Transcription is a central step in gene expression, in which the DNA template is processively read by RNA polymerase II (Pol II), synthesizing a complementary messenger RNA transcript. At each cycle, Pol II moves exactly one register along the DNA, a process known as translocation.  While X-ray crystal structures have greatly enhanced our understanding of the transcription process, the underlying molecular mechanisms of translocation remain unclear.  Here, we performed computer simulations to investigate the mechanisms of translocation.  The main challenge for molecular dynamics (MD) simulations is to reach biologically relevant timescales, which are orders of magnitude longer than most atomistic simulations. In order to overcome this timescale gap, we have applied Markov State Models (MSMs) to extract long timescale dynamics from many short MD simulations.  Using MSMs, we have observed multiple cycles of forward and backward translocation at a millisecond dynamics, and identify two novel intermediate states. We show that the Bridge Helix plays a key role accelerating the translocation of both the RNA:DNA Hybrid and Transition Nucleotide (TN) by directly interacting with them.  The conserved Bridge Helix residues, Thr831 and Tyr836, mediate these interactions.  To the date, our study delivers the most detailed picture of the mechanism of Pol II translocation at atomic level.  In addition, I will also briefly discuss other conformational changes in Pol II we have studied using MSMs.References:.1.  Da, L., Pardo, F., Wang, D., Huang, X., �A Two-State Model for the Dynamics of the Pyrophosphate Ion Release in Bacterial RNA Polymerase�, PLoS. Comp. Bio., 9(4): e1003020, (2013)2. Da, L., Wang, D., Huang, X., �Dynamics of Pyrophosphate Ion Release and Its Coupled Trigger Loop Motion from Closed to Open State in RNA Polymerase II�, J. Am. Chem. Soc., 134 (4), 2399, (2012)3.   Huang X., Wang D., Weiss D.H., Bushnell D. A., Westover K. D., Kornberg R. D., and Levitt M. 'RNA Polymerase II Trigger Loop Residues Stabilize and Position the Incoming NTP in Transcription', Proc. Nat. Acad. Sci. U.S.A. , 107 , 15745-15750, (2010)

Simulating millisecond dynamics of RNA polymerase II translocation at atomic resolution using Markov State models

247th National Meeting (2014)

The official archive and repository for all ACS Meetings & Expositions abstracts and select posters or presentations.