Fig. 2

Comparison of the persistence of the wild-type TWIST1/E12 (TE) dimer and mutated R154P TE dimer. a 3D representation of the conserved TWIST1 (grey ribbon)/E12 (green ribbon) complex. Description of the position of the basic domain residues is represented as a cartoon and CPK in grey for TWIST1 (from R110 to E126) and in green for E12 (R550 to N566). b The CA-CA distances between pairs of basic domain residues on TWIST1 and E12 were estimated during 10 ns in silico molecular dynamics (MD) simulations using the VMD 1.9.1 software. The graphical representation shows the calculated mean distances between pairs of TWIST1/E12 residues in angstroms (Å) in the mutated R154P TE model with (green line) or without (dashed green line) DNA anchor, and the TE model with (blue line) or without a DNA anchor (dashed blue line). c 3D representation of the conserved TWIST1 (grey ribbon)/E12 (green ribbon) complex bound to DNA along with the E-box sequence (CATCTG), carried out using the VMD 1.9.1 software. The residues are numbered in each strand of the 5′-CATCTG-3′ E-box core. The three pairs of residues are shown, namely M112-V552, L124-D564, and I134-L578, which were located at the bottom, in the middle and at the top of the dimer, respectively. d-f Box plots representing the distances (Å) between pairs of residues of the dimer as a function of time (total time = 10 ns, 1 frame per 10 ps), during the TE (black line) and TE R154P (grey line) 10 ns in silico molecular dynamics (MD) simulations. These distances were estimated during the MD simulations using the VMD 1.9.1 software (Graph of Labels Bonds). The lengths of H-bond interactions were represented via GraphPad Prism 5: “smooth, differentiate or integrate curve, with 8 neighbors”. Interactions between the (d) M112 of TWIST1 and V552 of E12 residue pair, close to the bottom of the dimer, (e) L124 of TWIST1 and D564 of E12 residue pair, close to the middle of the dimer, and (f) I134 of TWIST1 and L578 of E12 residue pair, close to the top of the dimer