Arnoux B, Ducruix A, Lecroisey A
Laboratoire de Cristallochimie, CNRS, Gif-Sur-Yvette, France.
Pathol Biol (Paris). 1990 Dec;38(10):975-81.
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.
来自招潮蟹（学名：Uca pugilator）的胶原酶解蛋白酶I是胰蛋白酶家族的丝氨酸蛋白酶之一。基于四种同源蛋白的序列和晶体结构构建了一个图形分子模型，这些同源蛋白相互叠加以识别结构保守区域。蛋白酶I的序列与参考蛋白的序列进行匹配，在这些区域不允许有任何缺失或插入。对于结构可变区域，选择了四种参考蛋白中最相似的序列。通过调整侧链构象来校正由于蛋白酶I侧链取代参考侧链而导致的分子内空间聚集。通过能量最小化对模型进行优化。该模型预测的蛋白酶I一级特异性口袋的构象表明其对P1疏水或带正电荷的底物具有偏好性。这一预测与生化研究结果一致。由于已证明大豆胰蛋白酶抑制剂（STI）可抑制蛋白酶I，因此构建了该复合物的初步模型并分析了蛋白酶I与STI可能的相互作用。
