Figure 1.
Structures and domain organization (PDB codes: 3V6P and 3V6T).
(A) The structures of dHax3 in the DNA-free state (left) and DNA-bound state (right). Each structure contains an 11.5-repeat domain, forming a right-handed superhelical assembly. The 11.5 repeats are colored separately. (B) The 11.5-repeat domain mediates DNA binding. Each repeat recognizes one specific nucleotide by using the RVD residues at positions 12 and 13. Single-letter abbreviations for the amino acid residues are as follows: A, Ala; C, Cys; D, Asp; E, Glu; F, Phe; G, Gly; H, His; I, Ile; K, Lys; L, Leu; M, Met; N, Asn; P, Pro; Q, Gln; R, Arg; S, Ser; T, Thr; V, Val; W, Trp; and Y, Tyr.
Figure 2.
Comparative MD analysis of DNA-free dHax3 (yellow) and DNA-bound dHax3 (dHax3: sky blue; DNA: orange) systems.
(A) The RMSD values of the dHax3 and DNA backbone atoms versus simulation time. (B) The probability distribution of RMSD calculated from the equilibrium trajectories. (C) The RMSF values of the dHax3 Cα atoms calculated from the equilibrium trajectories. (D) The cartoon representation of 11.5 TAL repeats for the dHax3 in the DNA-bound system. The residues in red have relatively higher RMSF values (>1.8 Å) while the ones in blue have relatively lower RMSF values (<1 Å). The other regions are colored white.
Table 1.
TALE-DNA direct hydrogen bonds in 11.5 repeats with occupancy over 40%.
Table 2.
Water-mediated hydrogen bonds in 11.5 repeats with occupancy over 40%.
Table 3.
Distances between the Cα of G13 and the 5-methyl group of thymine in all repeats with RVDs NG.
Figure 3.
The change of the specific hydrogen bonds between the TAL repeats and DNA bases at 6(A), 11 ns (B) and 16 ns (C) in the DNA-bound system.
The TAL repeats (yellow), DNA (pink) and water (blue) are depicted with ribbons, tube and CPK models, respectively. During the simulation, 1D13 (the residue Asp13 in repeat 1), 2D13, and 9D13 kept the specific hydrogen bond with 1dC (the base C1 in the DNA target sequence), 2dC, and 9dC, respectively. However, 11D13 lost the specific hydrogen bond with 11dC after 6 ns. Interestingly, 3D13 firstly interacted with 3dC (A). At 11 ns, 3D13 also formed water-mediated hydrogen bond with 4dT (B). Finally, 3D13 only indirectly contacted with 4dT (C).
Figure 4.
The first and second slowest motion modes of the DNA-free system (A and C) and DNA-bound system (B and D).
The length of cone is positively-correlated with motive magnitude, and the orientation of cone indicates motive direction. The two systems have the similar slow motions. The first slowest motion mainly appears as the open-close movements between the two ends of the superhelical structure (A and B). The second slowest motion shows a twisting around each end (C and D).
Figure 5.
Representation of the intramolecular angle and changes of the angles in the DNA-free and DNA-bound systems.
(A) The cartoon representation of 11.5 TAL repeats, with the intramolecular angle being defined by the Cα atoms of L357 (Leu357), N504 (Asn504) and E648 (Glu648). (B) The intramolecular angle change versus simulation time (solid line) and the value from crystal structure (dotted line) for the DNA-free dHax3. (C) The intramolecular angle change versus simulation time (solid line) and the value from crystal structure (dotted line) for the DNA-bound dHax3.
Figure 6.
Representation of the superhelical pitches and changes of the distances in the DNA-free and DNA-bound systems.
(A) The cartoon representation of 11.5 TAL repeats and the DNA. The superhelical pitch of dHax3 is assessed by the distance between the Cα atoms of G303 (Gly303) and G675 (Gly675) (left), and the pitch of DNA by the distance between the C3′ atoms of 1dC and 12dT (right). (B) The distance change versus simulation time (solid line) and the value from crystal structure (dotted line) in the DNA-free system. (C) The distance change versus simulation time (solid line) and the value from crystal structure (dotted line) in the DNA-bound system.
Figure 7.
Free energy contour map versus the principal components PC1 and PC2 at 310-free system (A) and DNA-bound system (B).
Deeper color indicates lower energy.
Figure 8.
Changes of axis bend angles along the DNA target sequence.
(A) Comparison of the average values (pink) of the axis bend calculated from the equilibrium trajectory along the d(CCCTTTATCTCT) with the corresponding crystal values (sky blue). (B) Fluctuations of axis bend for all dinucleotide steps along the d(CCCTTTATCTCT) during 20 ns trajectory. The color bar gives the variations in bend from 0° (dark blue) to 10° (dark red).
Figure 9.
Comparison of the average values (pink) of base pair step parameters calculated from the equilibrium trajectory along the d(CCCTTTATCTCT) with the corresponding crystal values (sky blue).
(A) Slide. (B) Roll angle. (C) Twist angle. (D) Rise.
Figure 10.
Comparison of the average values (pink) of groove widths calculated from the equilibrium trajectory along the d(CCCTTTATCTCT) with the corresponding crystal values (sky blue).
(A) Minor groove widths. (B) Major groove widths. The widening of the major groove is more remarkable at the sites of C2 and C9.