Research
When viruses infect cells, they establish a complex network of molecular interactions with host cellular factors to transform the cells into a fully habitable environment. These interactions include the initial attachment of viruses to the target cell surface through specific cell-entry receptors, hijacking of host macromolecular machinery for viral genome replication, and the evasion of host immunity through viral protein antagonists. For example, just a handful of genes encoded by human immunodeficiency virus (HIV) multitask to facilitate the infection, which involves numerous interactions with host proteins and nucleic acids. Targeting virus-host molecular interactions in infected cells represents an open area for the development of therapeutics for viral infectious diseases. To this end, comprehensive structural, functional, proteomic information on essential interactions between viral components and host factors is essential.
Our long-term goal is to gain atomic-level molecular insights into viral infection, host immune defense, and virus-host interactions by using structural biology techniques, such as cryo-electron microscopy (cryo-EM), complemented by functional biochemistry and virology.
Current Projects
Project 1: Molecular basis of HIV accessary protein complexes 
HIV-1 possesses a compact genome of 9.7 kb, encoding just nine genes. Besides the typical retroviral genes that encode viral enzymes and structural components, such as Gag, Pol, and Env, the HIV-1 genome contains four unique genes that encode accessory proteins Vpr, Vif, Vpu, and Nef. These HIV accessory proteins are not directly involved in the viral genome replication, virion assembly, or maturation, but they play essential roles in maintaining the infectivity and persistence of the virus. Typically, they promote virus infectivity by intercepting host cellular processes such as antiviral immune response. For example, Vif hijacks the host CUL5 E3 ubiquitin ligase complex to degrade antiviral restriction factor APOBEC3 cytidine deaminases in T-cells. Because of this, the deletion of vif gene from the HIV genome results in severely compromised infectivity of the virus in T-lymphoblast CEM cells. While the role of Vpr in HIV replication remains enigmatic, studies indicated that Vpr is required for viral replication in macrophages. These observations highlight the potential of targeting the accessory proteins in mitigating HIV pathogenicity.
In this project, we aim to comprehensively understand the molecular mechanisms governing the interactions of HIV accessory proteins and their host cellular partners. Capturing such virus-host molecular interactions would provide important insights into the intricate strategy that viruses adopt to combat host anti-viral factors and to exploit pro-viral factors during viral infection.
Project 2: Assembly and interactions of coronavirus replication-transcription complex
The replication–transcription complex (RTC) is the central machinery that performs the replication of single-stranded RNA genome in coronaviruses, such as SARS-CoV-2. The RTC is composed of multiple non-structural proteins (Nsps), including the RNA-dependent RNA polymerase (Nsp12), helicase (Nsp13), and several associated cofactors (e.g., Nsp7, Nsp8, Nsp9, Nsp10, Nsp14, and Nsp16), which assemble into a large, multifunctional molecular machine responsible for viral RNA synthesis, proofreading, and 5′-end capping.
Coronavirus Nsp15 endoribonuclease processes the viral RNA to evade innate immunity, and functionally couples with the RTC. The mechanism and timing of this coordination remain elusive. Moreover, emerging data indicates that the RTC incorporates multiple host proteins that may assist in viral replication during infection, yet the composition and architecture of these extended assemblies are not fully defined.
In this project, we aim to isolate and reconstitute the extended SARS-CoV-2 RTC with its host factors in near-physiological context and characterize the mechanistic basis of the complex. By visualizing the molecular architecture and regulatory mechanisms of this complex, we aim to reveal new insights into coronavirus replication and identify potential inhibitor sites that could disrupt RTC assembly or cellular activities for the future development of broad-spectrum antivirals.