Mechanistic bases of strain-specific virus-host interactions

Abstract Influenza A viruses (IAVs) are responsible for seasonal flu and pose a pandemic threat. The overarching goal of our research is to understand the structural and biophysical mechanisms at the molecular level by which nonstructural protein 1 (NS1) of IAVs interferes with host antiviral responses. NS1 is a major virulence factor of IAVs, counteracting host antiviral immune responses. Remarkably, NS1 has a multifaceted strategy to interfere with many host proteins involved in viral RNA (vRNA) sensing and degradation, apoptosis, and interferon production. Furthermore, NS1 is one of the most frequently mutating proteins in the IAV genome. Therefore, studying the evolution of NS1 and its role in immune evasion and modulation is essential for understanding the strain-specific virulence of IAVs. However, to understand the evolutionary development of NS1’s strain-specific functions, it is necessary to examine the interactions between newly acquired mutations and other residues within NS1, which are known as epistatic interactions. Addressing the molecular mechanisms of epistasis is a major challenge in the fields of protein science and evolution. Over the next five years, we will investigate how NS1 interferes with host immune responses in a strain-specific manner. In this proposed research, we will address the questions of how epistatic interactions contribute to the strain-specific interactions between NS1 and host proteins, and how NS1 employs its RNA-binding ability to antagonize vRNA sensors that initiate innate immune responses. To accomplish our goal, we will use an integrated approach including X-ray crystallography, cryo-electron microscopy (EM), NMR and fluorescence spectroscopies, chemical crosslinking using amber-codon suppression, molecular dynamics simulation, and cell-based experiments to parallel our structural and biophysical studies. This research will provide a mechanistic framework for a quantitative understanding of NS1's strain-specific immune evasion functions. As a result, this study is expected to have a positive impact on the development of antiviral agents targeting NS1-host protein interactions.