Clarification of Interaction Mechanism of Mouse Hepatitis Virus (MHV) N and nsp3 Protein with Homology Modeling and Protein-Protein Docking Analysis

The coronavirus Nucleocapsid (N) plays an important role in the virus structure, the replication, and the transcription of CoV. This protein, which has a helix and flexible structure, and is capable of binding on to the viral genomic RNA, is a non-structural protein (nsp3). Many studies suggest that the N protein interaction with nsp3 plays a critical role in the virus replication early in infection. Therefore, it is necessary to know the definition of the interaction mechanism of N and nsp3 protein in terms of the CoV replication transcription mechanism. We report on the homology modeling, molecular dynamics simulation, and docking studies to explain the structure-function relationship and the interaction mechanism. In addition, the prototype MHV is preferred in the wet experiment, so we also based our study on the MHV N and nsp3 proteins that belong to the experimental study. The amino acid sequences of MHV N and nsp3 proteins have similarity between human and severe acute respiratory syndrome coronavirus. Therefore, the 3D structure models of these proteins were built with using the crystal structure of the CoV family members as a template. By following these models, molecular dynamics simulations were applied to attain the most stable conformation. Finally, protein-protein docking was performed to prove accuracy of model structures of the MHV N and to clarify the interaction with nsp3. As a result, Lys 113, Arg 125, Tyr 127, Glu 173, Tyr 190 residues that play an important role in virus replication were determined.