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HtrA2-ligand complex unit C after 50 ns MD with reference to the initial structure.

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posted on 2016-08-29, 17:37 authored by Artur Gieldon, Dorota Zurawa-Janicka, Miroslaw Jarzab, Tomasz Wenta, Przemyslaw Golik, Grzegorz Dubin, Barbara Lipinska, Jerzy Ciarkowski

All but the top-right views have common orientation. PD N-terminal α1-α2 and C-terminal barrel are in the foreground (bottom, dark blue ribbon), while C-terminal α4 and N-terminal barrel are in the background (bottom, light blue ribbon). α1-α2 and α4 axes run roughly perpendicular to the figure plane. Important features of the structure and its dynamics are indicated. Top-left: Unit C as extracted from the trimer in Fig 4 left panel, and reoriented (see above). Bottom-left: As above, PD unwrapped form the surface. Top-right: Unit C is rotated 90° round the vertical axis to show relationships between the PDZ motion and exposure of the catalytic triad (olive green). Bottom-right: Visualization of a true uncovering of the catalytic triad after ca. 40° PDZ counterclockwise rotation (lid-opening) during the 50 ns MD, characterized in detail in the neighbor bottom-left panel and in Table 4.