Dynamic Conformational Change Regulates the Protein-DNA Recognition: An Investigation on Binding of a Y-Family Polymerase to Its Target DNA
Figure 3
The contacts between DPO4 and DNA at the EC.
Contact is based on a cut-off algorithm (See details in Text S1). (A) Average of the contacts of each residue in DPO4 and a contact-colored structure of DPO4 are shown. Since there are no contacts formed at the polymerase core, only the LF domain and the linker are shown. The color on the x-axis represents the different domains or regions in DPO4, the coloring scheme is same as that in Figure 1A. (B) Average contacts of each nucleotide in DNA are shown by primer and template strand, separately. The color on the x-axis represents the different regions of the DNA duplex: orange, the native recognition major groove; olive, the native recognition minor groove; dark cyan, the native recognition region at terminal of DNA. The native contacts are shown in Figure 9. (C) The DNA is colored by the average contacts of sugar, base and phosphate group. The color in the structure in (A) and (C) from blue to red corresponds to the number of contacts from zero to the largest.