Lokale und globale Dynamik im ungeordneten Synuklein‐Protein

Abstract

MD simulationAs described in [1] , the MD simulation of α-synuclein was performed using the Amber12 force field with the TIP4P-D water model. The simulation started from an extended conformation of α-synculein, solvated in an ~ 100 × 100 × 100 Å 3 box containing ~ 40000 water molecules and 0.1 M NaCl. The system was initially equilibrated at 300 K and 1 bar for 1 ns, then production run at 300 K and 1 bar was performed in the NPT ensemble with the Anton specialized hardware at 2.5 fs time step. Nonbonded interactions were truncated at 12 Å and the Gaussian split Ewald method with a 64 × 64 × 64 Å mesh was used to account for the long-range part of the electrostatic interactions. The MD frames were saved at 10 ps intervals.