Molecular dynamics simulation trajectories of S. pneumonia Pyruvate Kinase

This dataset contains the processed structural models and molecular dynamics (MD) simulation trajectories for the study of Streptococcus pneumoniae Pyruvate Kinase (SpPYK) allostery. 1. Prepared Input Structures The PYK_prepared_input_structures.zip archive contains the refined tetrameric models used to initialize all simulations. Structures were prepared using the Schrödinger Protein Preparation Wizard, including optimized hydrogen bonding networks and assigned protonation states at pH 7.0. The following ligation states are included: PYK-APO: The ligand-free apoenzyme (based on PDB: 8IAS). PYK-FBP: The enzyme bound to the allosteric effector fructose 1,6-bisphosphate (based on PDB: 8IAV, with modeled B-domains). PYK-PEP: The enzyme bound to the substrate phosphoenolpyruvate (generated as a symmetry-corrected tetramer from PDB: 8IAW). PYK-FBP-PEP: The fully liganded ternary complex (based on PDB: 8IAX). 2. Simulation Trajectories We provide three independent 500 ns replica trajectories (*simulation_trajectories.zip) for each of the four systems listed above (12 trajectories in total). Sampling Frequency: Coordinates were saved every 1 ns, resulting in 500 frames per replica. File Format: Trajectories are provided in AMBER NetCDF (.nc) format. All trajectories have been centered and fitted to the protein backbone to remove global rotational and translational motions. The corresponding .gro or .pdb topology files required for loading the trajectories are included in each system folder. These files are intended for the analysis of essential dynamics, subspace overlap, and allosteric network communication. Trajectories can be visualized using VMD and analyzed using tools such as CPPTRAJ.