C-Terminus Viability and Structural Adaptation of Sars-Cov-2 Leader Protein Enhancing its Network Suitability

Abstract

The leader SARS-CoV-2 protein (Nsp1; non-structural protein), acts at multiple functions towards the host cell that triggers host cell mRNA cleavage and decay. Nsp1 binds to the 40S ribosomal subunit and inhibits translation, as well as binds with different cyclophilins. Herein, we investigated the molecular properties of SARS-CoV-2 Nsp1 protein, applying different structural biology techniques and optimized the Nsp1 structure. During MD simulation the Nsp1 (apo-form) has shown a conformational switch in the (C-ter) region close to S166 residue, which is required to bind with the 40S ribosome. Among cyclophilins, the FKBP1B has high affinity and the PPIH has least interactions with Nsp1. Residues from 1-10 aa (N-terminal) and 155-165 aa (C-terminal) range were involved in the interactions with the cyclophilins. From the 40S-Nsp1 system, the uS3 and eS30 components formed an equivalent number of interactions with Nsp1. Residues E41, E87, E155, D156, E159, E176, and N178 from Nsp2 formed stable interactions with ribosomal proteins. The Rrp45 derived peptides (pep14; EEIIAEAEPP) that may act as a blocker or modulator for Nsp1, were proposed as the potential candidates for peptide-based vaccine approach. Along with identifying key interacting residues within different Nsp1-cyclophilins or 40S ribosome or RNA exosome complexes, we revealed that this viral protein has a versatile C-terminus region which changes its conformations according to its binding network. These findings identify novel binding-sites in the Nsp1 protein, which shall assist in future vaccine or drug discovery programmes aimed at targeting the coronavirus family of viruses.

Note:
Funding Information: U.K, is supported by The National Science Centre (Narodowe Centrum Nauki, Krakow, Poland) [grant no. 2020/36/C/NZ2/00108]. The International Centre for Cancer Vaccine Science project is carried out within the International Research Agendas programme of the Foundation for Polish Science co-financed by the European Union under the European Regional Development Fund. We gratefully acknowledge Poland’s high-performance computing infrastructure PLGrid (HPC Centers:) for providing computer facilities and support within computational grant no. PLG/2019/012567.

Declaration of Interests: The authors declare no conflict of interest.

Keywords: SARS-CoV-2, Covid-19, Nsp1, leader protein, 40S ribosomal, RNA exosome complex, pro-tein-protein docking, cyclophilins