In silico modelling of cascade enzymatic proteolysis is an exceedingly complex and challenging task. Here, we study partial proteolysis of insulin by pepsin: a process leading to the release of a highly amyloidogenic two chain ‘H-fragment’. The H-fragment retains several cleavage sites for pepsin. However, under favorable conditions H-monomers rapidly self-assemble into proteolysis-resistant amyloid fibrils whose composition provides snapshots of early and intermediate stages of the proteolysis. In this work, we report a remarkable agreement of experimentally determined and simulation-predicted cleavage sites on different stages of the proteolysis. Prediction of cleavage sites was based on the comprehensive analysis of the docking interactions from direct simulation of coupled folding and binding of insulin (or its cleaved derivatives) to pepsin. The most frequent interactions were found to be between the pepsin's active site, or its direct vicinity, and the experimentally determined insulin cleavage sites, which suggest that the docking interactions govern the proteolytic process.

在计算机模拟中级联酶解的建模是一项极其复杂且具有挑战性的任务。在这里，我们研究胃蛋白酶对胰岛素的部分蛋白水解作用：导致高度淀粉样蛋白生成的两条链“ H片段”释放的过程。H片段保留了胃蛋白酶的几个切割位点。然而，在有利条件下，H-单体迅速自组装成抗蛋白水解的淀粉样原纤维，其组成提供了蛋白水解早期和中间阶段的快照。在这项工作中，我们报告了在蛋白水解的不同阶段实验确定和模拟预测的裂解位点的显着一致性。裂解位点的预测是基于对接相互作用的综合分析，该对接相互作用是直接模拟胰岛素（或其裂解衍生物）与胃蛋白酶的偶联折叠和结合。