Research Article
RNA polymerase II flexibility during translocation from normal mode analysis
Michael Feig,
Zachary F. Burton,
Corresponding Author
Michael Feig
Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
Department of Chemistry, Michigan State University, East Lansing, Michigan 48824
Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824===Search for more papers by this authorZachary F. Burton
Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
Search for more papers by this authorMichael Feig,
Zachary F. Burton,
Corresponding Author
Michael Feig
Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
Department of Chemistry, Michigan State University, East Lansing, Michigan 48824
Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824===Search for more papers by this authorZachary F. Burton
Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
Search for more papers by this authorAbstract
The structural dynamics in eukaryotic RNA polymerase II (RNAPII) is described from computational normal mode analysis based on a series of crystal structures of pre- and post-translocated states with open and closed trigger loops. Conserved modes are identified that involve translocation of the nucleic acid complex coupled to motions of the enzyme, in particular in the clamp and jaw domains of RNAPII. A combination of these modes is hypothesized to be involved during active transcription. The NMA modes indicate furthermore that downstream DNA translocation may occur separately from DNA:RNA hybrid translocation. A comparison of the modes between different states of RNAPII suggests that productive translocation requires an open trigger loop and is inhibited by the presence of an NTP in the active site. This conclusion is also supported by a comparison of the overall flexibility in terms of root mean square fluctuations. Proteins 2010. © 2009 Wiley-Liss, Inc.
Supporting Information
Additional Supporting Information may be found in the online version of this article.
| Filename | Description |
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| PROT_22560_sm_suppmov1.mpg1.9 MB | Supporting Movie 1 |
| PROT_22560_sm_suppmov2.mpg2 MB | Supporting Movie 2 |
| PROT_22560_sm_suppmov3.mpg1.9 MB | Supporting Movie 3 |
| PROT_22560_sm_suppmov4.mpg1.9 MB | Supporting Movie 4 |
| PROT_22560_sm_suppmov5.mpg2 MB | Supporting Movie 5 |
| PROT_22560_sm_suppmov6.mpg2 MB | Supporting Movie 6 |
| PROT_22560_sm_suppmov7.mpg2 MB | Supporting Movie 7 |
| PROT_22560_sm_suppmov8.mpg1.9 MB | Supporting Movie 8 |
| PROT_22560_sm_suppmov9.mpg2 MB | Supporting Movie 9 |
| PROT_22560_sm_suppmov10.mpg2 MB | Supporting Movie 10 |
| PROT_22560_sm_suppfig1.pdf164.7 KB | Supporting Figure 1 |
Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
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