Molecular Dynamics of Compact and Extended Conformations of alpha-Synuclein Tetramer on Biological Membranes and with Micelles

The data contains starting and end structures (in their protein data bank or PDB format), input files and parameter files of molecular dynamics (MD) simulations of two conformations of alpha-Synuclein protein tetramer on two different membrane environments (POPS and mixed), and with two different kind of micelles (SDS and mixed). The tetramer-membrane pdb files are named as kind of tetramer conformation (Compact or Extended) followed by the membrane type (POPS or mixed) and finally followed by whether it is the start/beginning ('s') or end ('e') of MD simulations. The tetramer-micelle pdb files are named such that the sides of the tetramer in which the two micelles are placed (B for bottom towards the C-termini of tetramer, and S for side towards one of the lateral sides of the tetramer) followed by the type of tetramer (B for broken or compact conformation while E for extended conformation) followed by the type of micelle (SDS or mixed), and finally the start (s) or end (e) of the simulation. For instance, BSB_mixed_s.pdb means that the 'mixed' micelle is placed at the 'bottom' and the 'side' of the broken or compact tetramer at the start (s). The files ending with .mdp are the input files for different stages of MD simulations and the tar/gzipped folders are force field folders containing the parameters.