Collective motions of RNA polymerases. Analysis of core enzyme, elongation complex and holoenzyme.

The anisotropic network model (ANM), a coarse-grained normal mode analysis, is used to study the vibrational dynamics of RNA polymerases (RNAP) around the native states. The theoretical temperature factors obtained from ANM are in conformity with the experimental values for yeast and bacterial RNAP structures in free and complex forms. In the low-frequency collective modes that are related to biological function, both bacterial and yeast RNAPs with a crab claw shape display an opening/closing of the cleft due to the rigid-body motion of the clamp (bottom pincer), which has been also predicted by experiments, together with the motion of the top pincer. Even though slightly lower fluctuations are observed in the elongation complex of yeast RNAP, similar clamp motion still exists in collective modes, which should be concerted with the flexible switches and the bridge helix in driving the transcription process, pointing at the possibility of a ratchet-like mechanism. Two different bacterial holoenzyme (HE) structures are studied, which may have functional significance at different stages of transcription initiation. In a specific closed conformation of the HE, the clamp and top pincer are highly immobilized due to interactions with the sigma subunit. In contrast, the deformation of the top pincer is not inhibited in a relatively open conformation of another HE, which may help load the DNA into the cleft during transcription initiation, even though the clamp motion is still inhibited.