
Full text loading...
Polyamines are vital in regulating stress signaling pathways, inhibiting reactive oxygen species, and stabilizing the photosynthetic apparatus in plants, with their levels fluctuating under stress conditions. Among the key enzymes in polyamine biosynthesis is spermidine synthase, which synthesizes spermidine in the presence of putrescine and S-adenosyl 3-(methylsulfanyl) propylamine.
This study focused on the structural analysis of the maize spermidine synthase enzyme (SPDS-Maiz), highlighting its significance in plant stress tolerance. The enzyme's three-dimensional structure was modeled using the amino acid sequence and SWISS-MODEL, followed by refinement with the GalaxyRefine2 web server. Molecular docking studies were performed for its cofactor and substrate. Molecular dynamics simulations performed for 100 ns using Gromacs software confirmed the conformational stability of the apo and holoenzyme’s structure.
The structural model showed 90.3% of its amino acids in favored areas of the Ramachandran plot and obtained a notable score of 95.528% ERRAT. Molecular dynamics simulation confirmed the stability of the SPDS-Maiz structure by analyzing the physical movements of atoms and molecules. The docking studies showed that Asp226 is crucial in the interaction of putrescine and dc-SAM with the active site of the enzyme. Additional amino acids, including Gln122, Asp207, Ser227, Ser228, Glu236, Gln122, Asp226, Ser227, and Gln259, played a role in supporting the enzyme-dc-SAM-putrescine complex. Putrescine (PUT) exhibited stronger van der Waals interactions (-48.23 kcal/mol) and nonpolar solvation energy (-7.46 kcal/mol) compared to S-adenosylmethionine (dc-SAM). However, PUT incurred higher polar solvation penalties (+134.68 kcal/mol) due to its +2 charge, whereas dc-SAM benefited from slightly lower desolvation costs.
The study successfully modeled and refined the three-dimensional structure of the SPDS-Maiz enzyme, highlighting the critical role of Asp226 and other amino acids in substrate binding. Although dc-SAM had better electrostatic complementarity (-60.27 kcal/mol), the overall binding free energy (-20.58 kcal/mol for PUT vs. -11.22 kcal/mol for dc-SAM) indicated that PUT achieved stronger binding affinity, driven by its hydrophobic interactions. These findings provide insights into how the enzyme and substrate interact and the underlying molecular mechanisms in spermidine synthesis in plants.