Correlation among sites of limited proteolysis, enzyme accessibility and segmental mobility

The relationship among accessibility to an enzyme, flexibility, and limited proteolysis was explored. Regions accessible to large probes, comparable in size to proteolytic enzymes, were computed in the crystallographic structures of thermolysin, trypsinogen and ribonuclease. Positions of these accessible regions were compared with sites of autolytic/proteolytic attacks, and with locations of flexible backbone segments. All the proteolytic sites were found to be exceptionally accessible. Most of them were also flexible, but at least one prominent site in trypsinogen appeared to be rigid. Thus, surface exposure seems to be more essential to proteolysis than flexibility.