Our research focuses on the structure and mechanism of viral replication and infection machinery using X-ray crystallography and cryo-electron microscopy. Atomic resolution structures of large complexes (up to several thousand Å in diameter) can be obtained by the combination of these two techniques.
1. Viral genome replication
Virtually all RNA viruses carry out viral genome replication using a large replication complex composed of RNA, viral replicases (i.e., polymerase, helicase, protease), and cellular proteins. However, specific protein-protein and protein-RNA interactions are still poorly understood. We are interested in the structure of individual replication enzymes and their protein-protein, and protein-RNA complexes in human and animal viruses. These viruses include flavivirus (such as dengue virus), pestivirus, alphavirus, and arenavirus. Our structural studies will help develop antiviral therapeutics for animal and human diseases caused by these RNA viruses.
2. Virus-host interaction
Cells sense RNA virus infection and trigger a signaling cascade leading to innate and adaptive anti-viral responses. Viruses have evolved a multitude of strategies to counter the host's innate immune activation. In particular, many viruses target interferon pathways to counteract its downstream function. For example, pestivirus Npro induces degradation of a transcription factor that promotes interferon synthesis. We are working to determine the mechanism by which viral proteins subvert host innate immune response, which may ultimately lead to new antiviral strategies.
3. Virus structure and assembly
Tailed bacteriophages have to deliver their genetic information into the host cell's cytoplasm across cell membranes. The tail machinery, composed of multiple protein components, attaches to the cell membrane and transports genomic DNA into the cell. We use bacteriophage N4 as a model system to study the mechanism of genome and protein transport from the virus into the host cell. N4 packages dsDNA as well as one or two copies of a 3,500-amino acid RNA polymerase inside the capsid, which is then ejected into host cell upon infection. In collaboration with Dr. Lucia Rothman-Denes laboratory (University of Chicago), we are determining the structure of N4 virions, including their tail component proteins.
A. Crystal structure of dengue virus polymerase NS5. Dengue virus polymerase consists of methyltransferase (MTase) and RNA-dependent RNA polymerase (RdRp) domains, which catalyze 5’ RNA capping/methylation and RNA synthesis respectively. B. Structure of bacteriophage N4 determined by cryo-EM and 3D image reconstruction techniques.