Competitive interplay of cotton SELF PRUNING, FLOWERING LOCUS T, and FLOWERING LOCUS D proteins governing indeterminate flowering

Abstract Background Indeterminate cotton is capable of prolonged vegetative growth and increased fruiting; however, excessive plant height is often associated with fruit abscission, uneven nutrient supply, and difficulties in mechanized harvesting. Therefore, developing early-maturing, machine-harvestable cotton varieties with compact growth remains a long-standing objective for breeders. Members of the phosphatidylethanolamine-binding protein (PEBP) gene family play central roles in maintaining indeterminate growth in cotton. Results In this study, molecular docking coupled with molecular dynamics (MD) simulations was employed to characterize protein–protein interactions among PEBP family members FLOWERING LOCUS T (FT), SELF PRUNING (SP), and the bZIP transcription factor FLOWERING LOCUS D (FD) in Gossypium hirsutum . Docking analysis of Complex I (FD-SP) revealed a strong hydrogen bond (H-bond) and salt bridge between the GLU-242 residue of FD and the ARG-102 residue of SP, whereas in Complex II (FT-FD), the same FD residue (GLU-242) formed an H-bond and a salt bridge with the ARG-111 residue of FT, indicating that SP and FT compete for GLU-242 at FD’s interface. Complex III (FT-SP) displayed comparatively weaker interactions between FT GLU-166 and SP’s LYS-50 through hydrogen bonding and salt bridge formation, suggesting a less favorable interaction. Binding free energy (Δ G ) = –14.1 kcal·mol⁻ 1 and dissociation constant ( K D ) = 4.5 × 10 –11 M, represented consistent values for Complex I and Complex II, while Complex III indicated substantially weaker binding interactions with Δ G = 10.9 kcal·mol⁻ 1 and a K D score of 1.0 × 10 –8 M. Furthermore, MD simulations of the docked complexes (I and II) revealed a stable hydrogen-bonding network, low root mean square deviations (RMSDs) of 0.04 nm, and H-bond distances within 0.3 nm throughout the simulation period. In contrast, Complex III exhibited a reduced H-bond network and a late-stage RMSD spike, indicating structural instability compared to the stronger FD-mediated Complexes I and II. Conclusions These findings provide a structural framework for understanding the competitive interplay among PEBP family members, highlighting potential candidates for future functional validation and the development of improved cotton ideotypes.