Activation loop plasticity and active site coupling in the MAP kinase, ERK2: Supplementary Data, Trajectories, and Scripts

Conventional molecular dynamics (MD) simulations using the GPU-enabled CUDA version of the pmemd executable (pmemd.cuda) in AMBER were applied to explore the structure and dymanics of MAPK, ERK2. The role of dual phosphorylation was explored by comparing 0P-ERK2 with 2P-ERK2 (two phosphate groups added at T183 and Y185). Both 0P-ERK2 and 2P-ERK2 models were treated with the ff19SB forcefield immersed in a solution of 0.15 M NaCl in OPC water. The results showed that the A-loop can adopt multiple long-lived (>5 microseconds) conformational states. A set of primary and secondary seeds were used to explore these novel states of the activation loop. Analysis scripts, dataframes, and all trajectories (stripped of explicit water and NaCl ions) are provided here to enhance reproducibility of this complex study and aid future studies.