In-Silico Thermodynamic and Structural Profiling of Bacterial SoxB Thiohydrolase: Evaluating the Substrate Accommodation of Circular Potassium Thiosulfate in Sulfur-Deficient Alkaline Soils
- 1Vellore Institute of Technology Bhopal
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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BibTeX
@misc{choudhary2026insilico,
title = {{In-Silico Thermodynamic and Structural Profiling of Bacterial SoxB Thiohydrolase: Evaluating the Substrate Accommodation of Circular Potassium Thiosulfate in Sulfur-Deficient Alkaline Soils}},
author = {A. Choudhary and S. Budhwar},
howpublished = {bioRxiv},
year = {2026},
month = sep,
doi = {10.64898/2026.09.20.752951},
url = {https://www.biorxiv.org/content/10.64898/2026.09.20.752951v1},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - In-Silico Thermodynamic and Structural Profiling of Bacterial SoxB Thiohydrolase: Evaluating the Substrate Accommodation of Circular Potassium Thiosulfate in Sulfur-Deficient Alkaline Soils
AU - A. Choudhary
AU - S. Budhwar
PY - 2026
DA - 2026/09/20
PB - bioRxiv
DO - 10.64898/2026.09.20.752951
UR - https://www.biorxiv.org/content/10.64898/2026.09.20.752951v1
AB - 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.
ER -