[Model of protease I from the crab Uca pugilator]

Collagenolytic protease I from the fiddler crab Uca pugilator is one of the serine proteases of the trypsin family. A graphic molecular model was built on the basis of the sequences and crystalline structures of four homologous proteins which were superimposed in order to identify structurally conserved regions. The sequence of protease I was matched to sequences of the reference proteins, without allowing any deletions or insertions in these regions. For structurally variable regions, the most similar sequences of the four reference proteins were selected. Intramolecular steric clumping due to replacement of reference side-chains by protease I side-chains were corrected by adjusting side-chain conformations. The model was optimized by energy minimization. The conformation of the primary specificity pocket for protease I predicted by the model indicated a preference for P1 hydrophobic or positively charged substrates. This prediction is consistent with biochemical findings. Because soya bean trypsin inhibitor (STI) has been shown to inhibit protease I, a tentative model of the complex was constructed and possible protease I-STI interactions were analyzed.