Protein-RNA complex simulation

Simulation trajectory of TSEN/pre-tRNAArgTCT generated with GROMACS. A hybrid model of truncated TSEN/pre-tRNAArgTCT with the additional TSEN2 domain from AlphaFold Jumper et al, 2021 and in silico modeled intron bases 37 to 43 was subjected to all-atom molecular dynamics simulations for assessment of flexibility. Simulation trajectory can be visualised with PyMOL or VMD. The protein was described by the AMBER14ff (Maier, et al 2015), and the RNA with the OL3 force field (Zgarbova et al, 2011) and the TIP3P water model was employed (Jorgensen et al, 1983).