SARS-CoV-2 nucleocapsid and Nsp3 binding: an in silico study

Khan, Muhammad Tahir; Zeb, Muhammad Tariq; Ahsan, Hina; Ahmed, Abrar; Ali, Arif; Akhtar, Khalid Pervaiz; Malik, Shaukat Iqbal; Cui, Zhi; Ali, Sajid; Khan, Abdul Karim; Ahmad, Manzoor; Wei, Dong; Irfan, Muhammad

doi:10.1007/s00203-020-01998-6

Cited by 36 publications

(30 citation statements)

References 40 publications

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“…Notably, it is also reported that nucleocapsid (N) protein functions as the only structural protein shuttling inside/outside RTCs and facilitating the transcription and replication of coronavirus RNA (Cong et al, 2020;Surjit and Lal, 2008). Recently released structural information revealed the interaction of the C-terminal domain of N protein with the pore factor of DMVs (Khan et al, 2021). As a critical step toward understanding this process, it is necessary to investigate the interaction network among Nsps.…”

Section: Introductionmentioning

confidence: 99%

Compartmentalization-aided interaction screening reveals extensive high-order complexes within the SARS-CoV-2 proteome

Xu¹,

Pei²,

Liu³

et al. 2021

Cell Reports

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Bearing a relatively large single-stranded RNA genome in nature, SARS-CoV-2 utilizes sophisticated replication/transcription complexes (RTCs), mainly composed of a network of nonstructural proteins and nucleocapsid protein, to establish efficient infection. Here, we develop an innovative interaction screening strategy based on phase separation in cellulo , namely co mpartmentalization of p rotein-protein i nteractions in c ells (CoPIC). Utilizing CoPIC screening, we map the interaction network among RTC-related viral proteins. We identify a total of 47 binary interactions among 14 proteins governing replication, discontinuous transcription, and translation of coronaviruses. Further exploration via CoPIC leads to the discovery of extensive ternary complexes composed of these components, which infer potential higher-order complexes. Taken together, our results present an efficient, and robust interaction screening strategy, and indicate the existence of a complex interaction network among RTC-related factors, thus opening up opportunities to understand SARS-CoV-2 biology and develop therapeutic interventions for COVID-19.

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Section: Introductionmentioning

confidence: 99%

Compartmentalization-aided interaction screening reveals extensive high-order complexes within the SARS-CoV-2 proteome

Xu¹,

Pei²,

Liu³

et al. 2021

Cell Reports

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“…The N-terminal portion of nsp3 is comprised of a ubiquitin-like (Ubl) structured domain and a subsequent acidic IDR. Besides its ability to bind ssRNA ( Serrano et al, 2007 ), nsp3a has been reported to interact with the nucleocapsid ( Hurst et al, 2013 ; Khan et al, 2020 ), playing a potential role in virus replication. We here provide protocols for the purification of both the Ubl (aa 1–111) and fl nsp3a (aa 1–206), including the acidic IDR (Ubl + IDR Table 1 ).…”

Section: Resultsmentioning

confidence: 99%

Large-Scale Recombinant Production of the SARS-CoV-2 Proteome for High-Throughput and Structural Biology Applications

Altincekic

Korn

Qureshi

et al. 2021

Front. Mol. Biosci.

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The highly infectious disease COVID-19 caused by the Betacoronavirus SARS-CoV-2 poses a severe threat to humanity and demands the redirection of scientific efforts and criteria to organized research projects. The international COVID19-NMR consortium seeks to provide such new approaches by gathering scientific expertise worldwide. In particular, making available viral proteins and RNAs will pave the way to understanding the SARS-CoV-2 molecular components in detail. The research in COVID19-NMR and the resources provided through the consortium are fully disclosed to accelerate access and exploitation. NMR investigations of the viral molecular components are designated to provide the essential basis for further work, including macromolecular interaction studies and high-throughput drug screening. Here, we present the extensive catalog of a holistic SARS-CoV-2 protein preparation approach based on the consortium’s collective efforts. We provide protocols for the large-scale production of more than 80% of all SARS-CoV-2 proteins or essential parts of them. Several of the proteins were produced in more than one laboratory, demonstrating the high interoperability between NMR groups worldwide. For the majority of proteins, we can produce isotope-labeled samples of HSQC-grade. Together with several NMR chemical shift assignments made publicly available on covid19-nmr.com, we here provide highly valuable resources for the production of SARS-CoV-2 proteins in isotope-labeled form.

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“…SARS-CoV-2 NP is a 419 aa phosphoprotein that associates with the viral RNA genome as well as other proteins to form the ribonucleoprotein core (23). Like SARS-CoV, NP protein of SARS-CoV-2 consists of three distinct domains: an N-terminal RNA-binding domain (NTD) which associates with the RNA genome, an intrinsically disordered central Ser/Arg (SR)-rich linker and a C-terminal domain (CTD) which allows dimerization of NP proteins (24,25).…”

Section: Discussionmentioning

confidence: 99%

Identification of immunodominant epitopes on nucleocapsid and spike proteins of the SARS-CoV-2 in Iranian COVID-19 patients

Maghsood

Shokri

Jeddi-Tehrani

et al. 2021

Preprint

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Given the emergence of SARS-CoV-2 virus as a life-threatening pandemic, identification of immunodominant epitopes of the viral structural proteins, particularly the nucleocapsid (NP) protein and receptor binding domain (RBD) of spike protein, is important to determine targets for immunotherapy and diagnosis. In this study, epitope screening was performed using a panel of overlapping peptides spanning the entire sequences of the RBD and NP proteins of SARS-CoV-2 in the sera from 66 COVID-19 patients and 23 healthy subjects by enzyme-linked immunosorbent assay (ELISA). Also, three non-overlapping peptides belonging to the S2 domain of spike protein were assessed. Our results showed that while reactivity of patients’ sera with reduced recombinant RBD protein was significantly lower than the native form of RBD (p<0.001), no significant differences were observed for reactivity of patients’ sera with reduced and non-reduced NP protein. Pepscan analysis revealed weak to moderate reactivity towards different RBD peptide pools, which was more focused on peptides encompassing aa 181-223 of RBD. NP peptides, however, displayed strong reactivity with a single peptide covering aa 151-170. These findings were confirmed by peptide depletion experiments using both ELISA and Western blotting. Altogether, our data suggest the involvement of mostly conformational disulfide bond-dependent immunodominant epitopes in RBD-specific antibody response, while the IgG response to NP is dominated by linear epitopes. Identification of antigenic epitope in NP and RBD of SARS-CoV-2 could provide important advances for the development of passive and active immunotherapy as well as diagnostic tools for the control of COVID-19 infection.

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SARS-CoV-2 nucleocapsid and Nsp3 binding: an in silico study

Cited by 36 publications

References 40 publications

Compartmentalization-aided interaction screening reveals extensive high-order complexes within the SARS-CoV-2 proteome

Compartmentalization-aided interaction screening reveals extensive high-order complexes within the SARS-CoV-2 proteome

Large-Scale Recombinant Production of the SARS-CoV-2 Proteome for High-Throughput and Structural Biology Applications

Identification of immunodominant epitopes on nucleocapsid and spike proteins of the SARS-CoV-2 in Iranian COVID-19 patients

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