Fig. 5.

The Rad50 coiled-coil contains specific segments of increased flexibility. (a) Flexibility distribution along the Rad50 coiled-coil. Segments within 10 nm of the center of the globular R/M complex domain, marked I, are indicated by white bars. These regions do not contribute to the Rad50 coiled-coil. The last bin is also displayed in white because end effects distort its value. Gray bars represent segments along the coiled-coil. Two segments displaying increased flexibility are marked II and III. (b) Intrinsic curvature distribution along the Rad50 coiled-coil. The first bins, indicated in white and corresponding to the R/M complex globular domain, are not relevant with respect to the curvature analysis of the Rad50 coiled-coil; the last bin is affected by end effects. (c) Schematic cartoon of Rad50 in ribbon representation derived from the crystal structures of the ATPase domain (left) and the zinc hook (right) the Rad50 homologue in Pyrococcus furiosus (5, 20). The structure of the coiled-coil that connects these two features has not been determined and is indicated by the dotted line. (d) Probability of coiled-coil formation along the Rad50 amino acid chain is indicated by using a gray scale with black and white representing the lowest and highest probability of forming a coiled-coil, respectively. The amino acid chain is folded back onto itself at the position of the zinc hook, marked IV. The globular domain is marked I. Two positions, marked II and III, appear in the coiled-coil where both amino acid chains have a predicted decreased probability in coiled–coil formation. These positions colocalize with increased flexibility segments II and III in a.