Molecular docking and dynamic simulation of escherichia coli K-12 Elements as a Biosensor for Detecting...

Trinitrotoluene (TNT) is widely used in military and industrial fields due to its strong explosive properties and chemical stability. However, its persistence in the environment and harmful effects on living organisms make it important to develop sensitive and selective detection methods. Previous research has identified the Escherichia coli genes yadG and aspC as promising components for TNT biosensors, based on their increased gene expression in response to TNT exposure. Although these findings are promising, it is still unclear whether the proteins produced from these genes directly interact with TNT at the molecular level. This study focuses on analyzing the binding interactions between TNT and the protein products of yadG and aspC using computational methods. Molecular docking showed that TNT binds more strongly to yadG (- 6.81 ± 0.02 kcal/mol) than to aspC (- 6.23 ± 0.00 kcal/mol). Further analysis using molecular dynamics simulations with MM-GBSA calculations confirmed that the yadG-TNT complex is more stable, with a binding free energy (ΔG) of - 23.58 kJ/mol, in line with fluorescence data that also indicated stronger binding to yadG. TNT binding to yadG involves aromatic residues (Tyr-106, His-153) and hydrophobic contacts (Ala-150), which may promote π-π stacking and suggest reduced water occupancy. These features highlight key principles for protein engineering and suggest a clear route from computational findings to biosensor development.