Molecular Dynamics Trajectories Exploring the Impact of Phosphorylation on the Physiological Form of Human alpha-Synuclein in Aqueous Solution

Primary data for the publication "Impact of Phosphorylation on the Physiological Form of Human alpha-Synuclein in Aqueous Solution" by de Bruyn, Dorn, Rossetti, Fernandez, Outeiro, Schulz and Carloni. Submitted to the Journal of Chemical Information and Modeling.

Included are all GROMACS input files, parameterised topologies, starting and final configurations, and trajectories for the lowest temperature replica (at 300 K, lowest of 32 replicas between 300-500 K exchanging according to the REST2 algorithm (Wang et al. 2011)). The data is split into three archives:

1. all_atom_trajectories.zip
   • contains all input files and all atom trajectories including solvent
   • trajectories written at 100 ps intervals
2. protein+ion_trajectories.zip
   • contains configuration/non-parameterised topologies and trajectories excluding solvent, but including ions
   • trajectories written at 10 ps intervals
3. additional_simulations.zip
   • contains the all atom trajectories and input files, and
   • solvent-free trajectories above,
   • for the additional simulations in the Supplemental Information of the article:
     • includes the DES-Amber-based simulations with 64 replicas between 300-600 K, and
     • a99SB-disp-based simulations

Folders are named according to the following top level scheme:

• DES-Amber simulations/ Simulations created using the DES-Amber force field (Tucker et al. 2022)
• a99SB-disp simulations/ SImulations created using the a99SB-disp force field for Intrinsically Disordered Proteins (IDPs) (Robustelli et al. 2018)

Sub-folders follow the following scheme:

• AS/ Simulations of the physiological form of wild-type Human α-Synuclein
  • unphosphorylated
• pAS/ Simulations of the physiological form of wild-type Human α-Synuclein
  • phosphorylated at S129
  • with double negative charge
• pASH/ Simulations of the physiological form of wild-type Human α-Synuclein (a99SB-disp simulations only)
  • phosphorylated at S129
  • with a single negative charge (monoprotonated)