Satellite Tobacco Mosaic Virus: Revealing Environmental Drivers of Capsid and Nucleocapsid Plasticity using High-Resolution Simulations

The Satellite Tobacco Mosaic Virus (STMV) serves as a model system for elucidating how electrostatic and mechanical forces shape single-stranded (ss) RNA viral architecture. Lever-aging a cumulative total of 1.5 µ s of simulation with a polarizable force field including 1.2 µ s of conventional Molecular Dynamics (MD) supplemented by Gaussian accelerated MD (GaMD), and well-tempered metadynamics (WTMetaD) enhanced sampling techniques, we examined how pH and ionic composition regulate the structural dynamics of preassembled STMV capsids. Six ∼1M-atom assemblies spanning physiological and stress-mimicking environments were modeled to capture the interplay among protein–protein, protein–RNA, and ion-mediated interactions. A representative GaMD trajectory, corresponding to the up to µ s-equivalent regime of conventional MD, revealed that the capsid undergoes coordinated radial fluctuations, with collective expansion and contraction of the icosahedral shell. WTMetaD free-energy surfaces, computed for all six assemblies, delineated distinct condition-specific minima, defining thermodynamically accessible conformations for each environment. During the early relaxation dynamics revealed in conventional MD, RNA-free capsids preserved their icosahedral symmetry in physiological salt, where monovalent ions screened intra-capsid electrostatics. RNA encapsidation further modulated this balance through divalent-ion coordination at the protein–RNA interface. Under acidic conditions, a reversible Na ⁺ /Mg ²⁺ exchange reorganized interfacial charge networks while maintaining the overall capsid architecture. Transient chloride binding intermittently disrupted key inter-monomer salt bridges, exposing a regulatory mechanism for capsid plasticity and permeability. Our findings establish STMV as an inherently dynamic, ion-responsive structural assembly whose conformational adaptability emerges from finely balanced electrostatic coupling between the capsid and its RNA, providing an atomistic framework for how ssRNA icosahedral viruses sense and adjust to environmental changes.