Structure and dynamics of RNA polymerase II elongation complex Atsushi Suenaga a, * , Noriaki Okimoto a , Noriyuki Futatsugi a , Yoshinori Hirano b , Tetsu Narumi a , Yousuke Ohno a , Ryoko Yanai a , Takatsugu Hirokawa c , Toshikazu Ebisuzaki b , Akihiko Konagaya a , Makoto Taiji a, * a Bioinformatics Group, RIKEN Genomic Sciences Center, 61-1 Ono-cho, Tsurumi, Yokohama, Kanagawa 230-0046, Japan b Computational Astrophysics Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan c Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-43-17F Aomi, Koutou-ku, Tokyo 135-0064, Japan Received 1 February 2006 Available online 2 March 2006 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. Ó 2006 Elsevier Inc. All rights reserved. Keywords: Molecular dynamics; Molecular modeling; RNA polymerase II; Transcription; Molecular motor RNA polymerase (Pol) II catalyzes synthesis of messen- ger RNA in eukaryotes thereby playing important roles in the regulation of gene expression and cell growth. Within the Pol II–DNA transcribing complex, double-stranded DNA (dsDNA) is separated from unwound template and non-template strands, and the Pol II synthesizes messenger RNA based on the code on the template strand by moving along the DNA. Thus, the Pol II is an interesting enzyme not only as a molecular machine for transcription but also as a molecular motor. On the structural bases, several X-ray crystallographic studies have revealed the protein– DNA, protein–RNA, and DNA–RNA interactions of the Pol [1–13]. On the bacterial Pol, the model structures of the Pol–DNA/RNA complex have been built [14,15], and they provide insight into the protein–DNA interactions that is critical for understanding the mode of the actions. However, the complete information about the interactions between the eukaryotic Pol II and DNA/RNA, especially interactions between the Pol II and unwound non-template DNA strand/upstream rewound DNA, has remained unsolved. According to current research on the Pol II, there are two mysterious questions: how an unwound bubble of DNA established and maintained at the active center and how the Pol II moved along the DNA. To solve these questions, we constructed a model structure of the Pol II complexed with the 50 base pairs of DNA-24 bases of RNA including the unwound bubble of DNA and investigated the complete structure of the Pol II elongation complex. As the template structure for our modeling, we used the (incomplete) X-ray structure of the Pol II elongation complex [3]. In the X-ray structure, 0006-291X/$ - see front matter Ó 2006 Elsevier Inc. All rights reserved. doi:10.1016/j.bbrc.2006.02.124 * Corresponding authors. Fax: +81 45 507 2524. E-mail addresses: suenaga@gsc.riken.jp (A. Suenaga), taiji@gsc. riken.jp (M. Taiji). www.elsevier.com/locate/ybbrc Biochemical and Biophysical Research Communications 343 (2006) 90–98 BBRC