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

    Metadata Updated: December 15, 2023

    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.

    Access & Use Information

    Public: This dataset is intended for public access and use. License: See this page for license information.

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    Dates

    Metadata Created Date December 15, 2023
    Metadata Updated Date December 15, 2023
    Data Update Frequency irregular

    Metadata Source

    Harvested from NIST

    Other Data Resources

    Additional Metadata

    Resource Type Dataset
    Metadata Created Date December 15, 2023
    Metadata Updated Date December 15, 2023
    Publisher National Institute of Standards and Technology
    Maintainer
    Identifier ark:/88434/mds2-2988
    Language en
    Data Last Modified 2023-10-18 00:00:00
    Category Mathematics and Statistics:Modeling and simulation research
    Public Access Level public
    Data Update Frequency irregular
    Bureau Code 006:55
    Metadata Context https://project-open-data.cio.gov/v1.1/schema/data.json
    Schema Version https://project-open-data.cio.gov/v1.1/schema
    Catalog Describedby https://project-open-data.cio.gov/v1.1/schema/catalog.json
    Harvest Object Id 70ced50b-f516-49e6-be22-f227ef2f4dd6
    Harvest Source Id 74e175d9-66b3-4323-ac98-e2a90eeb93c0
    Harvest Source Title NIST
    Homepage URL https://data.nist.gov/od/id/mds2-2988
    License https://www.nist.gov/open/license
    Program Code 006:045
    Source Datajson Identifier True
    Source Hash 28c60eca711e7dc3b8f650db06f5f2722d428c1803aa1ce9004c6b2804f6f7b3
    Source Schema Version 1.1

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