A Cylindrical Assembly Model and Dynamics of the Ebola Virus VP40

Abstract

The Ebola virus, a member of the filovirus family, causes a severe hemorrhagic fever with a high fatality rate in humans. Of the seven proteins that are encoded by the Ebola virus, VP40 is the primary matrix protein and exists in different conformational and oligomeric states. VP40 plays crucial roles in viral assembly and budding at the plasma membrane of the infected cells. This matrix protein is capable of forming virus-like particles without the need for other Ebola proteins. The budding and formation of new virus-like particles requires VP40 hexamers to arrange side-by-side into a cylinder, as well as end-to-end to extend the cylinder to a long filament. However, no experimental three-dimensional structure for any filovirus VP40 cylindrical assembly matrix is currently available. Here, we developed cylindrical assembly models of 42 nm and 92 nm diameters with varying numbers of VP40 hexamers using a protein-protein docking approach. These models match well with the 2D averages of cryo-electron tomograms of authentic virions. In addition, our models form a multilayered matrix that is in good agreement with the experimental observations. Using a pair of hexamer from the models, we studied the energetics of the interactions between the hexamers for different side-by-side arrangements, which indicated the most important residues in the protein-protein binding site responsible for the cylindrical matrix assembly. We also investigated the stability and dynamics of the cylindrical hexamer models using implicit all-atom molecular dynamics simulations, which revealed the flexibility of the cylinders. Our models will provide helpful information to better understand the assembly processes of filoviruses and such structural studies could also lead to the design and development of antiviral drugs.