A Jump-from-Cavity Pyrophosphate Ion Release Assisted by a Key Lysine Residue in T7 RNA Polymerase Transcription Elongation
Fig 5
The side chain swing of Lys472 assists the PPi release.
(A) The molecular view of Lys472 side chain that swings from pointing inside toward PPi in the active site (S1) to pointing outside to the solvent (S2). The two major configurations of the side chain were sampled from the long simulation (i and iii) and from the SMD simulations. (B) The Lys472-MgA distance measured from the long simulation (i) and (iii), with and without PPi, respectively. (C) The 2D density map (-ln P) generated from many short simulations used for the MSM construction. The map is depicted along the distance between Lys472 (NZ) and MgA and along the PPi RMSD. (D) The Lys472-MgA distance change along with the PPi-MgA distance change, obtained from three SMD simulations for nanoseconds, ran from different initial conditions/directions to pull PPi out.