Ligand-Specific Conformational Dynamics and Interaction Landscapes of hnRNPA2B1 Reveal a Structural Basis for Its Functional Regulation

The RNA-binding protein hnRNPA2B1 is critical for mRNA processing, transport, metabolism, and antiviral innate immunity. Its activity is modulated by various ligands, including RNA, single-stranded DNA (ssDNA), and the small-molecule agonist PAC5, but the structural dynamics of these ligand-specific modulations are not fully understood. We hypothesized that each ligand triggers distinct conformational shifts that dictate functional outcomes. Starting from available crystal structures, we built three complex models and performed 100-ns molecular-dynamics simulations, analyzing RMSD, RMSF, radius of gyration, free-energy landscapes, MM-PBSA binding affinities, PCA projections, and trajectory clustering. Our analyses reveal common and distinct interaction footprints between hnRNPA2B1 and the three ligands. Residues 24, 62, and 97 engage all ligands, whereas residues 28 and 30 form pronounced contacts with ssDNA yet only weakly interact with RNA and PAC5. Conversely, residues 102 and 108 are stably anchored to RNA but not to ssDNA. Radius-of-gyration and RMSF analyses further indicate that the backbone flexibility of hnRNPA2B1 is ligand-dependent: the protein is most expanded when bound to PAC5 and most compact when bound to ssDNA. Consistently, the binding free energy is highest for PAC5 and lowest for ssDNA. Finally, PCA shows that the PAC5-bound ensemble splits into two distinct conformational clusters whose overlap with the ssDNA-bound state (39.26 %) markedly exceeds that with the RNA-bound state (16.12 %), suggesting that PAC5 may promote hnRNPA2B1 dimerization by mimicking the ssDNA-bound conformation. These findings illuminate the ligand-dependent conformational and interaction landscapes of hnRNPA2B1, establishing a robust structure–thermodynamics framework for rational drug discovery. • The key highlights of our findings are: • Distinct conformational changes of the three distinct ligands. We demonstrate that each ligand induces distinct conformational states in hnRNPA2B1. PAC5 binding expands the protein backbone, ssDNA compacts it, and RNA yields intermediate flexibility. These dynamics are linked to functional outcomes—ssDNA promotes dimerization, while PAC5 mimics this state, potentially explaining its role in activating antiviral signaling. • Ligand-specific binding thermodynamics and interaction landscapes. Binding free energy calculations show strongest affinity for ssDNA (-101.75 kcal/mol), followed by RNA (-95.29 kcal/mol) and PAC5 (-21.22 kcal/mol). Residue-level analysis identifies common and unique interaction footprints, highlighting how ligand specificity is achieved at the atomic level. Despite having the weakest binding affinity, PAC5 still stably anchors to the RRM1 domain. • Structural mimicry by PAC5: Crucially, Principal Component Analysis (PCA) demonstrated that the PAC5-bound conformational ensemble exhibits a significantly greater overlap with the ssDNA-bound state (39.26% in the PC1/PC2 space) than with the RNA-bound state (16.12 %). This strong conformational similarity suggests that PAC5 may promote hnRNPA2B1 dimerization by structurally mimicking the ssDNA-bound conformation, providing a structural explanation for its function as an activator of the antiviral pathway.