Preorganized RdRp-Thumb Dynamics Drives SARS-CoV-2 Polymerase Function

The SARS-CoV-2 RNA-dependent RNA polymerase drives viral genome replication and is a major antiviral target. How intrinsic conformational dynamics organize functional states of the polymerase, however, remains incompletely understood. Here, molecular dynamics (MD) simulations combined with free-energy landscape analysis reveal that the apo polymerase samples preexisting conformational states defined by coordinated thumb-subdomain motions. Projection of experimental structures, representative of the polymerase nucleic acid cycle, onto the conformational landscape identified discrete basins spanning apo-like and elongation-like states and revealed a coherent structural axis coupling global polymerase compaction (radius of gyration, Rg) with thumb-interface separation (center-of-mass distance, COM). These motions connect catalytic motifs, RNA-binding regions, and distal regulatory elements across the polymerase ensemble. The observed conformational organization is not apparent from static structures alone and supports a model in which functional transitions arise from intrinsic collective dynamics of the apo enzyme. Intermediate conformational ensembles combine structural stability with retained inter-domain flexibility, identifying mechanically responsive states favorable for allosteric modulation. Together, these findings define structurally coupled regulatory regions within the coronavirus polymerase and support conformational trapping of thumb-subdomain dynamics as a potential strategy for antiviral design targeting RNA virus replication machinery.