School of Life Sciences, University of Technology Sydney, PO Box 123, Broadway, NSW 2007 Australia.
Sci Rep. 2016 Mar 15;6:23174. doi: 10.1038/srep23174.
MCoTI-I and II are plant defence proteins, potent trypsin inhibitors from the bitter gourd Momordica cochinchinensis. They are members of the Knottin Family, which display exceptional stability due to unique topology comprising three interlocked disulfide bridges. Knottins show promise as scaffolds for new drug development. A crystal structure of trypsin-bound MCoTI-II suggested that loop 1, which engages the trypsin active site, would show decreased dynamics in the bound state, an inference at odds with an NMR analysis of MCoTI-I, which revealed increased dynamics of loop 1 in the presence of trypsin. To investigate this question, we performed unrestrained MD simulations of trypsin-bound and free MCoTI-II. This analysis found that loop 1 of MCoTI-II is not more dynamic in the trypsin-bound state than in the free state. However, it revealed an intermediate conformation, transitional between the free and bound MCoTI-II states. The data suggest that MCoTI-II binding involves a process in which initial interaction with trypsin induces transitions between the free and intermediate conformations, and fluctuations between these states account for the increase in dynamics of loop 1 observed for trypsin-bound MCoTI-I. The MD analysis thus revealed new aspects of the inhibitors' dynamics that may be of utility in drug design.
MCoTI-I 和 II 是植物防御蛋白，是来自苦瓜 Momordica cochinchinensis 的强效胰蛋白酶抑制剂。它们是 Knottin 家族的成员，由于包含三个互锁二硫键的独特拓扑结构，显示出异常的稳定性。Knottins 有望成为新药开发的支架。与胰蛋白酶结合的 MCoTI-II 的晶体结构表明，与胰蛋白酶活性位点结合的 loop 1 在结合状态下的动力学会降低，这一推断与对 MCoTI-I 的 NMR 分析不一致，后者表明在存在胰蛋白酶的情况下 loop 1 的动力学增加。为了研究这个问题，我们对与胰蛋白酶结合和游离的 MCoTI-II 进行了无约束的 MD 模拟。该分析发现，与游离状态相比，胰蛋白酶结合状态下的 MCoTI-II 的 loop 1 并没有更具动态性。然而，它揭示了一种中间构象，介于游离和结合的 MCoTI-II 状态之间。数据表明，MCoTI-II 的结合涉及一个过程，即与胰蛋白酶的初始相互作用诱导游离和中间构象之间的转变，并且这些状态之间的波动解释了与胰蛋白酶结合的 MCoTI-I 中观察到的 loop 1 动力学增加。因此，MD 分析揭示了抑制剂动力学的新方面，这可能对药物设计有用。
