Structural and Functional Analysis of Dengue Virus Non-Structural Protein 5 (NS5) Using Molecular Dynamics

• Published in: Crystals (Basel) 2023-01, Vol.13 (1), p.63
• Main Authors: Fidel, Darylle Ann, Macalino, Stephani Joy Y., Posadas, George, Carrillo, Maria Constancia O.
• Format: Article
• Language: English
• Subjects: Crystal structure; dengue; Dengue fever; Domains; Dynamic structural analysis; Eigenvectors; Functional analysis; Hydrogen bonds; Infections; Information flow; Ligands; molecular docking; Molecular dynamics; Molecular structure; Monomers; Mutation; network analysis; non-structural protein 5; principal component analysis; Principal components analysis; Proteins; Public health; Residues; RNA polymerase; Simulation; Viruses
• ISSN: 2073-4352; 2073-4352
• DOI: 10.3390/cryst13010063

Dengue is an infection transmitted by the Aedes mosquito and is considered a major public health concern in many tropical and Asian countries, including the Philippines. It is caused by the dengue virus (DENV) which belongs to the Flaviviridae family and has four serotypes. The non-structural protein 5 (NS5), which consists of an MTase domain and an RdRp domain, is the largest and most conserved protein among flaviviruses and thus a potential target against DENV. However, there are very limited studies on the functional homodimer structure of NS5. Through molecular dynamics, it was found that residues 458–470, 583–586, 630–637, 743–744, and 890–900 of monomer A and residues 14–24, 311–315, and 462–464 of monomer B undergo essential motions for the conformational changes in the RdRp template tunnel and GTP binding in the MTase domain. Through the analysis of these motions, it was also proposed that in the dimeric structure of NS5 only one pair of domains contribute to the function of the protein. Other essential residues, specifically A-ASP533, A-LYS689, A-ARG620, A-ARG688, A-SER710, B-ARG620, B-LYS689, A-GLU40, A-ARG262, A-GLU267, A-ARG673, and B-ARG673, were also identified to play important roles in the information flow necessary for the function of the protein. In particular, shortest paths analysis led to the identification of ARG673 as an essential residue for the communication between RdRp and MTase catalytic sites. Mutation of this residue led to changes in the conformational flexibility of the RdRp finger subdomain, which may influence the RdRp catalytic function. These findings serve as a basis for future studies on the mechanism and inhibition of the NS5 dimer for dengue drug discovery.