Krüger P, Verheyden S, Declerck P J, Engelborghs Y
Laboratory of Biomolecular Dynamics, Katholieke Universiteit Leuven, 3001 Leuven, Belgium.
Protein Sci. 2001 Apr;10(4):798-808. doi: 10.1110/ps.40401.
Plasminogen activator inhibitor type 1 (PAI-1) is an inhibitor of plasminogen activators such as tissue-type plasminogen activator or urokinase-type plasminogen activator. For this molecule, different conformations are known. The inhibiting form that interacts with the proteinases is called the active form. The noninhibitory, noncleavable form is called the latent form. X-ray and modeling studies have revealed a large change in position of the reactive center loop (RCL), responsible for the interaction with the proteinases, that is inserted into a beta-sheet (s4A) in the latent form. The mechanism underlying this spontaneous conformational change (half-life = 2 h at 37 degrees C) is not known in detail. This investigation attempts to predict a transition path from the active to the latent structure at the atomic level, by using simulation techniques. Together with targeted molecular dynamics (TMD), a plausible assumption on a rigid body movement of the RCL was applied to define an initial guess for an intermediate. Different pathways were simulated, from the active to the intermediate, from the intermediate to the latent structure and vice versa under different conditions. Equilibrium simulations at different steps of the path also were performed. The results show that a continuous pathway from the active to the latent structure can be modeled. This study also shows that this approach may be applied in general to model large conformational changes in any kind of protein for which the initial and final three-dimensional structure is known.
纤溶酶原激活物抑制剂1型（PAI-1）是组织型纤溶酶原激活物或尿激酶型纤溶酶原激活物等纤溶酶原激活物的抑制剂。对于这种分子，已知有不同的构象。与蛋白酶相互作用的抑制形式称为活性形式。非抑制性、不可裂解的形式称为潜伏形式。X射线和建模研究表明，负责与蛋白酶相互作用的反应中心环（RCL）的位置发生了很大变化，在潜伏形式中它插入到一个β折叠（s4A）中。这种自发构象变化（37℃下半衰期 = 2小时）的潜在机制尚不清楚。本研究试图通过使用模拟技术在原子水平预测从活性结构到潜伏结构的转变路径。结合靶向分子动力学（TMD），对RCL的刚体运动应用了一个合理假设来定义中间体的初始猜测。在不同条件下模拟了从活性结构到中间体、从中间体到潜伏结构以及反之亦然的不同路径。还对路径不同步骤进行了平衡模拟。结果表明，可以构建从活性结构到潜伏结构的连续路径。这项研究还表明，这种方法通常可应用于为已知初始和最终三维结构的任何类型蛋白质的大构象变化建模。
