Figure 1.

MD simulation on T7 RNAP at the posttranslocated state. (a) (Left) A structure of T7 RNAP elongation complex. (Silver) Nucleic acids. Each protein subdomain is colored differently. (Blue) N-terminus (residues 1∼325); (red) thumb (326∼411); (purple) palm-I (412∼553); (green) fingers (554∼784); (brown) palm-II (785∼883). (Right) The RMSD values of the protein subdomains with corresponding colors. The active site (yellow star) for the nucleotide addition is located on the palm-I subdomain. The O-helix (cyan) on the fingers subdomain close to the active site is also indicated. (b) (Left) The stacking of Tyr⁶³⁹ (red) to the end bp of the DNA-RNA hybrid (blue and green) in cartoon representation. Tyr⁶³⁹ locates on the C-terminal of the O-helix, with its side chain inserted in the active site (pink oval) and close to the preinsertion site (yellow oval). (Right) The interaction energy between Tyr⁶³⁹ and the end bp. The nonbonded interaction energies (black) between Tyr⁶³⁹ and the end bp, along with the electrostatic (ele) (blue) and vdW (red) contributions, are shown in time series (from the 100-ns simulation) and histograms (measured −2.0 ± 1.2 kcal/mol for nonbonded, 0.2 ± 0.6 kcal/mol ele, and −2.2 ± 1.0 kcal/mol vdW).