Viewing SARS-CoV-2 Nucleocapsid Protein in Terms of Molecular Flexibility

Abstract

Simple Summary Nucleocapsid protein is one of the essential proteins for viral replication including the coronavirus SARS-CoV-2, which causes coronavirus disease 2019 (COVID-19) pneumonia leading to the ongoing pandemic. Whereas this protein has emerged as a potential drug target, its physicochemical properties and the molecular mechanism of how this protein is involved in viral replication remain unclear. In this review, structural and dynamical aspects of the SARS-CoV-2 nucleocapsid protein (NCoV2), which should play a key role in a new drug development and in the interaction with RNA and other proteins are summarized. The structural feature of NCoV2 is first described. Next, simulation studies on the interaction between potential drug molecules and NCoV2 are summarized, which show the importance of molecular flexibility. Then, liquid-liquid phase separation phenomenon involving NCoV2, which has recently been reported, is described. This phenomenon also suggests the importance of molecular flexibility of NCoV2. Finally, a promising method using neutron scattering to characterize the structure and structural fluctuation of the droplets, which are formed through this phenomenon, is presented. Abstract The latest coronavirus SARS-CoV-2, which causes coronavirus disease 2019 (COVID-19) pneumonia leading to the pandemic, contains 29 proteins. Among them, nucleocapsid protein (NCoV2) is one of the abundant proteins and shows multiple functions including packaging the RNA genome during the infection cycle. It has also emerged as a potential drug target. In this review, the current status of the research of NCoV2 is described in terms of molecular structure and dynamics. NCoV2 consists of two domains, i.e., the N-terminal domain (NTD) and the C-terminal domain (CTD) with a disordered region between them. Recent simulation studies have identified several potential drugs that can bind to NTD or CTD with high affinity. Moreover, it was shown that the degree of flexibility in the disordered region has a large effect on drug binding rate, suggesting the importance of molecular flexibility for the NCoV2 function. Molecular flexibility has also been shown to be integral to the formation of droplets, where NCoV2, RNA and/or other viral proteins gather through liquid-liquid phase separation and considered important for viral replication. Finally, as one of the future research directions, a strategy for obtaining the structural and dynamical information on the proteins contained in droplets is presented.