title: Structure and dynamics of RNA polymerase II elongation complex.
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.
authors.affiliation: Bioinformatics Group, RIKEN Genomic Sciences Center, 61-1 Ono-cho, Tsurumi, Yokohama, Kanagawa 230-0046, Japan. suenaga@gsc.riken.jp
authors.forename: Atsushi
authors.initials: A
authors.lastname: Suenaga
authors.forename: Noriaki
authors.initials: N
authors.lastname: Okimoto
authors.forename: Noriyuki
authors.initials: N
authors.lastname: Futatsugi
authors.forename: Yoshinori
authors.initials: Y
authors.lastname: Hirano
authors.forename: Tetsu
authors.initials: T
authors.lastname: Narumi
authors.forename: Yousuke
authors.initials: Y
authors.lastname: Ohno
authors.forename: Ryoko
authors.initials: R
authors.lastname: Yanai
authors.forename: Takatsugu
authors.initials: T
authors.lastname: Hirokawa
authors.forename: Toshikazu
authors.initials: T
authors.lastname: Ebisuzaki
authors.forename: Akihiko
authors.initials: A
authors.lastname: Konagaya
authors.forename: Makoto
authors.initials: M
authors.lastname: Taiji
mesh_terms: D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry*; D005656:Fungal Proteins / Q000737:chemistry*; D011487:Protein Conformation; D012319:RNA Polymerase II / Q000737:chemistry*; D014158:Transcription, Genetic
chemical_list: D005656:Fungal Proteins; D004247:DNA; D012319:RNA Polymerase II