Hubbard S J, Thornton J M, Campbell S F
Department of Biochemistry and Molecular Biology, University College, London, UK.
Faraday Discuss. 1992(93):13-23. doi: 10.1039/fd9929300013.
The molecular recognition of limited proteolytic site substrates by serine proteinases has been compared and contrasted to the recognition of serine proteinase inhibitors, utilising the coordinate sets contained in the Brookhaven Protein Databank. Most families of these inhibitors are known to possess a structurally conserved recognition motif at their reactive site-binding loops. Structural comparisons with trypsin limited proteolytic sites revealed that the in situ conformation of these substrates bears little resemblance to the inhibitor-binding loops. Assuming that both inhibitors and substrates bind to the proteinase in the same manner, segmental mobility would be required to permit substrates to adopt an 'inhibitor-like' binding conformation, which is presumed to be necessary for proteolysis. Modelling experiments have been conducted to attempt to introduce such a conformation into tryptic limited proteolytic segments of the native proteins, to test the ability of the limited proteolytic sites to alter their geometry. Further to this, the conformational parameters of accessibility, protrusion, mobility and secondary structure have been analysed and incorporated into a predictive algorithm to assign likely limited proteolytic sites within native protein structures.
利用布鲁克海文蛋白质数据库中的坐标集，对丝氨酸蛋白酶对有限蛋白水解位点底物的分子识别与丝氨酸蛋白酶抑制剂的识别进行了比较和对比。已知这些抑制剂的大多数家族在其活性位点结合环处具有结构保守的识别基序。与胰蛋白酶有限蛋白水解位点的结构比较表明，这些底物的原位构象与抑制剂结合环几乎没有相似之处。假设抑制剂和底物以相同方式与蛋白酶结合，则需要片段移动性以使底物采用“抑制剂样”结合构象，据推测这对于蛋白水解是必需的。已进行建模实验，试图将这种构象引入天然蛋白质的胰蛋白酶有限蛋白水解片段中，以测试有限蛋白水解位点改变其几何形状的能力。除此之外，还分析了可及性、突出性、移动性和二级结构的构象参数，并将其纳入预测算法中，以在天然蛋白质结构中确定可能的有限蛋白水解位点。
