RNA polymerase

RNA polymerase

During transcription RNA polymerase copies genes from DNA to RNA to be used as a template for protein synthesis. RNA polymerase is a highly complex molecular machine that can unwind DNA, synthesize complementary RNA in a regulated manner with low error rates, and even correct errors when they do occur.

We are using molecular dynamics simulations, normal mode analysis, Markov state modeling, and kinetic network modeling to understand the detailed mechanism of RNA polymerase and in particular how this enzyme is able to efficiently select the correctly matched nucleotide out of four possible ribonucleotides at each RNA elongation cycle.

Related Publications:

2017
  9. Beibei Wang, Rachel E. Sexton, Michael Feig: Kinetics of Nucleotide Entry via Secondary Pore into RNA Polymerase II Active Site Provides Mechanism for Efficiency and Fidelity BBA Gene Regulatory Mechanisms (2017) in press,
2015
  8. Beibei Wang, Kristopher Opron, Zachary F. Burton, Robert I. Cukier, Michael Feig: Five checkpoints maintaining the fidelity of transcription by RNA polymersases in structural and energetic detail Nucleic Acids Research (2015) 43, 1133-1146 Abstract PDF
2013
  7. Beibei Wang, Michael Feig, Robert Cukier, Zachary Burton: Computational simulation strategies for analysis of multi-subunit RNA polymerases Chemical Reviews (2013) 113, 8546-8566 Abstract PDF
  6. Beibei Wang, Alexander Predeus, Zachary Burton, Michael Feig: Energetic and Structural Details of Trigger Loop Closing Transition in RNA Polymerase II Biophysical Journal (2013) 105, 767-775 Abstract PDF
2010
  5. Michael Feig, Zachary F. Burton: RNA Polymerase II with Open and Closed Trigger Loops: Active Site Dynamics and Nucleic Acid Translocation Biophysical Journal (2010) 99, 2577-2586 Abstract PDF
  4. Steve Seibold, Badri Nath Singh, Chunfen Zhang, Maria Kireeva, Celine Domecq, Annie Bouchard, Anthnoy Nazione, Michael Feig, Robert Cukier, Benoit Coulombe, Mikhail Kashlev, Michael Hampsey, Zachary Burton: Conformational coupling, bridge helix dynamics and active site dehydration in catalysis by RNA polymerase Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms (2010) 1799, 575-587 Abstract PDF
  3. Michael Feig, Zachary F. Burton: RNA Polymerase II Flexibility During Translocation From Normal Mode Analysis Proteins (2010) 78, 434-446 Abstract PDF
2005
  2. Xue Q. Gong, Chunfen Zhang, Michael Feig, Zachary F. Burton: Dynamic Error Correction and Regulation of Downstream Bubble Opening by Human RNA Polymerase II Molecular Cell (2005) 18, 461-470 Abstract PDF
  1. Zachary F. Burton, Michael Feig, Xue Qian Gong, Chunfen Zhang, Yuri A. Nedialkov, Yalin Xiong: NTP-driven translocation and regulation of downstream template opening by multi-subunit RNA polymerases Biochemistry And Cell Biology (2005) 83, 486-496 Abstract PDF