Structure and dynamics of RNA polymerase II elongation complex.
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.
Suenaga
Atsushi
A
Bioinformatics Group, RIKEN Genomic Sciences Center, 61-1 Ono-cho, Tsurumi, Yokohama, Kanagawa 230-0046, Japan. suenaga@gsc.riken.jp
Okimoto
Noriaki
N
Futatsugi
Noriyuki
N
Hirano
Yoshinori
Y
Narumi
Tetsu
T
Ohno
Yousuke
Y
Yanai
Ryoko
R
Hirokawa
Takatsugu
T
Ebisuzaki
Toshikazu
T
Konagaya
Akihiko
A
Taiji
Makoto
M
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
D005656:Fungal Proteins; D004247:DNA; D012319:RNA Polymerase II