Computational analysis of putative SULTR3–NLP interactions reveals potential structural basis for sulfur–nitrogen crosstalk in Arabidopsis thaliana

Sulfur (S) and nitrogen (N) metabolism in plants are tightly co-regulated at transcriptional and biochemical levels, yet the molecular interface linking both pathways is incompletely defined. NIN-like proteins (NLP1–NLP7) are major transcriptional activators of nitrate responses, whereas sulfate transporter 3 (SULTR3) governs intracellular and inter-organ sulfate partitioning. Here, we used comparative molecular docking to elucidate potential protein–protein interactions between SULTR3 and NLP1–NLP7, analyzing four energetic paradigms - balanced, electrostatic, hydrophobic, and van der Waals + electrostatic (VdW + Elec). For all paralogs, hydrophobic docking resulted in the deepest binding energy minima (−2550 to −2960 kcal mol −1 ), contributing >75% of the total stabilization energy. The complex with NLP3 (−2960 kcal mol −1 ) and NLP7 (−2817 kcal mol −1 ) were most stable complexes, followed by those with NLP4 and NLP5. Electrostatic energies (−1750 to −2050 kcal mol −1 ) gave specificity of orientation, while VdW + Elec terms (−395 to −470 kcal mol −1 ) brought out steric complementarity. Structural mapping showed hydrophobic clustering between the SULTR3 trans-membrane helices (TMs 3–6) and the PB1/RWP-RK domains of NLPs. Functionally, such hydrophobic complementarity could facilitate transient assemblies of signals, such as SULTR3–NLP, connects sulfur transport and nitrate-regulated transcription. This study integrates the first computational prediction suggesting of hydrophobic dominance among the evaluated docking models in sulfur–nitrogen crosstalk and provides a mechanistic basis for engineering nutrient-efficient crops. The current work will be used as a guide for experimental validation and crop improvement.