The illustrated movies were generated on the basis of different protein conformations that we observed in various crystal structures. In combination, these structures reveal the remarkable dynamics of protease and chaperone machines and demonstrate that protein crystallography does much more than only providing static pictures. It's still fiction - but beautiful scientific fiction.
The DegP hexamer (DegP6) was observed in two different conformations in the obtained crystal form. The corresponding particles were present in an "open" and a "closed" conformation with the PDZ domains (orange) controlling access to the inner cavity, where the proteolytic sites are. The movie suggests that DegP6 is a real eating machine (movie, 1 MB).
Upon substrate binding, the DegP hexamer (DegP6) re-assembles and forms a DegP12 or DegP24 particle. This oligomer conversion is paralleled by a remodeling of the proteolytic site from an inactive into the active state. Hmmh, looks like a protease tango in the active site (movie, 1 MB).
The RIP protease CtpB was observed in 4 different conformations providing an almost complete enzymatic motion picture. Most likely, the indicated conformational switching is induced by substrate binding to the PDZ domain - highlighted in magenta - thereby opening the proteolytic tunnel. To fully enjoy this mechanism, you can watch the movie in different modes (fast, medium, slow, all about 9 MB).
The RIP protease CtpB was observed in 4 different conformations providing an almost complete enzymatic motion picture. This motion picture illustrates the elegant opening of the protease tunnel, as induced by substrate binding to the PDZ domain that is shown in yellow (movie, 1 MB).
Most likely, the conformational switching of CtpB is induced by substrate binding to the PDZ domain. A corresponding mechanism is illustrated in this movie - highlighting the additional stabilization of the open tunnel in the substrate-bound state (movie, 2 MB).
DegS is another PDZ-protease that is allosterically regulated by peptide binding to its PDZ domain. In this case, the bound OMP C-terminus (spheres) induce remodeling of the proteolytic site, i.e. of loop L3 (orange) and loops L1, L2 and LD of the activation domain (green). Strikingly, protease activation is reversible as illustrated the two movies (fast, slow, 2 and 7 MB).