Figure 1.
Structural representation of DPO4 and free energy landscapes.
The structure of the A-, I- and B-states of DPO4 are shown in (A), (B) and (C), colored by: the F domain, blue; the P domain, red; the T domain, green; the LF domain, purple; the linker between the LF and T domain, grey. The specific interactions formed by the LF domain with the T domain in the A-state and the F domain in the B-state are drawn by orange lines in (A) and (C), and the number of the specific interactions are indicated in parentheses, respectively. The unstructured loop in the F domain is shown by the blue broken lines in (A) and (B). (D) The binding free energy is shown as a function of QiDNA and DCOM at . QiDNA describes the native similarity of binding of DPO4 to DNA, DCOM describes the distance between DPO4 and DNA. The four free energy minima correspond to different binding stages: the US, EC, IS and BS. A constant temperature simulation at
was performed and the trajectory is shown to validate the continuity of the adjacent stages in free energy landscapes. (E–H) The free energy landscapes of conformational dynamics in DPO4 are shown as a function of QA and QiB at each binding stage. QA, QiB measures the native similarity of the LF domain interacting with the T domain in the A-state and the F domain in the B-state, respectively. The A-, I- and B-states of DPO4 can be observed in the US, EC and IS, with different population distributions at different binding stages. Only the I- and B-state of DPO4 can be observed in the BS. The populations of the three states of DPO4 at each binding state are plotted as pie-charts in (D) near the corresponding free energy minima.
Figure 2.
Conformational dynamics of DPO4 change with temperature.
The population distributions of the A- (red lines), I- (green lines) and B-state (blue lines) in the (A) US, (B) EC, (C) IS and (D) BS are shown as a function of temperature. Temperature is energy unit ().
Table 1.
Protein-DNA interaction energy in each binding state at .
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.
Figure 4.
Native contacts between DPO4 and DNA as well as the structural illustrations of DPO4-DNA complex in the IS.
(A) The average of inter-chain native contacts for each residue in DPO4 are shown. The fraction of native contacts, which measures the degree of the formation of the native contacts, is shown in the insert figure. (B) The fraction of native contacts is shown for each nucleotide of either the primer or the template strand. The color on the x-axis in (A) and (B) is the same as that in Figure 3. (C) Typical structures of the A-, I- and B-state of DPO4 binding with DNA in the IS are shown. The coloring strategy for DPO4 is the same as that in Figure 1A.
Figure 5.
CSalt is the salt concentration. The error bar represents the standard error of the corresponding MPT.
Figure 6.
MPT and the conformational dynamics of DPO4 change with the flexibility of the linker.
is the parameter which controls the flexibility of the linker. There are two groups of
shown. The filled symbols correspond to the linker biased to the B-state while the empty symbols correspond to the linker biased to the A-state. (A) MPT as a function of
. (B) The conformational population distribution of the A-, I- and B-state of DPO4 in the US, EC, IS and BS with different
. Notice that when
equals 10.0 and 100.0, the BS cannot be observed in the simulations when the linker is biased to the A-state. MPT is calculated as the largest observation time. The error bar represents the standard error of the corresponding MPT.
Figure 7.
MPT changes with the conformational dynamics.
is the strength of the specific native contacts between the LF and F domain in B-state of DPO4.
controls the conformational dynamics of DPO4. (A) MPT as a function of
. (B) The conformational distribution of the A-, I- and B-state of DPO4 in the US, EC, IS and BS with different
. The error bar represents the standard error of the corresponding MPT.
Figure 8.
MPT of dissociation of DPO4-DNA binary complex as a function of temperature.
The error bar represents the standard error of the corresponding MPT. Temperature is in energy unit ().
Figure 9.
Native contacts between DPO4 and DNA in native bound structure.
(A) Native contacts for each nucleotide in DNA. DPO4 interacts with DNA in native bound structure at three different regions, which are colored orange, olive green and dark cyan, corresponding to the major groove, minor groove and the terminal of the DNA duplex, respectively. (B) Native contacts for the sugar, base and phosphate group in DNA. (C, D) The native structure of DPO4-DNA binary complex. In (C), the sugar, base and phosphate groups in DNA are colored from blue to red, corresponding to contact number from 0 to 5; while DPO4 is colored grey. In (D), the residues in DPO4 are colored from blue to red, corresponding to the DPO4-DNA contact number from 0 to 5, while DNA is colored grey. The DPO4-DNA contacts are drawn by orange lines in (C) and (D).