Wroblowski B, Díaz J F, Schlitter J, Engelborghs Y
Laboratorium voor Chemische en Biologische Dynamica, Katholieke Universiteit Leuven, Belgium.
Protein Eng. 1997 Oct;10(10):1163-74. doi: 10.1093/protein/10.10.1163.
The conformational change of alpha-chymotrypsin from an inactive, chymotrypsinogen like structure at high pH to an active conformation around pH 8.5 is used here as a model system to generate possible pathways for the transition by use of two different theoretical methods. One method, the 'targeted molecular dynamics' algorithm (TMD) adds a constraint in the direction of the target to a molecular dynamics force field and gives two different paths, one for every direction of the reaction (Schlitter,J., Engels,M., Krüger,P.J., Mol. Graphics (1994) 12, 84-89). The second method, the 'self penalty walk' algorithm (SPW), refines an initially guessed path by minimizing the sum of the energies of its structures (Elber,R. and Karplus,M., Chem. Phys. Lett. (1987) 139, 375-380). Thus, starting from a linear path as a first approximation, it produces a reaction coordinate of the transition. The structures of the TMD and SPW paths are similar only in the beginning while the middle part of the SPW path links the two TMD branches. The activation of alpha-chymotrypsin in the TMD path starts with a movement of loop VII (residues 215-225), pulling on loop VI (residues 186-194). Then the side chain of Met192 turns to the surface and Ile16 approaches Asp194 to form a salt bridge. In the TMD deactivation path, loop VII also moves and pushes loop VI to the protein core. The Met192 side chain adopts three intermediate conformations, till the salt bridge Ile16-Asp194 is broken and loop VI rearranges to its final conformation. In the SPW pathway both the formation of the salt bridge and the movement of Met192 happen simultaneously between two consecutive steps.
α-胰凝乳蛋白酶在高pH值下从无活性的、类似胰凝乳蛋白酶原的结构转变为pH 8.5左右的活性构象，在此被用作一个模型系统，通过使用两种不同的理论方法来生成可能的转变途径。一种方法是“靶向分子动力学”算法（TMD），它在目标方向上对分子动力学力场添加一个约束，并给出两条不同的路径，反应的每个方向各一条（施利特，J.，恩格斯，M.，克鲁格，P.J.，《分子图形学》（1994年）12卷，84 - 89页）。第二种方法是“自罚行走”算法（SPW），通过最小化其结构能量之和来优化最初猜测的路径（埃尔伯，R.和卡尔普斯，M.，《化学物理快报》（1987年）139卷，375 - 380页）。因此，从作为一阶近似的线性路径开始，它产生转变的反应坐标。TMD和SPW路径的结构仅在开始时相似，而SPW路径的中间部分连接了两个TMD分支。在TMD路径中α-胰凝乳蛋白酶的激活始于环VII（残基215 - 225）的移动，拉动环VI（残基186 - 194）。然后Met192的侧链转向表面，Ile16靠近Asp194形成盐桥。在TMD失活路径中，环VII也移动并将环VI推向蛋白质核心。Met192侧链采取三种中间构象，直到盐桥Ile16 - Asp194断裂且环VI重新排列至其最终构象。在SPW途径中，盐桥的形成和Met192的移动在两个连续步骤之间同时发生。
