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Biochim Biophys Acta Gene Regul Mech. 2017 Apr;1860(4):482-490. doi: 10.1016/j.bbagrm.2017.02.008. Epub 2017 Feb 24.

Kinetics of nucleotide entry into RNA polymerase active site provides mechanism for efficiency and fidelity.

Author information

1
Department of Biochemistry & Molecular Biology, 603 Wilson Rd., Room 218 BCH, Michigan State University, East Lansing, MI 48824, USA. Electronic address: bbwang@msu.edu.
2
Department of Biochemistry & Molecular Biology, 603 Wilson Rd., Room 218 BCH, Michigan State University, East Lansing, MI 48824, USA. Electronic address: sextonra@msu.edu.
3
Department of Biochemistry & Molecular Biology, 603 Wilson Rd., Room 218 BCH, Michigan State University, East Lansing, MI 48824, USA. Electronic address: feig@msu.edu.

Abstract

During transcription, RNA polymerase II elongates RNA by adding nucleotide triphosphates (NTPs) complementary to a DNA template. Structural studies have suggested that NTPs enter and exit the active site via the narrow secondary pore but details have remained unclear. A kinetic model is presented that integrates molecular dynamics simulations with experimental data. Previous simulations of trigger loop dynamics and the dynamics of matched and mismatched NTPs in and near the active site were combined with new simulations describing NTP exit from the active site via the secondary pore. Markov state analysis was applied to identify major states and estimate kinetic rates for transitions between those states. The kinetic model predicts elongation and misincorporation rates in close agreement with experiment and provides mechanistic hypotheses for how NTP entry and exit via the secondary pore is feasible and a key feature for achieving high elongation and low misincorporation rates during RNA elongation.

KEYWORDS:

Markov state model; Molecular dynamics simulation; NTP discrimination; Network model; Secondary pore

PMID:
28242207
PMCID:
PMC5393355
DOI:
10.1016/j.bbagrm.2017.02.008
[Indexed for MEDLINE]
Free PMC Article

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