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Review
. 2013 Nov 13;113(11):8546-66.
doi: 10.1021/cr400046x. Epub 2013 Aug 29.

Computational simulation strategies for analysis of multisubunit RNA polymerases

Beibei Wang  1 , Michael Feig, Robert I Cukier, Zachary F Burton
Affiliations
Review

Computational simulation strategies for analysis of multisubunit RNA polymerases

Beibei Wang et al. Chem Rev. .
No abstract available

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Figures

Figure 1
Figure 1
Multisubunit RNAP (S. cerevisiae RNAP II). (A) Complex subunit structure and main enzyme channel. (B) Cutaway image (parts of Rpb1 and Rpb2 are missing) to show the transcription bubble, secondary pore (lime green; blue indicates basic residues important in PPi release), and buried active site. RNA is red, template DNA is blue, nontemplate DNA is yellow, the closed trigger loop conformation is orange, and the open trigger loop conformation is cyan. Images to the right indicate that a TEC with a closed trigger loop (orange) mostly closes the pore, and a TEC with an open trigger loop (cyan) has a more open pore with a diameter comparable to a diffusing GTP substrate. (C) RNAP active site with closed and open trigger loop conformations overlaid. Colors are as in panel B. The bridge helix is dark green. PDB structures 2E2H and 2E2J (with the open trigger loop modeled) and a PDB file from Jens Michaelis showing the intact bubble were used to make the images, by use of the program Visual Molecular Dynamics..
Figure 2
Figure 2
RNAPs and DNAPs have analogous 2-Mg2+ mechanisms. (A) Proposed mechanism for S. cerevisiae RNAP II. In the model, 3′-HORNA is deprotonated by OH– proposed to be derived from solvent. Rpb1 His1085 is proposed to transfer a proton to a β-phosphate oxygen. (B) Recently proposed mechanism for human DNAP η. Water is recruited beneath the 2′-H2 (i site sugar), interacting with the 3′-HODNA (i site) and the dNTP (i + 1 site) α-phosphate oxygens, which interact with Arg61. After extraction of the 3′-HODNA (i site) proton, the sugar pucker changes from 2′-endo to 3′-endo. Attack of 3′-O–DNA on the α-phosphate occurs. Arg61 shifts position and a third Mg2+ is recruited to PPi.
Figure 3
Figure 3
Phosphodiester bond addition cycle of S. cerevisiae RNAP II. Bridge helix is pink, trigger loop is green, NTP substrate is orange, RNA is purple, template DNA strand is blue, and nontemplate DNA strand is silver. The image is adapted from PDB files 2E2H (closed trigger loop) and 2E2J (open trigger loop). Reprinted with permission from ref (7a): Feig M.; Burton Z. F.. RNA polymerase II with open and closed trigger loops: Active site dynamics and nucleic acid translocation. Biophysical Journal 2010, 99(8), 2577.. Copyright 2010 Elsevier.
Figure 4
Figure 4
Simplified outline of a multisubunit RNAP elongation mechanism indicating potential rate-determining steps. Estimated or determined rate constants for elemental steps can be found in the text and references. EDTA-r/s: EDTA-resistant or -sensitive intermediates.
Figure 5
Figure 5
Model for histidine and arginine microswitches in RNAP translocation. Histidine can protonate on a DNA or RNA phosphate, deprotonate during translocation, and then reprotonate on the next phosphate downstream. Arginine remains protonated, so it requires a charge relay system and conformational effects for switching during template sliding. Red indicates negative charge; blue indicates positive charge; white indicates no charge.
Figure 6
Figure 6
RNAP inhibitors. (A) Rifamycin, a main-line drug against TB. (B) α-Amanitin, a deadly mushroom toxin that is heavily modified through secondary enzymatic reactions. (C) Microcin J25, a naturally occurring, plasmid-encoded bacterial antibiotic. Images of α-amanitin and microcin J25 are drawn to indicate similarities in structure, including a covalently closed eight-amino-acid ring, 2-Gly residues located in analogous positions, Pro residues in analogous positions, and ring cross-bridges projecting an aromatic amino acid with a hydroxyl group.
See this image and copyright information in PMC

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