Figure 7.

Reorientation of the Arg-150 side chain during the Anton MD simulations rationalizes the exclusive preference for a 5´ C·G base pair in sequences observed in the ITC study. For clarity, the Thy base from the TAAT sequence (labeled with a red ‘Thy’) and the nucleobase on the opposing strand in the 5´-flanking base pair (labeled with the appropriate three-letter code in blue) are displayed in color in all panels, whereas all other nucleobases are shown in white. Hydrogen bonds between Arg-150 (labeled in black) and the DNA nucleobases are indicated by dashed red lines. The nucleobase atom serving as a hydrogen bond acceptor is also designated in the color-coded nucleotide labels for the accepting bases. (A) The co-crystal structure of Pdx1 bound to consensus DNA shows Arg-150 to be the only residue capable of making direct contact with nucleotides 5´ to the core TAAT element. Contrary to the observation of selectivity for a C·G base pair observed by ITC, the co-crystal only shows Arg-150 in direct contact with the first T of the core element – no contact to the C·G base pair is made (inset). (B) During the Anton MD trajectory, Arg-150 rapidly reorients to simultaneously hydrogen bond with the Thy-O2 of the first position in the TAAT core element and with the Gua-N3 on the opposing strand in the 5´ C·G base pair. (C) Arg-150 retains a conformation similar to that of the co-crystal structure when Pdx1 is simulated in complex with the TTAAT mutant DNA, never making temporally stable contact with the 5´ T·A base pair. In both the (D) 5´ G·C and (E) 5´ A·T mutant trajectories, interactions of the Arg-150 side chain with nucleobase hydrogen-bond acceptors in the minor groove of the DNA duplex are especially unstable. In all cases, the snapshot recorded after 3.5 µs of production dynamics displays the predominant orientation of the Arg-150 side chain and is selected for representation.