genomic characterization and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding, Lancet
Millet, Kien, Cheung, Siu, Chan et al., Ezrin interacts with the SARS coronavirus spike protein and restrains infection at the entry stage, PLoS One,
doi:10.1371/journal.pone.0049566Miteva, Guyon, Tufféry, Frog2: Efficient 3D conformation ensemble generator for small compounds, Nucleic Acids Res. Jul
Morris, Huey, Lindstrom, Sanner, Belew et al., Autodock4 and AutoDockTools4: automated docking with selective receptor flexibility, J. Computational Chemistry
Nose, A unified formulation of the constant temperature molecular dynamics methods, The Journal of Chemical Physics
Paules, Marston, Fauci, Coronavirus infections-more than just the common cold, JAMA
Petit, Chouljenko, Iyer, Colgrove, Farzan et al., Palmitoylation of the cysteine-rich endodomain of the SARS-coronavirus spike glycoprotein is important for spike-mediated cell fusion, Virology Apr
Phang, Harrop, Duff, Sokolova, Crossett et al., Structural characterization suggests models for monomeric and dimeric forms of full length ezrin, Biochem. J
Ramadan, Mayilsamy, Mcgill, Ghosh, Giulianotti et al., Identification of SARS-CoV-2 Spike Palmitoylation Inhibitors That Results in Release of Attenuated Virus with Reduced Infectivity, Viruses
Schwede, Kopp, Guex, Peitsch, SWISS-MODEL: an automated protein homology-modelling server, Nucleic Acids Res. Jul
Shaw Research, Maestro-Desmond Interoperability Tools, version 3.6
Smith, Nassar, Bretscher, Cerione, Andrew et al., Structure of the active N-terminal domain of Ezrin. Conformational and mobility changes identify keystone interactions, J. Biol. Chem. Feb,
doi:10.1074/jbc.M210601200Turunen, Wahlström, Vaheri, Ezrin has a COOH-terminal actin-binding site that is conserved in the ezrin protein family, J. Cell Biol
Van Zundert, Melquiond, Bonvin, Integrative Modeling of Biomolecular Complexes: HADDOCKing with Cryo-Electron Microscopy Data, Structure
Wiederstein, Sippl, ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins, Nucleic Acids Research
Xia, Domains and Functions of Spike Protein in Sars-Cov-2 in the Context of Vaccine Design, Viruses,
doi:10.3390/v1301010Xue, Rodrigues, Kastritis, Bonvin, Vangone, PRODIGY: a web server for predicting the binding affinity of protein-protein complexes, Bioinformatics
Zhang, Holmes, A genomic perspective on the origin and emergence of SARS-CoV 2, Cell
