Figure 1

The cartoon rendering of the crystal structure of staphylococcal nuclease (PDB ID 1stn), refined at 1.7Å resolution, is shown in (a). KINARI-Web was used to calculate the protein's rigidity properties, visualized in (b); color clusters represent atoms that are rigidly connected (only clusters made up of more than 15 atoms are shown). KINARI uses chemical bonds and stabilizing interactions to identify bodies, which are sets of atoms rigidly attached to each other. The three atoms identified in the purple region in (c) form a rigid body because the covalent bonds and distances imposed by angle constraints (shown as dotted lines) remove all degrees of freedom among the three atoms. The rigid units are used to construct a mechanical model of the molecule, in which two rigid bodies that have a rotatable bond in common are represented as hinges, as shown in yellow in (d). In (d), rigid body 1 corresponds to atoms N₁, C_1α, and C in (c), and rigid body 2 corresponds to atoms C_1α, C, and O; the two bodies share the covalent bond between C_1αand C. The pebble game paradigm associates rigid bodies of a mechanical model to a node in a graph, a hinge in the mechanical model as 5 bars between two nodes, and bars, which represent constraints such as hydrogen bonds and hydrophobic interactions in the mechanical model, to single bars among nodes in the graph. The pebble game algorithm is used to analyze the graph, the results of which are used to infer rigid clusters of atoms in the biomolecule. A complete explanation of how modeling is performed by KINARI is described in [16].