Hubbard S J, Campbell S F, Thornton J M
Department of Biochemistry and Molecular Biology, University College, London, U.K.
J Mol Biol. 1991 Jul 20;220(2):507-30. doi: 10.1016/0022-2836(91)90027-4.
The conformations of known tryptic limited proteolytic sites have been analysed and compared to the structures of the binding regions of serine proteinase inhibitors, as they are found when complexed to a serine proteinase. Conformational parameters studied include main-chain torsion angles, root-mean-square fits, accessibility, mobility and protrusion indices. As observed before, the inhibitors share a common main-chain conformation at the binding loop from P3-P'3 (Schechter & Berger notation), which is maintained throughout all the serine proteinase inhibitor families for which X-ray data is available, despite lack of similarity in the rest of the protein. This canonical structure is not found amongst the limited proteolytic sites (or nicksites), which differ markedly from the inhibitor binding loop conformation, and also amongst themselves. The experimentally determined nicksites are in general both accessible and protruding; as are the inhibitor binding loops, as well as being typically flexible regions of structure, as denoted by elevated temperature factors from crystallographic determinations. For cleavage by serine proteinases these loops must radically alter their local conformations and a large motion of the loop relative to the structure, in some cases, would be required to orientate these sites for cleavage.
已知胰蛋白酶有限蛋白水解位点的构象已被分析，并与丝氨酸蛋白酶抑制剂结合区域的结构进行了比较，这些结构是在与丝氨酸蛋白酶形成复合物时发现的。研究的构象参数包括主链扭转角、均方根拟合、可及性、流动性和突出指数。如之前所观察到的，抑制剂在结合环（从P3 - P'3，Schechter & Berger表示法）处共享一个共同的主链构象，尽管蛋白质的其余部分缺乏相似性，但在所有有X射线数据的丝氨酸蛋白酶抑制剂家族中都保持这种构象。在有限蛋白水解位点（或切口位点）中未发现这种典型结构，这些位点与抑制剂结合环构象明显不同，并且它们彼此之间也有差异。实验确定的切口位点通常既具有可及性又突出；抑制剂结合环也是如此，并且它们通常是结构的柔性区域，这由晶体学测定中升高的温度因子表示。为了被丝氨酸蛋白酶切割，这些环必须从根本上改变其局部构象，并且在某些情况下，环相对于结构的大幅度移动将是使这些位点定向进行切割所必需的。
