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 <i>Cornus wilsoniana</i> 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 <i>C. wilsoniana</i> FAD2 homologs and highlight access-pathway dynamics as a mechanistic feature potentially contributing to O/L formation.