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bioRxiv · 10.64898/2026.09.20.752951

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

Choudhary, A.·Budhwar, S.
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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 Angstrom). Energetic decomposition indicated that ligand association is governed predominantly by electrostatic interactions (delta-E_elec ~ -40 kcal/mol) with basic residues (His146, His269, Trp147; RMSF < 0.60 Angstrom), 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.

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Choudhary, A., Budhwar, S.. 2026-09-25. In-Silico Thermodynamic and Structural Profiling of Bacterial SoxB Thiohydrolase: Evaluating the Substrate Accommodation of Circular Potassium Thiosulfate in Sulfur-Deficient Alkaline Soils. https://doi.org/10.64898/2026.09.20.752951

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