Structural characterization of transition state ensembles

<p><b>.</b> Native state-specific contacts with different probability formed in are mapped onto the open and apo-closed structures (upper right subfigure). For the contact probability map (lower left subfigure), the upper triangle and lower triangle correspond to probability map of the O-specific and A-specific native contacts, respectively. Note that the NTD is used to superimpose the open and closed conformations. For clarity, the O-specific mapped structures and A-specific mapped structures are shown separately in upper left and lower right corners respectively. For O-specific mapped structures (upper left subfigure), which are turned for the illustration of the back of active site groove, the CTD for apo-closed structure is represented by transparent cartoon in red. For the A-specific mapped structures (lower right subfigure), the CTD for the open structure is represented by the transparent cartoon in green. Blue squares (A and B regions) label the O-specific interactions which are not broken in . These broken O-specific interactions are highlighted by magenta squares (C and D regions). Red squares (E and F regions) and black squares (G and H regions) highlight the formed and unformed A-specific interactions respectively. The green squares in the contact probability map and green dashed lines in the mapped structure are used to label the O-specific contacts (F88-V255 and V106-A299) between linker1 and NTD at the bottom of the ligand bind cleft, which are not broken in TS.