Sucrose and Gibberellic Acid Binding Stabilize the Inward-Open Conformation of AtSWEET13: A Molecular Dynamics Study

In plants, sugar will eventually be exported transporters (SWEETs) facilitate the translocation of mono- and disaccharides across membranes and play a critical role in modulating responses to gibberellin (GA3), a key growth hormone. However, the dynamic mechanisms underlying sucrose and GA3 binding and transport remain elusive. Here, we employed microsecond-scale molecular dynamics (MD) simulations to investigate the influence of sucrose and GA3 binding on SWEET13 transporter motions. While sucrose exhibits high flexibility within the binding pocket, GA3 remains firmly anchored in the central cavity. Binding of both ligands increases the average channel radius along the transporter's principal axis. In contrast to the apo form, which retains its initial conformation throughout the simulation, ligand-bound complexes undergo a significant conformational transition characterized by further opening of the intracellular gate relative to the inward-open crystal structure (5XPD). This opening is driven by ligand-induced bending of helix V, stabilizing the inward-open state. Sucrose binding notably enhances the flexibility of the intracellular gate and amplifies anticorrelated motions between the N- and C-terminal domains at the intracellular side, suggesting an opening-closing motion of these domains. Principal component analysis revealed that this gating motion is most pronounced in the sucrose complex and minimal in the apo form, highlighting sucrose's ability to induce high-amplitude gating. Our binding free energy calculations indicate that SWEET13 has lower binding affinity for sucrose compared to GA3, consistent with its role in sugar transport. These results provide insight into key residues involved in sucrose and GA3 binding and transport, advancing our understanding of SWEET13 dynamics.