Fig. 8: Molecular dynamics simulation of TBP2 with DNA G4s.
From: A non-B DNA binding peptidomimetic channel alters cellular functions
A Top and side views of the final structures of TBP2, interacting with the top and bottom tetrad of c-MYC (1XAV) and h-TELO (1KF1) G-quadruplexes, as observed from two MD simulation trajectories. B Number of H-bonds between TBP2 and G-quadruplexes. C Free energies of binding between TBP2 and the two G-quadruplexes. Since the TBP2 molecule undergoes adsorption at different distances from the two G-quadruplexes, therefore, for a direct comparison, the reaction coordinate is represented as δ = d-d0, where, d and d0 are the distances at any time instant and the initial distance of adsorption, respectively.
