RESUMO
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 ß-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.
Assuntos
COVID-19/virologia , Ácidos Nucleicos/metabolismo , Proteínas do Nucleocapsídeo/metabolismo , Domínios e Motivos de Interação entre Proteínas , SARS-CoV-2/fisiologia , Sítios de Ligação , DNA/química , DNA/metabolismo , Regulação Viral da Expressão Gênica , Interações Hospedeiro-Patógeno , Humanos , Ligação de Hidrogênio , Modelos Moleculares , Ácidos Nucleicos/química , Proteínas do Nucleocapsídeo/química , Ligação Proteica , RNA/química , RNA/metabolismo , Análise Espectral , Relação Estrutura-AtividadeRESUMO
Tuberculosis is one of the deadliest diseases worldwide affecting approximately 10 million people in 2018. This classifies tuberculosis as epidemic in several countries and leads to an increasing number of multidrug-resistant strains. Thus, the development of new drugs is essential to effective treatments. A potential drug target is the ribose-5-phosphate isomerase, a ubiquitous enzyme important to nucleotide and cofactor biosynthesis. Here, we report the backbone assignment of ribose-5-phosphate isomerase of Mycobacterium tuberculosis (MtRpiB) that has been performed by triple resonance sequential approach using a [13C, 15N, 2H]-labeled protein. This is the first ribose-5-phosphate isomerase, an enzyme previously classified as highly druggable, to be assigned. These data will be important to further screening studies to find inhibitors and determine their interaction with MtRpiB.