Molecular dynamics simulation data for TC and SMX degradation
Description
We devised an effective strategy for Laccase–mediator systems (LMS) design by deciphering the mechanisms of degradation of tetracycline and sulfamethoxazole in the presence of different mediators via molecular dynamics simulation. The dataset includes input topology files, simulation parameters, result, and structure. The molecular dynamics simulation result files, including root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), and molecular mechanics/Poisson–Boltzmann surface area (MM/PBSA) calculations. The abbreviations for antibiotics and mediators used in the uploaded files are tetracycline hydrochloride (TC), sulfamethoxazole (SMX), syringaldehyde (SA), gallic acid (GA), syringic acid (Syr), p-coumaric acid (p-CA), caffeic acid (CA), and vanillic acid (VA).
Files
Steps to reproduce
MD simulations were performed using the GROMACS 2025.0 software in combination with the AMBER14SB force field. Degradation of laccase–tetracycline and laccase–sulfamethoxazole in the presence of natural mediators, including VA, SA, p-CA, GA, CA, and Syr, was analyzed. Here is a concise abbreviation of your paragraph: > A 10 nm cubic box with a mediator (2 mM) was solvated with TIP3P water and neutralized with Na⁺/Cl⁻. Energy minimization used the steepest descent algorithm (0.01 kcal·mol⁻¹; 50,000 steps). Short-range interactions used a 1.2 nm cut-off; long-range electrostatics were treated with PME. Equilibration included NVT (100 ps; V-rescale at 298.15 K) and NPT (100 ps; Parrinello–Rahman at 1 bar) with a 2 fs timestep. A 100 ns MD simulation followed, saving energies every 10.0 ps. Trajectories were analyzed for RMSD, RMSF, Rg, and secondary structure. Free energy landscapes (FEL) were derived from RMSD and Rg. Binding free energies were calculated using the MM/PBSA method (g_mmpbsa). Binding pockets were predicted using CavityPlus.
Institutions
- Hubei UniversityHubei, Wuhan