AN INTERACTIVE COMPUTER-GRAPHICS STUDY OF THERMOLYSIN-CATALYZED PEPTIDE CLEAVAGE AND INHIBITION BY N-CARBOXYMETHYL DIPEPTIDES
AN INTERACTIVE COMPUTER-GRAPHICS STUDY OF THERMOLYSIN-CATALYZED PEPTIDE CLEAVAGE AND INHIBITION BY N-CARBOXYMETHYL DIPEPTIDES
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DOI：
10.1021/bi00319a011
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发表时间：
1984-01-01
期刊：
影响因子：
2.9
通讯作者：
MATTHEWS, BW
中科院分区：
文献类型：
--
作者：
HANGAUER, DG;MONZINGO, AF;MATTHEWS, BW
利用交互式计算机图形学研究了锌内肽酶嗜热菌蛋白酶对模型底物Z-Phe-Phe-Leu-Trp的切割机理。研究了两种米氏络合物和三种四面体中间体与嗜热菌蛋白酶晶体结构的结合取向。结果表明，米氏络合物，它不涉及协调的易裂肽的锌，是与现有的实验数据和最合理的2个配合物。四面体中间复合物，其中水合易裂肽的2个氧以二齿方式跨在锌上，导致与活性位点的最有利的相互作用。优选的四面体中间体和米氏络合物为已发表的底物数据提供了合理化。提出了从米氏络合物到四面体中间体的轨迹。该轨迹涉及与锌结合的水分子的同时激活，同时攻击易分裂的肽。并给出了详细的有序产品发布机制。这些研究表明，一些修改和一些扩展的机制提出了较早的。嗜热菌蛋白酶抑制剂N-（1-羧基-3-苯基丙基）-L-亮氨酰-L-色氨酸的结合模式进行了比较，与优选的四面体中间体，提供洞察这种抑制剂的设计。
Interactive computer graphics was used as a tool in studying the cleavage mechanism of the model substrate Z-Phe-Phe-Leu-Trp by the Zn endopeptidase thermolysin. Two Michaelis complexes and 3 binding orientations of the tetrahedral intermediate to the crystal structure of thermolysin were investigated. The results indicate that a Michaelis complex, which does not involve coordination of the scissile peptide to the Zn, is consistent with available experimental data and the most plausible of the 2 complexes. A tetrahedral intermediate complex wherein the 2 oxygens of the hydrated scissile peptide straddle the Zn in a bidentate fashion results in the most favorable interactions with the active site. The preferred tetrahedral intermediate and Michaelis complex provide a rationalization for the published substrate data. A trajectory for proceeding from the Michaelis complex to the tetrahedral intermediate is proposed. This trajectory involves a simultaneous activation of the Zn-bound water molecule concurrent with attack on the scissile peptide. A detailed ordered product release mechanism is also presented. These studies suggest some modifications and a number of extensions to the mechanism proposed earlier. The binding mode of the thermolysin inhibitor N-(1-carboxy-3-phenylpropyl)-L-leucyl-L-tryptophan is compared with that of the preferred tetrahedral intermediate, providing insight into this inhibitor design.