Structure insights, thermodynamic profiles, dsDNA melting activity, and liquid-liquid phase separation of the SARS-CoV-2 nucleocapsid N-terminal domain binding to DNA
ABSTRACT 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), either with or without the SR-rich motif (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 specificity for N-NTD/N-NTD-SR interaction with TRS, including an unfavorable energetic contribution to binding along with hydrogen bonds between the triple-thymidine (TTT) motif in the dsTRS and β-sheet II due to the defined position and orientation of the DNA duplex, a well-defined pattern (ΔH > 0 and ΔS > 0 for ssTRS, and ΔH < 0 and ΔS < 0 for dsTRS) for the thermodynamic profile of binding, and a preference for TRS in the formation of liquid condensates when compared to a non-specific sequence. 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..
Medienart: |
Preprint |
---|
Erscheinungsjahr: |
2021 |
---|---|
Erschienen: |
2021 |
Enthalten in: |
bioRxiv.org - (2021) vom: 24. Juli Zur Gesamtaufnahme - year:2021 |
---|
Sprache: |
Englisch |
---|
Links: |
Volltext [kostenfrei] |
---|
doi: |
10.1101/2021.07.21.453232 |
---|
funding: |
|
---|---|
Förderinstitution / Projekttitel: |
|
PPN (Katalog-ID): |
XBI032246285 |
---|
LEADER | 01000caa a22002652 4500 | ||
---|---|---|---|
001 | XBI032246285 | ||
003 | DE-627 | ||
005 | 20230429100553.0 | ||
007 | cr uuu---uuuuu | ||
008 | 210724s2021 xx |||||o 00| ||eng c | ||
024 | 7 | |a 10.1101/2021.07.21.453232 |2 doi | |
035 | |a (DE-627)XBI032246285 | ||
035 | |a (biorXiv)10.1101/2021.07.21.453232 | ||
040 | |a DE-627 |b ger |c DE-627 |e rakwb | ||
041 | |a eng | ||
082 | 0 | |a 570 |q DE-84 | |
100 | 1 | |a Caruso, Icaro Putinhon |e verfasserin |4 aut | |
245 | 1 | 0 | |a Structure insights, thermodynamic profiles, dsDNA melting activity, and liquid-liquid phase separation of the SARS-CoV-2 nucleocapsid N-terminal domain binding to DNA |
264 | 1 | |c 2021 | |
336 | |a Text |b txt |2 rdacontent | ||
337 | |a Computermedien |b c |2 rdamedia | ||
338 | |a Online-Ressource |b cr |2 rdacarrier | ||
520 | |a ABSTRACT 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), either with or without the SR-rich motif (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 specificity for N-NTD/N-NTD-SR interaction with TRS, including an unfavorable energetic contribution to binding along with hydrogen bonds between the triple-thymidine (TTT) motif in the dsTRS and β-sheet II due to the defined position and orientation of the DNA duplex, a well-defined pattern (ΔH > 0 and ΔS > 0 for ssTRS, and ΔH < 0 and ΔS < 0 for dsTRS) for the thermodynamic profile of binding, and a preference for TRS in the formation of liquid condensates when compared to a non-specific sequence. 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. | ||
700 | 1 | |a dos Santos Almeida, Vitor |e verfasserin |4 aut | |
700 | 1 | |a Juliani do Amaral, Mariana |e verfasserin |4 aut | |
700 | 1 | |a de Andrade, Guilherme Caldas |e verfasserin |4 aut | |
700 | 1 | |a de Araújo, Gabriela Rocha |e verfasserin |4 aut | |
700 | 1 | |a de Araújo, Talita Stelling |e verfasserin |4 aut | |
700 | 1 | |a de Azevedo, Jéssica Moreira |e verfasserin |4 aut | |
700 | 1 | |a Barbosa, Glauce Moreno |e verfasserin |4 aut | |
700 | 1 | |a Bartkevihi, Leonardo |e verfasserin |4 aut | |
700 | 1 | |a Bezerra, Peter Reis |e verfasserin |4 aut | |
700 | 1 | |a dos Santos Cabral, Katia Maria |e verfasserin |4 aut | |
700 | 1 | |a Lourenço, Isabella Otênio |e verfasserin |4 aut | |
700 | 1 | |a Malizia-Motta, Clara L. F. |e verfasserin |4 aut | |
700 | 1 | |a de Luna Marques, Aline |e verfasserin |4 aut | |
700 | 1 | |a Mebus-Antunes, Nathane Cunha |e verfasserin |4 aut | |
700 | 1 | |a Neves-Martins, Thais Cristtina |e verfasserin |4 aut | |
700 | 1 | |a de Sá, Jéssica Maróstica |e verfasserin |4 aut | |
700 | 1 | |a Sanches, Karoline |e verfasserin |4 aut | |
700 | 1 | |a Santana-Silva, Marcos Caique |e verfasserin |4 aut | |
700 | 1 | |a Vasconcelos, Ariana Azevedo |e verfasserin |4 aut | |
700 | 1 | |a da Silva Almeida, Marcius |e verfasserin |4 aut | |
700 | 1 | |a de Amorim, Gisele Cardoso |e verfasserin |4 aut | |
700 | 1 | |a Anobom, Cristiane Dinis |e verfasserin |4 aut | |
700 | 1 | |a Da Poian, Andrea T. |e verfasserin |4 aut | |
700 | 1 | |a Gomes-Neto, Francisco |e verfasserin |4 aut | |
700 | 1 | |a Pinheiro, Anderson S. |e verfasserin |4 aut | |
700 | 1 | |a Almeida, Fabio C. L. |e verfasserin |4 aut | |
773 | 0 | 8 | |i Enthalten in |t bioRxiv.org |g (2021) vom: 24. Juli |
773 | 1 | 8 | |g year:2021 |g day:24 |g month:07 |
856 | 4 | 0 | |u http://dx.doi.org/10.1101/2021.07.21.453232 |z kostenfrei |3 Volltext |
912 | |a GBV_XBI | ||
912 | |a SSG-OLC-PHA | ||
951 | |a AR | ||
952 | |j 2021 |b 24 |c 07 | ||
953 | |2 045F |a 570 |