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

Description

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 the reproducibility of this complex study and aid future studies. Trajectories As described in the associated publication, individual trajectories were run for (5-25) microseconds and totaled 727 microseconds. Multiple primary seeds (285 K, 300 K, 315 K, and 330 K) and secondary trajectory seeds (300 K) were run; all are available in this data publication. All frames for each trajectory were aligned to backbone atoms of residues 10-161 and 182-343 of the minimized 2ERK X-ray structures (0P and 2P). Modeled residue numbers are 1-353 and correspond to residues 6-358 of 2ERK and 5UMO (rat sequence numbering). The model built from 2Y9Q, which is a human kinase, was converted to correspond to the rat-derived models (2ERK, 5UMO) as described in the associated publication. Most primary seeds are greater than 10 microseconds while most secondary seeds are 5.7 microseconds. Angstrom units (0.1 nm) are used for trajectory coordinate storage and analysis. Three sets of trajectories are provided for convenience: 1. The canonical set of trajectories are netcdf files (extension .nc) that are stripped of NaCl and water molecules and down-sampled to 2.5 ns between frames. 2. The set of trajectory seeds with hydrogens removed and further down-sampling to 250 ns between frames is provided as DCD trajectory files. This is the smallest download that will be most convenient for visualization and initial development. 3. Frames from the 300 K trajectories collated by the A-loop states. These trajectories should be treated as collections of frames without regard for any time information stored. Structures from RCSB.org The associated publication analyzed the crystal packing environment of the activation loop. The structural data were collected in November 2021. All pdb files downloaded at that time are included in this data publication to aid the reproducibility of the analysis. The RCSB (Research Collaboratory for Structural Bioinformatics, https://www.rcsb.org) was the source of information and should be used directly for current versions of the associated entries. The RCSB entries pdbid 2ERK, pdbid 5UMO, and pdbid 2Y9Q were the structures used to build initial models for MD simulations. Scripts Representative scripts are provided to aid future work. See README.md Units Q-Aloop values are fractions. RMSD, distances, and coordinates are all reported in Angstroms (0.1 nm). Angles are reported in degrees. NOTE: Trade names are provided only to specify the source of information and procedures adequately and do not imply endorsement by the National Institute of Standards and Technology. Similar products by other developers may be found to work as well or better.

Resources

Name Format Description Link
57 aligned_trajectories_seeds_250.zip https://data.nist.gov/od/ds/ark:/88434/mds2-2988/aligned_trajectories/aligned_trajectories_seeds_250.zip
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2988/data/contact_maps.zip.sha256
57 DataGraph.zip https://data.nist.gov/od/ds/ark:/88434/mds2-2988/main-text%20figures/DataGraph.zip
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2988/main-text%20figures/VMD_FIGURES.zip.sha256
0 2erk_0p_bb.pdb https://data.nist.gov/od/ds/ark:/88434/mds2-2988/notebooks/2erk_0p_bb.pdb
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2988/setup/2erk_2P_mmpbsa.prmtop.sha256
57 partop_solv.zip https://data.nist.gov/od/ds/ark:/88434/mds2-2988/setup/partop_solv.zip
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2988/setup/partop_solv.zip.sha256
5 production_300.mdin https://data.nist.gov/od/ds/ark:/88434/mds2-2988/setup/production_300.mdin
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2988/setup/production_300.mdin.sha256
0 setup_README.md https://data.nist.gov/od/ds/ark:/88434/mds2-2988/setup/setup_README.md
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2988/setup/setup_README.md.sha256
8 Aloop_MKI_xtal_summary.csv https://data.nist.gov/od/ds/ark:/88434/mds2-2988/Xtal_survey/Aloop_MKI_xtal_summary.csv
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2988/Xtal_survey/xtal_survey.zip.sha256
0 xtal_survey_README.md https://data.nist.gov/od/ds/ark:/88434/mds2-2988/Xtal_survey/xtal_survey_README.md
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2988/notebooks/2erk_0p_bb.pdb.sha256
5 all_0p.pc12.nmd https://data.nist.gov/od/ds/ark:/88434/mds2-2988/notebooks/all_0p.pc12.nmd
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2988/notebooks/all_0p.pc12.nmd.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2988/notebooks/all_2p.pc12.nmd.sha256
0 l16_bb.pdb https://data.nist.gov/od/ds/ark:/88434/mds2-2988/notebooks/l16_bb.pdb
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2988/notebooks/l16_bb.pdb.sha256
5 https://data.nist.gov/od/ds/ark:/88434/mds2-2988/notebooks/PCA_final.ipynb
5 https://data.nist.gov/od/ds/ark:/88434/mds2-2988/notebooks/TRAJECTORY%20TIMES.ipynb
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2988/notebooks/TRAJECTORY%20TIMES.ipynb.sha256
0 README.md https://data.nist.gov/od/ds/ark:/88434/mds2-2988/README.md
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2988/README.md.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2988/reference_structures/reference_structures.zip.sha256
0 reference_structures_README.md https://data.nist.gov/od/ds/ark:/88434/mds2-2988/reference_structures/reference_structures_README.md
57 scripts.zip https://data.nist.gov/od/ds/ark:/88434/mds2-2988/scripts.zip
5 https://data.nist.gov/od/ds/ark:/88434/mds2-2988/setup/2erk_0P_mmpbsa.prmtop
57 contact_maps.zip https://data.nist.gov/od/ds/ark:/88434/mds2-2988/data/contact_maps.zip
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2988/Xtal_survey/xtal_survey_README.md.sha256
57 measures.zip https://data.nist.gov/od/ds/ark:/88434/mds2-2988/data/measures.zip
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2988/data/measures.zip.sha256
57 reference_structures.zip https://data.nist.gov/od/ds/ark:/88434/mds2-2988/reference_structures/reference_structures.zip
0 data_README.md https://data.nist.gov/od/ds/ark:/88434/mds2-2988/data/data_README.md
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2988/notebooks/PCA_final.ipynb.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2988/aligned_trajectories/aligned_trajectories_seeds_250.zip.sha256
57 aligned_trajectories_states_2.5.zip https://data.nist.gov/od/ds/ark:/88434/mds2-2988/aligned_trajectories/aligned_trajectories_states_2.5.zip
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2988/aligned_trajectories/aligned_trajectories_states_2.5.zip.sha256
5 all_2p.pc12.nmd https://data.nist.gov/od/ds/ark:/88434/mds2-2988/notebooks/all_2p.pc12.nmd
0 aligned_trajectories_README.md https://data.nist.gov/od/ds/ark:/88434/mds2-2988/aligned_trajectories/aligned_trajectories_README.md
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2988/main-text%20figures/DataGraph.zip.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2988/aligned_trajectories/aligned_trajectories_README.md.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2988/data/data_README.md.sha256
57 Q_analysis.zip https://data.nist.gov/od/ds/ark:/88434/mds2-2988/data/Q_analysis.zip
57 VMD_FIGURES.zip https://data.nist.gov/od/ds/ark:/88434/mds2-2988/main-text%20figures/VMD_FIGURES.zip
5 https://data.nist.gov/od/ds/ark:/88434/mds2-2988/setup/2erk_2P_mmpbsa.prmtop
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2988/aligned_trajectories/aligned_trajectories_seeds_2.5.zip.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2988/Xtal_survey/Aloop_MKI_xtal_summary.csv.sha256
57 xtal_survey.zip https://data.nist.gov/od/ds/ark:/88434/mds2-2988/Xtal_survey/xtal_survey.zip
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2988/reference_structures/reference_structures_README.md.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2988/scripts.zip.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2988/data/Q_analysis.zip.sha256
57 aligned_trajectories_seeds_2.5.zip https://data.nist.gov/od/ds/ark:/88434/mds2-2988/aligned_trajectories/aligned_trajectories_seeds_2.5.zip
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2988/setup/2erk_0P_mmpbsa.prmtop.sha256

Tags

  • allostery
  • activation-loop
  • molecular-dynamics
  • kinase
  • erk2
  • mapk-signaling
  • phosphorylation

Topics

Categories