Native-Based Simulations of the Binding Interaction Between RAP74 and the Disordered FCP1 Peptide

By dephosphorylating the C-terminal
domain (CTD) of RNA polymerase
II (Pol II), the Transcription Factor IIF (TFIIF)-associating CTD
phosphatase (FCP1) performs an essential function in recycling Pol
II for subsequent rounds of transcription. The interaction between
FCP1 and TFIIF is mediated by the disordered C-terminal tail of FCP1,
which folds to form an α-helix upon binding the RAP74 subunit
of TFIIF. The present work reports a structure-based simulation study
of this interaction between the folded winged-helix domain of RAP74
and the disordered C-terminal tail of FCP1. The comparison of measured
and simulated chemical shifts suggests that the FCP1 peptide samples
40–60% of its native helical structure in the unbound disordered
ensemble. Free energy calculations suggest that productive binding
begins when RAP74 makes hydrophobic contacts with the C-terminal region
of the FCP1 peptide. The FCP1 peptide then folds into an amphipathic
helix by zipping up the binding interface. The relative plasticity
of FCP1 results in a more cooperative binding mechanism, allows for
a greater diversity of pathways leading to the bound complex, and
may also eliminate the need for “backtracking” from
contacts that form out of sequence.