title: RNA polymerase II flexibility during translocation from normal mode analysis.
abstract: The structural dynamics in eukaryotic RNA polymerase II (RNAPII) is described from computational normal mode analysis based on a series of crystal structures of pre- and post-translocated states with open and closed trigger loops. Conserved modes are identified that involve translocation of the nucleic acid complex coupled to motions of the enzyme, in particular in the clamp and jaw domains of RNAPII. A combination of these modes is hypothesized to be involved during active transcription. The NMA modes indicate furthermore that downstream DNA translocation may occur separately from DNA:RNA hybrid translocation. A comparison of the modes between different states of RNAPII suggests that productive translocation requires an open trigger loop and is inhibited by the presence of an NTP in the active site. This conclusion is also supported by a comparison of the overall flexibility in terms of root mean square fluctuations.
authors.affiliation: Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA. feig@msu.edu
authors.forename: Michael
authors.initials: M
authors.lastname: Feig
authors.forename: Zachary F
authors.initials: ZF
authors.lastname: Burton
mesh_terms: D020134:Catalytic Domain; D008958:Models, Molecular; D009038:Motion; D009696:Nucleic Acids / Q000737:chemistry; D011487:Protein Conformation; D012319:RNA Polymerase II / Q000737:chemistry*; D012441:Saccharomyces cerevisiae / Q000201:enzymology*
chemical_list: D009696:Nucleic Acids; D012319:RNA Polymerase II