Catalytic Tunnel Dynamics Explain Functional Divergence of FAD2 Homologs Underlying the Oleic-to-Linoleic Ratio in Cornus wilsoniana

The oleic-to-linoleic acid ratio (O/L) is a key determinant of oil quality, yet its molecular basis in Cornus wilsoniana remains unclear. Here, we combined fatty-acid profiling with molecular dynamics (MD) simulations and catalytic tunnel analysis to compare four annotated FAD2 homologs. Sequence alignment revealed a major variable segment at residues 160–185, including a small deletion in CW09G04700 and an extensive deletion in CW04G07690. Docking against oleic acid supported excluding CW04G07690 due to weak binding. Eighty-nanosecond MD simulations showed that CW02G01750 and CW09G27260 rapidly converged to stable conformational ensembles with lower core flexibility, whereas CW09G04700 exhibited higher internal mobility around residues 180–220. CAVER analysis further indicated increasingly accessible catalytic tunnels for CW02G01750 and CW09G27260 during simulation, while CW09G04700 displayed transient tunnel narrowing accompanied by ligand conformational readjustments. These results nominate CW02G01750 as a leading structural candidate among C. wilsoniana FAD2 homologs and highlight access-pathway dynamics as a mechanistic feature potentially contributing to O/L formation.