RNA polymerase II trigger loop residues stabilize and position the incoming nucleotide triphosphate in transcription.

ABSTRACT: A structurally conserved element, the trigger loop, has been suggested to play a key role in substrate selection and catalysis of RNA polymerase II (pol II) transcription elongation. Recently resolved X-ray structures showed that the trigger loop forms direct interactions with the beta-phosphate and base of the matched nucleotide triphosphate (NTP) through residues His1085 and Leu1081, respectively. In order to understand the role of these two critical residues in stabilizing active site conformation in the dynamic complex, we performed all-atom molecular dynamics simulations of the wild-type pol II elongation complex and its mutants in explicit solvent. In the wild-type complex, we found that the trigger loop is stabilized in the "closed" conformation, and His1085 forms a stable interacti

SUBMITTER: Huang X 

PROVIDER: S-EPMC2936645 | biostudies-literature | 2010 Sep

REPOSITORIES: biostudies-literature