Figure 2.

Protein and DNA motions in pol μ simulations. (a) Protein motions (left) and DNA motions (right) of pol μ in selected simulations (red, simulation I; green, simulation II; blue, simulation III; black, simulation V). For clarity, DNA bases other than A5 in simulations II, III, and V are not shown. (b) DNA position in simulation XIV (shifted-DNA model), before (brown) and after simulation (purple), compared with simulation II (green). (c) Protein conformation in simulation XV (open-thumb model), before (brown) and after (purple) simulation, compared with simulation II (green). The motion of α-helix N in the thumb is shown. (d) Protein motions (left) and DNA motions (right) of pol μ in mutant simulations compared with wild-type simulation I (red, simulation I; cyan, simulation XI; orange, simulation XII; purple, simulation XIII). DNA bases other than A5 in simulations XI, XII, and XIII are not shown. The shift of A5 base is indicated. (e) Interactions between DNA and residues Arg⁴⁴⁴, Arg⁴⁴⁷, and Arg⁴⁴⁸. Only residues A5–A6 in the DNA template are shown. Dashed lines indicate hydrogen bonds. (f) The insertion frameshift error observed in simulation XIII (R448A, purple) compared to wild-type simulation I (red). The frameshift behavior can be described in three steps: 1), A5 and A6 rotate/shift toward the downstream side; 2), Gln⁴⁴⁰ flips to A5; and 3), dTTP shifts toward the upstream side and flips to A6. Nucleotides are drawn with a smaller bond radius. Dashed lines indicate hydrogen bonds.