Dynamics of pyrophosphate ion release and its coupled trigger loop motion from closed to open state in RNA polymerase II.

ABSTRACT: Pyrophosphate ion (PP(i)) release after nucleotide incorporation is a necessary step for RNA polymerase II (pol II) to enter the next nucleotide addition cycle during transcription elongation. However, the role of pol II residues in PP(i) release and the mechanistic relationship between PP(i) release and the conformational change of the trigger loop remain unclear. In this study, we constructed a Markov state model (MSM) from extensive all-atom molecular dynamics (MD) simulations in the explicit solvent to simulate the PP(i) release process along the pol II secondary channel. Our results show that the trigger loop has significantly larger intrinsic motion after catalysis and formation of PP(i), which in turn aids PP(i) release mainly through the hydrogen bonding between the trigger loop re

SUBMITTER: Da LT 

PROVIDER: S-EPMC3273452 | biostudies-literature | 2012 Feb

REPOSITORIES: biostudies-literature