Membrane lipid composition and amino acid sequence determine binding of SARS-CoV-2 fusion peptides

Membrane fusion during SARS-CoV-2 entry is initiated by the fusion peptide (FP) domain of the spike protein, which binds to the host membrane and lowers the energetic barrier for merging the viral and cellular membranes. Although several FP segments-FP1 (816-837), FP2 (835-856), and FP4 (885-909)-have been identified, the molecular mechanism of fusion initiation, driven by peptide-lipid interactions, remains poorly understood. We hypothesize that lipid composition and packing density modulate FP binding, insertion, and local membrane deformation during fusion initiation. Coarse-grained molecular dynamics simulations were performed to study FP1, FP2, and FP4 interactions with lipid monolayers of controlled composition and packing density, mimicking the extracellular leaflet of the plasma membrane. These models enabled systematic evaluation of peptide binding, aggregation, and induced curvature under variable interfacial conditions. The simulations reveal sequence-dependent fusion mechanisms governed by lipid composition and electrostatics. Cholesterol-rich and tightly packed monolayers hinder peptide interface migration, while charged environments facilitate it. FP1 and FP2 form surface aggregates that induce convex curvature, consistent with stalk or hemifusion intermediates, whereas FP4 exhibits a distinct binding mode, forming aggregates that promote transient pore formation rather than bending. Together, these findings demonstrate how peptide sequence, lipid organization, and interfacial packing cooperatively control the earliest steps of SARS-CoV-2 membrane fusion, providing molecular-level insights for designing antiviral strategies. This work highlights the relevance of lipid monolayers as precise interfacial models for elucidating peptide-membrane interactions underlying complex biological fusion processes.