1. Insights into the specificity for the interaction of the promiscuous SARS-CoV-2 nucleocapsid protein N-terminal domain with deoxyribonucleic acids
- Author
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Icaro Putinhon Caruso, Vitor dos Santos Almeida, Mariana Juliani do Amaral, Guilherme Caldas de Andrade, Gabriela Rocha de Araújo, Talita Stelling de Araújo, Jéssica Moreira de Azevedo, Glauce Moreno Barbosa, Leonardo Bartkevihi, Peter Reis Bezerra, Katia Maria dos Santos Cabral, Isabella Otênio de Lourenço, Clara L.F. Malizia-Motta, Aline de Luna Marques, Nathane Cunha Mebus-Antunes, Thais Cristtina Neves-Martins, Jéssica Maróstica de Sá, Karoline Sanches, Marcos Caique Santana-Silva, Ariana Azevedo Vasconcelos, Marcius da Silva Almeida, Gisele Cardoso de Amorim, Cristiane Dinis Anobom, Andrea T. Da Poian, Francisco Gomes-Neto, Anderson S. Pinheiro, Fabio C.L. Almeida, Federal University of Rio de Janeiro, Universidade Estadual Paulista (UNESP), Multidisciplinary Center for Research in Biology (NUMPEX), Oswaldo Cruz Foundation (FIOCRUZ), and Rio BioNMR Network
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Gene Expression Regulation, Viral ,Models, Molecular ,Binding Sites ,SARS-CoV-2 ,Spectrum Analysis ,COVID-19 ,Hydrogen Bonding ,General Medicine ,DNA ,Nucleocapsid Proteins ,DNA/RNA binding protein ,Biochemistry ,Article ,Binding specificity ,Structure-Activity Relationship ,SARS-CoV-2 nucleocapsid protein ,Structural Biology ,Nucleic Acids ,Host-Pathogen Interactions ,Humans ,RNA ,Protein Interaction Domains and Motifs ,Molecular Biology ,Protein Binding - Abstract
Made available in DSpace on 2022-04-28T19:50:20Z (GMT). No. of bitstreams: 0 Previous issue date: 2022-04-01 Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ) Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) The SARS-CoV-2 nucleocapsid protein (N) is a multifunctional promiscuous nucleic acid-binding protein, which plays a major role in nucleocapsid assembly and discontinuous RNA transcription, facilitating the template switch of transcriptional regulatory sequences (TRS). Here, we dissect the structural features of the N protein N-terminal domain (N-NTD) and N-NTD plus the SR-rich motif (N-NTD-SR) upon binding to single and double-stranded TRS DNA, as well as their activities for dsTRS melting and TRS-induced liquid-liquid phase separation (LLPS). Our study gives insights on the specificity for N-NTD(-SR) interaction with TRS. We observed an approximation of the triple-thymidine (TTT) motif of the TRS to β-sheet II, giving rise to an orientation difference of ~25° between dsTRS and non-specific sequence (dsNS). It led to a local unfavorable energetic contribution that might trigger the melting activity. The thermodynamic parameters of binding of ssTRSs and dsTRS suggested that the duplex dissociation of the dsTRS in the binding cleft is entropically favorable. We showed a preference for TRS in the formation of liquid condensates when compared to NS. Moreover, our results on DNA binding may serve as a starting point for the design of inhibitors, including aptamers, against N, a possible therapeutic target essential for the virus infectivity. Institute of Medical Biochemistry Federal University of Rio de Janeiro Multiuser Center for Biomolecular Innovation (CMIB) Department of Physics São Paulo State University (UNESP) National Center of Nuclear Magnetic Resonance (CNRMN) CENABIO Federal University of Rio de Janeiro Faculty of Pharmacy Federal University of Rio de Janeiro Protein Advanced Biochemistry (PAB) CENABIO Federal University of Rio de Janeiro Department of Biochemistry Institute of Chemistry Federal University of Rio de Janeiro Multidisciplinary Center for Research in Biology (NUMPEX) Campus Duque de Caxias Federal University of Rio de Janeiro Laboratory of Toxinology Oswaldo Cruz Foundation (FIOCRUZ) Rio BioNMR Network Multiuser Center for Biomolecular Innovation (CMIB) Department of Physics São Paulo State University (UNESP) FAPERJ: 202.279/2018 FAPERJ: 204.432/2014 FAPERJ: 210.361/2015 FAPERJ: 239.229/2018 FAPERJ: 255.940/2020 CNPq: 309564/2017-4 CNPq: 439306/2018-3
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- 2021