Investigation on the Molecular Mechanism of ORF7a Suppressing BST-2 Antiviral Activity through Structural Modeling of Their Protein–Protein Interface

In the present work, a structural model for the protein-protein interface of bone marrow stromal cell antigen 2 (BST-2) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) open reading frame 7a (ORF7a) is predicted using multiscale molecular dynamic simulations. Coarse-grained simulations enabled broad conformational sampling, and all-atom simulations refined the resulting structures. A machine learning-based clustering analysis was applied to the simulation ensemble to categorize the dominant heterodimeric conformations that captured the principal interaction geometries. Across these dominant conformations, BST-2 and ORF7a form a tightly packed transmembrane core stabilized by complementary hydrophobic and polar interactions. The cytoplasmic region contributes additional anchoring through recurrent hydrogen bonds, salt bridges, and cation-π interactions between BST-2's N-terminal residues and ORF7a's short cytoplasmic extending stabilization beyond the TM interface. On the other hand, the extracellular interface is reinforced by an overlapping dense network of polar and aromatic contacts. Central hubs such as N49, D55, E62, R64, N65, and H93 engage multiple ORF7a partners (R25, K32, R76, K85, and E95), creating a robust and redundant interaction architecture. Our simulations indicate that ORF7a disrupts BST-2 homodimerization through transmembrane domain competition, extracellular interface hijacking, and cytoplasmic tail anchoring. This not only destabilizes tetherin's canonical dimer but also creates a robust heterodimeric BST-2-ORF7a complex. Functionally, this structural reorganization undermines BST-2's ability to cross-link budding virions at the cell surface, thereby antagonizing its antiviral tethering function. Overall, our model provides structural insight into the molecular mechanism underlying the ORF7a-mediated antagonism.