Open Access Highly Accessed Research article

Molecular dynamics and mutational analysis of the catalytic and translocation cycle of RNA polymerase

Maria L Kireeva1, Kristopher Opron2, Steve A Seibold234, Céline Domecq5, Robert I Cukier3, Benoit Coulombe56, Mikhail Kashlev1 and Zachary F Burton2*

Author Affiliations

1 Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, MD, 21702-1201, USA

2 Department of Biochemistry and Molecular Biology, Michigan State University, E. Lansing, MI, 48824-1319, USA

3 Department of Chemistry, Michigan State University, E. Lansing, MI, 48824, USA

4 Department of Chemistry, University of Saint Mary, Leavenworth, KS, 66048, USA

5 Gene Transcription and Proteomics Laboratory, Institut de Recherches Cliniques de Montréal (IRCM), 110, Avenue des Pins Ouest, Montréal, Québec, H2W 1R7, CANADA

6 Department of Biochemistry, Université de Montréal, Montréal, Québec, H3C 3J7, CANADA

For all author emails, please log on.

BMC Biophysics 2012, 5:11  doi:10.1186/2046-1682-5-11

Published: 7 June 2012

Additional files

Additional file 1:

Supplementary figures and legends.

Format: PDF Size: 3.7MB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 2:

Movie M1. Closed-Mg (closed trigger loop; bonded Mg atoms) Tt RNAP TEC (Thermus thermophilus RNA polymerase ternary elongation complex). DNA is gold. RNA is red. ATP is red (stick). The bridge helix is green transparent. The trigger loop is green opaque. G1230 (H1), G1233 (H1), G1255 (H2), G1076 (H3), G1080 (H4) and G1081 (H4) are shown in space-filling representation. Bridge helix bending mode B1 is established and held stably through the simulation. At the beginning of the movies, closed-Mg and open RNAP TECs are very similar in conformation except for the trigger loop conformation.

Format: MPEG Size: 10.2MB Download file

Playing the movie within this page requires QuickTime 6.4 or later and JavaScript. Read more

Open Data

Additional file 3:

Movie M2. Open (open trigger loop) Tt RNAP TEC. DNA is gold. RNA is red. ATP is red. The bridge helix is blue transparent. The trigger loop is blue opaque. G1230 (H1), G1233 (H1), G1255 (H2), G1076 (H3), G1080 (H4) and G1081 (H4) are shown in space-filling representation. Bridge helix bending mode B2 is established rapidly and held stably through the simulation. At the beginning of the movies, closed-Mg and open RNAP TECs are very similar in conformation except for the trigger loop conformation.

Format: MPEG Size: 10.1MB Download file

Playing the movie within this page requires QuickTime 6.4 or later and JavaScript. Read more

Open Data