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RNA polymerase II flexibility during translocation from normal mode analysis
Author(s) -
Feig Michael,
Burton Zachary F.
Publication year - 2009
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.22560
Subject(s) - chromosomal translocation , transcription (linguistics) , rna , polymerase , dna , biology , microbiology and biotechnology , rna polymerase , biophysics , chemistry , genetics , computational biology , gene , linguistics , philosophy
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. Proteins 2010. © 2009 Wiley‐Liss, Inc.