Conformational elasticity can facilitate TALE-DNA recognition - PubMed (original) (raw)

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Conformational elasticity can facilitate TALE-DNA recognition

Hongxing Lei et al. Adv Protein Chem Struct Biol. 2014.

Abstract

Sequence-programmable transcription activator-like effector (TALE) proteins have emerged as a highly efficient tool for genome engineering. Recent crystal structures depict a transition between an open unbound solenoid and more compact DNA-bound solenoid formed by the 34 amino acid repeats. How TALEs switch conformation between these two forms without substantial energetic compensation, and how the repeat-variable di-residues (RVDs) discriminate between the cognate base and other bases still remain unclear. Computational analysis on these two aspects of TALE-DNA interaction mechanism has been conducted in order to achieve a better understanding of the energetics. High elasticity was observed in the molecular dynamics simulations of DNA-free TALE structure that started from the bound conformation where it sampled a wide range of conformations including the experimentally determined apo and bound conformations. This elastic feature was also observed in the simulations starting from the apo form which suggests low free energy barrier between the two conformations and small compensation required upon binding. To analyze binding specificity, we performed free energy calculations of various combinations of RVDs and bases using Poisson-Boltzmann surface area (PBSA) and other approaches. The PBSA calculations indicated that the native RVD-base structures had lower binding free energy than mismatched structures for most of the RVDs examined. Our theoretical analyses provided new insight on the dynamics and energetics of TALE-DNA binding mechanism.

Keywords: Bound; Elasticity; Specificity; TALE; Unbound.

© 2014 Elsevier Inc. All rights reserved.

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Conflict of interest statement

The authors have no conflicts of interest to declare.

Figures

Figure 1

Figure 1

RMSD profiles from the three 50-ns MD simulations with the TALE-DNA complex (PDB code: 3V6T, the complete system).

Figure 2

Figure 2

The profiles of RMSD (left) and radius of gyration (Rg, right) from the three 50-ns MD simulations with the ligand-free TALE starting from the apo structure (PDB code: 3V6P). In the RMSD profiles, the RMSDs against the apo structure are shown in black, the RMSDs against the bound structure are shown in green.

Figure 3

Figure 3

The profiles of RMSD (left) and Rg (right) from the three 200-ns MD simulations with the ligand-free TALE starting from the bound structure (PDB code: 3V6T, DNA removed). In the RMSD profiles, the RMSDs against the bound structure are shown in green, the RMSDs against the apo structure are shown in black.

Figure 4

Figure 4

Three representative snapshots from the MD simulation trajectory shown in the top panel of Figure 3(left, 68.25 ns, highly extended; middle, 73.95 ns, close to the apo form; and right, 130.29 ns, close to the bound form). The structures from the simulation are show in red, the reference bound structure is shown in green.

Figure 5

Figure 5

Conformational sampling of the ligand-free TALE from the three MD simulations shown in Figure 3.

Figure 6

Figure 6

Binding free energy evaluation of 16 RVDs and all four possible bases for each RVD by PBSA. For each RVD, the lowest binding free energy was set to zero while others were assigned to positive energy based on the energy difference. For NG and HG, a second template with NG at the central RVD of the original structure was used for energy evaluation (shown as NG’ and HG’).

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