Work

Domain-specific variants reshape terpene synthase conformational dynamics and ligand binding in Coffea arabica populations from Saudi Arabia

Year: 2026

Type: article

Abstract: Coffea arabica is an allotetraploid crop with limited genetic diversity, while terpene synthases (TPSs) contribute to specialized metabolism, ecological adaptation, and aroma formation. Whole-genome sequencing of Saudi Arabian C. arabica identified variants in five of 69 TPS genes, including eight missense substitutions in LOC113689980 (XP_071904867.1). Their structural consequences and the influence of TPS lid architecture were investigated using molecular modeling, docking, and three independent 300-ns molecular dynamics simulations per system. p.Glu424Val in 04867_cof_E424V_FPF preserved the global protein fold but altered ligand dynamics, Mg²⁺ coordination, and long-range catalytic coupling. The eight-substitution 04867_cof_mutant_FPF construct reduced ligand RMSD relative to 04867_cof_E424V_FPF (3.162 ± 0.743 vs. 3.831 ± 0.273 Å) and partially restored residue-424 coupling with DDXXD (− 0.138 to + 0.121; WT + 0.245) and NSE/DTE (+ 0.152 to + 0.208; WT + 0.404). However, the predefined statistical criterion for compensatory epistasis was not met (BH-FDR q = 0.549), indicating directional rather than statistically supported compensation. Lid architecture produced a stronger effect: the lid-containing 09630_cof_FPF complex showed significantly lower ligand RMSD (2.910 ± 0.122 vs. 4.166 ± 0.311 Å; q = 0.011) and ligand-contact residue RMSF (0.736 ± 0.064 vs. 1.973 ± 0.158 Å; q = 0.003) than the lid-absent 07178_cof_FPF. PCA/FEL further revealed system- and replicate-dependent redistribution of conformational ensembles rather than uniform changes in global flexibility. Collectively, these findings show that naturally occurring TPS variation can remodel catalytic-site dynamics while preserving overall structural integrity, whereas lid architecture strongly influences ligand confinement. The computationally constructed multi-variant model showed directional compensation in structural and dynamical properties relative to 04867_cof_E424V_FPF; however, this trend was neither statistically supported as positive epistasis nor reflected as stable energetic compensation in the ensemble QM/MM analysis. These findings provide a mechanistic basis for future haplotype-resolved analyses and experimental validation.

Source: Scientific Reports

DOI: 10.1038/s41598-026-77731-y