| rigid-body docking solely on the basis of experimental data;
sidechain dynamics. |
Coordinates of both proteins were taken from the PDB entry 2PCC. Sequences differ slightly from the experiment. Structure refinement was based on PRE-derived distance restraints for backbone atoms as a sole input. Only two energy terms, corresponding to restraints and van der Waals forces, are specified during the refinement procedure, which consist of two steps. First, a rigid-body docking of the protein molecules is carried out with van der Waals parameters for MTSL atoms set to zero. For each run performed, a single cluster of low-energy solutions is consistently produced. During the second step, 30 to 40 best structures are subjected to energy minimization and side-chain dynamics with fixed positions of backbone atoms for both proteins and active van der Waals parameters for MTSL. For the refined structures, the entire docking procedure is repeated until no further reduction in energy is observed. Best twenty structures of the final solution show an average rmsd from the lowest energy structure of 0.7 (0.2) Angstrom for the backbone atoms of cytochrome c after superposition of the peroxidase molecules. |
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