Structure and dynamics of RNA polymerase II elongation complex

Biochemical and Biophysical Research Communications
Atsushi SuenagaMakoto Taiji

Abstract

RNA polymerase (Pol) II is a fundamental and important enzyme in the transcription process. However, two mysterious questions have remained unsolved: how an unwound bubble of DNA is established and maintained, and how the enzyme moves along the DNA. To answer these questions, we constructed a model structure of the Pol II elongation complex with the 50 base pairs of DNA-24 bases of RNA including the unwound bubble of DNA and performed a molecular dynamics simulation. We obtained a reliable model structure of the Pol II elongation complex in the pre-translocation state which has not yet been determined by the X-ray crystallographic study. The model structure revealed that multiple protein loops work concertedly to form and maintain the bubble structure. We also found that the conformational change of a loop in the Pol II, fork loop 1, couples with the unidirectional movement of the Pol II along the DNA.

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Citations

Dec 25, 2009·Bioinformatics·Shang-Hong Zhang, Ya-Zhi Huang
Sep 1, 2011·Molecular Biology and Evolution·Ashley FarlowChristian Schlötterer
Nov 10, 2006·Proceedings of the National Academy of Sciences of the United States of America·Guenter Albrecht-Buehler
May 19, 2010·Biochimica Et Biophysica Acta·Steve A SeiboldZachary F Burton
Feb 19, 2008·Current Opinion in Structural Biology·Alexander D Mackerell, Lennart Nilsson
Nov 26, 2015·Frontiers in Molecular Biosciences·Jian WuHai-Feng Chen
Nov 6, 2009·Current Opinion in Structural Biology·Vladimir Svetlov, Evgeny Nudler
Sep 2, 2009·Genomics·Robert Carter, Guy Drouin
Sep 6, 2014·Biostatistics·Vera AfreixoCarlos A C Bastos
Jun 28, 2016·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Konstantinos Apostolou-KarampelisYannis Almirantis
Nov 3, 2006·Biopolymers·S Elizabeth McDowellNils G Walter
May 14, 2016·G3 : Genes - Genomes - Genetics·Gildas Lepennetier, Francesco Catania
May 14, 2017·G3 : Genes - Genomes - Genetics·Gildas Lepennetier, Francesco Catania

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