Living Cell Surfacome Lysine Footprinting (LiFT) Captures Virus-Induced Conformational Dynamics and Uncovers Influenza A Virus Host Factors

Understanding virus-host interactions at the cell surface remains a fundamental challenge due to the transient and conformational nature of receptor engagement. Existing methods often lack spatial specificity or fail to capture dynamic structural remodeling in living cells at the proteome-wide level. Building on our previously developed cell surface lysine labeling strategy, we here present LiFT (Living Cell Surfacome Lysine Footprinting), a chemical proteomic strategy enabling direct, high-specificity mapping of ligand-induced conformational changes through profiling the accessibility of extracellular lysines on living cells. LiFT was validated using model systems, including HSA-ibuprofen and EGFR-EGF, accurately detecting ligand-binding interfaces and conformational dynamics. When applied to influenza A virus (IAV) attachment on a host cell, LiFT revealed widespread lysine accessibility alterations across 362 host cell surface proteins and identified IGF1R as an IAV host factor. LiFT provides a living cell compatible and surface-specific approach for profiling functional receptor interactions and conformational dynamics, offering new insights into viral entry and receptor biology.