FIGURE 4.

Distance-restrained docking: applications to RNAP. (A) (left) Structures of Rif and Rif SV. (right) Fluorescein emission spectrum (solid line), Rif absorption spectrum (dashed line), and Rif SV absorption spectrum (dotted line). (B) Model of RNAP-Rif and RNAP-Rif SV complexes generated using experimental FRET-derived distance restraints for Rif (Table 1) and distance-restrained docking (two orthogonal views: view of upstream face of RNAP, left; view into the RNAP active-center cleft, right). Green spheres, possible positions of Rif chromophore (top 50% of solutions); red sphere, crystallographically defined position of Rif chromophore (Campbell et al., 2001); white and yellow spheres, attachment sites of donor chromophores on RNAP core and σ⁷⁰, respectively. (C) The same as for panel B, but model generated using experimental FRET-derived distance restraints for Rif SV (Table 1). (D) The same as for panel B, but model generated using combined experimental FRET-derived distance restraints for Rif and Rif SV (Table 1). Figures were prepared using PyMOL (DeLano, 2002).