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.