Synergistic Protein–Protein and Protein–Lipid Interactions Drive SARS-CoV-2 Envelope Assembly

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) assembles its viral envelope at the endoplasmic reticulum-Golgi intermediate compartment (ERGIC), yet the minimal molecular requirements for forming a stable viral envelope remain unclear. Here, we used coarse-grained molecular dynamics simulations to systematically examine how protein and lipid compositions and protein orientation influence membrane remodeling during viral envelope formation. Starting from bicelle membrane patches, we compared lipid-only systems and membranes containing the matrix (M) and spike (S) proteins under different lipid environments and orientations. Lipid-only membranes closed stochastically, whereas systems containing either M or S proteins reliably formed vesicles but failed to establish correct membrane topology. In contrast, systems containing both M and S proteins in heterogeneous ERGIC-like lipid mixtures consistently produced stable vesicles with correct topology. Mechanistic analyses revealed that protein orientation modulates membrane curvature generation and cholesterol redistribution, while persistent M-S contacts organize protein positioning during closure. Disrupting any of these interactions resulted in failed closure or severely deformed structures. Together, these results support an obligate-synergy model in which three interaction classes─M-S protein-protein contacts, M-lipid interactions, and S-lipid interactions─cooperate to drive robust coronavirus envelope assembly. These findings identify minimal physical requirements for viral envelope formation and provide mechanistic insights that may guide the rational design of coronavirus virus-like particle (VLP) assembly systems.