In-Silico Thermodynamic and Structural Profiling of Bacterial SoxB Thiohydrolase: Evaluating the Substrate Accommodation of Circular Potassium Thiosulfate in Sulfur-Deficient Alkaline Soils

Abstract

Characterizing the enzymatic accommodation of circular agricultural fertilizers is critical for informing strategies to remediate widespread soil sulfur hunger. Here, we present an exploratory in-silico investigation evaluating the active-site cleft of sulfate thiohydrolase (SoxB) across representative soil Proteobacteria. Following the crystallographic precedent of uncomplexed thiosulfate in PDB 2WDE, site-directed molecular docking indicated that the free thiosulfate polyanion binds favorably within the catalytic pocket (predicted affinity: −3.506 kcal/mol), yielding a substantially lower empirical energy barrier than hydrophobic elemental sulfur (S8, −1.409 kcal/mol). Comparative evaluation against the alkaline-adapted Thiobacillus denitrificans homolog revealed an elevated predicted binding affinity of −4.610 kcal/mol, suggesting a potential structural accommodation in high-pH calcareous soils (pH >8.0). Unrestrained 5.0 ns all-atom molecular dynamics in explicit TIP3P solvent demonstrated initial structural stability of the unliganded host backbone (RMSD = 1.10 ± 0.15 Å). Energetic decomposition indicated that ligand association is governed predominantly by electrostatic interactions (ΔEelec ≈ −40 kcal/mol) with basic residues (His146, His269, Trp147; RMSF < 0.60 Å), with a single-trajectory unbinding event observed at 3.2 ns. These computational observations provide an exploratory baseline characterizing the active-site electrostatic landscape of SoxB, generating working hypotheses for downstream empirical soil microcosm and in-planta trials.