A Jump-from-Cavity Pyrophosphate Ion Release Assisted by a Key Lysine Residue in T7 RNA Polymerase Transcription Elongation
Fig 3
The MSM construction for the PPi release in the T7 RNAP elongation.
(A) A structural view of the PPi distribution (shown in spheres) sampled from the MD simulations. Each sphere represents the center of the mass of the PPi group. The distribution was generated from randomly chosen MD snapshots for states S1a (in purple sphere), S1b (in green), and S2 (in orange). (B) The three-state macrostate representation generated from the MSM construction. The equilibrium populations from the MSM are indicated. (C) Distance analyses between several key residues and the PPi group in the three-state representation.