Molecular dynamics simulation study of conformational changes of transcription factor TFIIS during RNA polymerase II transcriptional arrest and reactivation

Abstract

Transcription factor IIS (TFIIS) is a protein known for catalyzing the cleavage reaction of the 3'-end of backtracked RNA transcript, allowing RNA polymerase II (Pol II) to reactivate the transcription process from the arrested state. Recent structural studies have provided a molecular basis of protein-protein interaction between TFIIS and Pol II. However, the detailed dynamic conformational changes of TFIIS upon binding to Pol II and the related thermodynamic information are largely unknown. Here we use computational approaches to investigate the conformational space of TFIIS in the Pol II-bound and Pol II-free (unbound) states. Our results reveal two distinct conformations of TFIIS: the closed and the open forms. The closed form is dominant in the Pol II-free (unbound) state of TFIIS, whereas the open form is favorable in the Pol II-bound state. Furthermore, we discuss the free energy difference involved in the conformational changes between the two forms in the presence or absence of Pol II. Additionally, our analysis indicates that hydrophobic interactions and the protein-protein interactions between TFIIS and Pol II are crucial for inducing the conformational changes of TFIIS. Our results provide novel insights into the functional interplay between Pol II and TFIIS as well as mechanism of reactivation of Pol II transcription by TFIIS.

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.

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.