DNA deformation by wildtype and mutant TBP.

<p>(A) DNA roll angle profile of TBP in the simulations of wildtype and mutant TBP proteins (the wildtype crystal structure 1cdw is shown as reference). The DNA sequence is shown as x-axis indicating that there are two kinks formed between a TA and an AG base step, respectively. (B) Time course of the roll angles for all base steps over the MD simulation. The two base steps exhibiting the largest kinks are highlighted by boxes at the y-axis. The vertical black line denotes the boundary between the two independent 250-ns MD simulations performed for each system, which are presented in a single panel. Colors of boxes match line colors of average roll angle plots of corresponding systems in (A). The type of mutation present in the individual systems is structurally depicted at the top of each panel.