Periodic rigidity of protein crystal structures

We initiate in silico rigidity-theoretical studies of protein crystal structures, with the goal to determine if, and how, the interactions among neighboring crystal cells affect the flexibility of biological unit. We use an efficient graph-based algorithm for rigidity analysis, and other tools available through the KINARI-Web server developed in our group. For the RNase A protein (PDB file 5RSA), which has the remarkable property of being functionally active even when crystallized, we found that the individual protein and its crystal form retain the flexibility parameters between the two states. By contrast, other proteins in our data set aggregated in larger rigid clusters when analyzed as crystals.