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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

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Citation and License

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

Published: 7 June 2012

Abstract

Background

During elongation, multi-subunit RNA polymerases (RNAPs) cycle between phosphodiester bond formation and nucleic acid translocation. In the conformation associated with catalysis, the mobile “trigger loop” of the catalytic subunit closes on the nucleoside triphosphate (NTP) substrate. Closing of the trigger loop is expected to exclude water from the active site, and dehydration may contribute to catalysis and fidelity. In the absence of a NTP substrate in the active site, the trigger loop opens, which may enable translocation. Another notable structural element of the RNAP catalytic center is the “bridge helix” that separates the active site from downstream DNA. The bridge helix may participate in translocation by bending against the RNA/DNA hybrid to induce RNAP forward movement and to vacate the active site for the next NTP loading. The transition between catalytic and translocation conformations of RNAP is not evident from static crystallographic snapshots in which macromolecular motions may be restrained by crystal packing.

Results

All atom molecular dynamics simulations of Thermus thermophilus (Tt) RNAP reveal flexible hinges, located within the two helices at the base of the trigger loop, and two glycine hinges clustered near the N-terminal end of the bridge helix. As simulation progresses, these hinges adopt distinct conformations in the closed and open trigger loop structures. A number of residues (described as “switch” residues) trade atomic contacts (ion pairs or hydrogen bonds) in response to changes in hinge orientation. In vivo phenotypes and in vitro activities rendered by mutations in the hinge and switch residues in Saccharomyces cerevisiae (Sc) RNAP II support the importance of conformational changes predicted from simulations in catalysis and translocation. During simulation, the elongation complex with an open trigger loop spontaneously translocates forward relative to the elongation complex with a closed trigger loop.

Conclusions

Switching between catalytic and translocating RNAP forms involves closing and opening of the trigger loop and long-range conformational changes in the atomic contacts of amino acid side chains, some located at a considerable distance from the trigger loop and active site. Trigger loop closing appears to support chemistry and the fidelity of RNA synthesis. Trigger loop opening and limited bridge helix bending appears to promote forward nucleic acid translocation.