Structure and dynamics of RNA polymerase II elongation complex

Biochem Biophys Res Commun. 2006 Apr 28;343(1):90-8. doi: 10.1016/j.bbrc.2006.02.124. Epub 2006 Mar 2.

Abstract

RNA polymerase (Pol) II is a fundamental and important enzyme in the transcription process. However, two mysterious questions have remained unsolved: how an unwound bubble of DNA is established and maintained, and how the enzyme moves along the DNA. To answer these questions, we constructed a model structure of the Pol II elongation complex with the 50 base pairs of DNA-24 bases of RNA including the unwound bubble of DNA and performed a molecular dynamics simulation. We obtained a reliable model structure of the Pol II elongation complex in the pre-translocation state which has not yet been determined by the X-ray crystallographic study. The model structure revealed that multiple protein loops work concertedly to form and maintain the bubble structure. We also found that the conformational change of a loop in the Pol II, fork loop 1, couples with the unidirectional movement of the Pol II along the DNA.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Crystallography, X-Ray
  • DNA / chemistry*
  • Fungal Proteins / chemistry*
  • Protein Conformation
  • RNA Polymerase II / chemistry*
  • Transcription, Genetic*

Substances

  • Fungal Proteins
  • DNA
  • RNA Polymerase II