Figure 1.
Schematic diagrams of the Pol II Elongation Complex (EC).
(A) Transcribing state. (B) Backtracking state. (C) Reactivation intermediate state. The arrows in (A) and (B) indicate the moving direction of the Pol II relative to the RNA. Here, NTP stands for nucleoside triphosphate, a building block of RNA.
Table 1.
AA and CG Model Systems.
Figure 2.
MD simulation results of Pol II-TFIIS complex and apo TFIIS.
The initial (left) and final (right) structures of Pol II-TFIIS complex (A) and apo TFIIS (B) from all-atom MD simulations. MD simulation results for all-atom models (C) and coarse-grained model (D). In (C) and (D), the black and red curves represent the cases of the Pol II-TFIIS complex and apo TFIIS, respectively.
Figure 3.
PMF and SASA of apo TFIIS and Pol II-TFIIS complex.
(A) PMF of coarse-grained TFIIS as a function of the distance between the domains II and III, and (B) hydrophobic and hydrophilic solvent accessible surface area (SASA) of coarse-grained TFIIS in the absence of Pol II. Note that, at small distances (<∼20 Å), the PMF increases while the hydrophobic SASA decreases. The increase in the PMF is due to the steric repulsion between the two domains. The value of PMF at the largest distance (∼78 Å) is set to be zero. (C) PMF and (D) SASA in the presence of Pol II. The value of PMF at the metastable states (d = ∼25 Å) is set to be zero.
Figure 4.
Schematic diagram of the reactivation process from the arrested state of Pol II.
(A) TFIIS in solution. (B) Backtracked state of Pol II. (C) State of Pol II with an initial partially-bound TFIIS. (D) State of Pol II with a partially-bound TFIIS for the insertion of catalytic domain. (E) State of Pol II with a fully-bound TFIIS. (F) Elongation state of Pol II with a partially-bound TFIIS. (G) Normal elongation state of Pol II.