Figure 1.
mDCC and DCC among residues of the (Ets1)2–DNA complex.
(A) The maps of mDCC values and their differences from the DCC values (the upper and lower triangles, respectively). The color gradation from blue to red corresponds to mDCC values and their differences from DCC values from −1.0 to 1.0. The horizontal and vertical axes denote residues in the system, including two Ets1 molecules and a double-stranded DNA. The colored bars along each axis provided a guide for the secondary structures of residues: green, orange, cyan, and pink denote α-helix, β-strand, loop or turn, and DNA, respectively. Parts marked by the rectangles a–j, and residues marked at the top and right of the map are discussed in the main text. (B) Histogram of residue-wise mDCC and DCC values, shown in pink and cyan, respectively.
Figure 2.
Examples of transiently formed intermolecular interactions.
(A, B, and C) Interactions among the Nδ atom of the Asn380B side-chain, and the Cβ atoms of Ala324A and Ala327A. (A) The time course of interatomic distances, where red and blue plots denote Ala324A–Asn380B and Ala327A–Asn380B, respectively. (B) Spatial distributions of the coordinates of the three atoms. Color gradations of the plots, green to blue, yellow to red, and cyan to magenta, correspond to the time evolution of the simulation from 10 to 200 ns, for Ala324A, Ala327A, and Asn380B, respectively. (C) Contours of probability density functions of the Gaussian mixture models learned from the distributions in (B). The green, red and cyan meshes denote the contours for Ala324A, Ala327A, and Asn380B, respectively. (D, E, and F) Interactions among the Oη atom of Tyr396B, the backbone nitrogen atom of Leu337B, and an oxygen atom of the phosphate group of C11. (D) Time course of interatomic distances, where red, blue, and green plots denote Tyr396B–C11, Leu337B–Tyr396, and Leu337B–C11 pairs, respectively. (E) Contours of probability density functions of the Gaussian mixture models. The cyan, red, and blue meshes denote the contours of Tyr396B, Leu337B, and C11, respectively. (F) Snapshots at 0 ns (green) and 200 ns (cyan). The structures of the three residues focused on here are shown as sticks.
Figure 3.
A correlation network in (Ets1)2–DNA model.
(A) A simplified correlation network diagram in two-dimension (2D) as a sub-network of the original one shown in Fig. S7. Each node indicates a residue and each edge indicates a proximal residue pair with a highly positive correlation (the maximum value of mDCC ≥0.5 and the distance between the center positions of the modes <5.0 Å). The two circles correspond to the two Ets1 proteins (chain A and chain B correspond to the left circle and right circles, respectively), and the pink nodes are the DNA. The colors of the Ets1 nodes represent secondary structures: green, orange, and cyan indicate α-helix, β-strand, and others, respectively. The sizes of nodes denote the Betweenness values of residues. Important interactions mentioned in the manuscripts are shown as colored edges with bold arrows. (B) A 3D representation of the core network. The colors of atoms and ribbons represent their Betweenness values, and the atoms in the top 5% Betweenness are shown as spheres. Red lines indicate the shortest paths among all of the spheres. (C) The 3D structure around the recognition (H3) helix and the intermolecular interfaces. The pairs of residues corresponding to colored edges in Fig. 3A are shown as cylinders.
Figure 4.
Comparisons of mDCC maps between the (Ets1)2–DNA and single Ets1–DNA models.
The upper triangle shows mDCC values in the single Ets1–DNA model, with the color gradation from blue to red corresponding to mDCC values from −1.0 to 1.0. The lower triangle shows differences of the mDCC values in the single Ets1–DNA model from those in the (Ets1)2–DNA model with the color gradation corresponding from−0.7 to 0.7. For the lower triangle, negative values (blue) indicate correlations that decreased by the removal of the partner Ets1 molecule.
Figure 5.
Summary of the correlation network in the (Ets1)2–DNA complex.
The colored bold arrows indicate interactions of important residues that exhibited high Betweenness values. The colors of these arrows are consistent with those in the other figures. The red dashed arrows indicate the intermolecular pairs with highly positive correlations between the Ets1 molecules. The blue dashed arrows indicate the pairs with significant gains of correlations by the loss of the partner Ets1 molecule.