Bing D H, Laura R, Robison D J, Furie B, Furie B C, Feldmann R J
Ann N Y Acad Sci. 1981;370:496-510. doi: 10.1111/j.1749-6632.1981.tb29758.x.
A computer graphic molecular display system has been used to construct a three-dimensional model of the B chain of bovine thrombin. The model is derived from the bovine alpha-chymotrypsin structure as determined by X-ray crystallographic studies. The amino acid sequence of bovine thrombin has been substituted for that of alpha-chymotrypsin, preserving the beta-barrel structure and maximizing homology of the amino acid sequence of the two proteins. With the exception of an area in the vicinity of the specificity binding pocket, most of the changes observed in thrombin occur on the surface of the molecule. The most notable changes observed in the model are the increases on the surface of positively charged (arginine and lysine) and negatively charged (glutamate and aspartate) residues. A glutamate replaces methionine 192 near the entrance to the specificity binding pocket. The nature of this site was further altered by the substitution of an aspartate for serine 189 and an alanine for serine 190. The structure of the resulting specificity binding pocket is consistent with that of serine proteases, which have trypsin-like substrate specificity. The computer graphics molecular display system has been used to insert models of synthetic thrombin inhibitors into the active site of the thrombin B chain model. With the model, it has been possible to correlate the interaction of thrombin with the observed binding constants of two inhibitors of trypsin-like serine proteases, p-amidinophenylmethylsulfonylfluoride (Ki = 1.27 x 10(-6) M) and m-[m-(trifluoromethyl)phenoxypropoxy]benzamidine (KD = 2.9 x 10(-6) M).
一种计算机图形分子显示系统已被用于构建牛凝血酶B链的三维模型。该模型源自通过X射线晶体学研究确定的牛α-胰凝乳蛋白酶结构。牛凝血酶的氨基酸序列已被替换为α-胰凝乳蛋白酶的氨基酸序列，保留了β-桶状结构并使两种蛋白质的氨基酸序列同源性最大化。除了特异性结合口袋附近的区域外，在凝血酶中观察到的大多数变化都发生在分子表面。在模型中观察到的最显著变化是带正电荷（精氨酸和赖氨酸）和带负电荷（谷氨酸和天冬氨酸）的残基在表面上的增加。在特异性结合口袋入口附近，一个谷氨酸取代了甲硫氨酸192。通过用天冬氨酸取代丝氨酸189和用丙氨酸取代丝氨酸190，该位点的性质进一步改变。所得特异性结合口袋的结构与具有胰蛋白酶样底物特异性的丝氨酸蛋白酶的结构一致。计算机图形分子显示系统已被用于将合成凝血酶抑制剂的模型插入到凝血酶B链模型的活性位点。利用该模型，已能够将凝血酶的相互作用与两种胰蛋白酶样丝氨酸蛋白酶抑制剂对脒基苯甲基磺酰氟（Ki = 1.27×10^(-6) M）和间-[间-(三氟甲基)苯氧基丙氧基]苯甲脒（KD = 2.9×10^(-6) M）的观察到的结合常数相关联。
