Molecular dynamics simulation

We performed two systems PykF/PykF K382la-FBP for 100 ns Molecular dynamics (MD) simulations for three times. The initial coordinates of the systems were obtained from X-ray crystal structures with PDB ID 1PKY. All MD simulations were performed using GROMACS 2019.6 (set defaults values as parameters). The software package with Gromos 54A7 force field was applied to describe the PykF, and Gromos 54A8 force field was used for the PykF K382la. Gromos 54A7 and Gromos 54A8 were downloaded from Vienna-PTM. The ligand FBP force fields were obtained from the Automated Topology Builder (ATB) (Version 3.0) database (https://atb.uq.edu.au/molecule.py?molid=1134439#panel-md). The complex systems were analyzed by MD simulations in a cubic box with the SPC water model. To neutralize the systems, chloride and sodium ions were randomly added to the simulation box. During the MD simulations, the long-range coulombic interactions were handled using the particle mesh Ewald (PME) method. The energy minimization of the whole system was carried out for 50,000 steps with the steepest descent method. Subsequently, 500 ps of NVT (Berendsen temperature coupled with constant particle number, volume, and temperature) and 500 ps of NPT (Parrinello–Rahman pressure coupled with constant particle number, pressure, and temperature) were performed to maintain the stability of the system (300 K, 1 bar). After stabilizing all thermodynamic properties, the molecular system was simulated for 100 ns with a time interval of 2 fs, whereas the coordinates for all models were stored every 2 ps. Root mean square deviations (RMSD) and distances between the nitrogen atom of K382 side chain and the central carbon atom of FBP were evaluated using the analysis tools within GROMACS 2019.6. All visualization is done through PyMOL and Xmgrace 2.3.7 software. Codes files, input parameters files and initial and final configurations files related to two MD simulations systems (PykF-FBP and PykF K382la-FBP) are provided as a MD simulation Source Data.