Molecular Dynamics Simulation of EpCAM Ectodomain Dimer

As a starting point crystal structure of EpEX dimer was used (PDB ID 4MZV) to prepare a complete simulated system (structure PDB and topology PSF file) where the dimer was embedded in an electro-neutral water cube. After minimization, the simulation was run at a pressure of 1 atm and a temperature of 310 K for 20 ns with 2 fs timestep.

For simulation, NAMD 2.11 was used. The resulting trajectory file (DCD format) was used to analyze frequency of inter-subunit contacts (Cytoscape network file, also supplied as PDF), and structure fluctuations (provided as list of per-residue Calpha RMSD values). The dataset also contains structure snapshots extracted from the trajectory (100 snapshots for subunits, and 100 for the dimer) corresponding to timepoints separated by 200 ps.