Zhang Yuebin, Niu Huiyan, Li Yan, Chu Huiying, Shen Hujun, Zhang Dinglin, Li Guohui
State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Rd, Dalian 116023, P.R. China.
Department of Geriatrics, Shengjing Hospital, China Medical University, 36 Sanhao Street, Heping, Shenyang 110004, P. R. China.
Sci Rep. 2015 Feb 12;5:8405. doi: 10.1038/srep08405.
Dramatic functional changes of enzyme usually require scores of alterations in amino acid sequence. However, in the case of guanylate kinase (GK), the functional novelty is induced by a single (S→P) mutation, leading to the functional transition of the enzyme from a phosphoryl transfer kinase into a phosphorprotein interaction domain. Here, by using molecular dynamic (MD) and metadynamics simulations, we provide a comprehensive description of the conformational transitions of the enzyme after mutating serine to proline. Our results suggest that the serine plays a crucial role in maintaining the closed conformation of wild-type GK and the GMP recognition. On the contrary, the S→P mutant exhibits a stable open conformation and loses the ability of ligand binding, which explains its functional transition from the GK enzyme to the GK domain. Furthermore, the free energy profiles (FEPs) obtained by metadymanics clearly demonstrate that the open-closed conformational transition in WT GK is positive correlated with the process of GMP binding, indicating the GMP-induced closing motion of GK enzyme, which is not observed in the mutant. In addition, the FEPs show that the S→P mutation can also leads to the mis-recognition of GMP, explaining the vanishing of catalytic activity of the mutant.
酶的显著功能变化通常需要氨基酸序列发生数十处改变。然而，对于鸟苷酸激酶（GK）而言，单个（S→P）突变就能引发功能上的新奇变化，导致该酶从磷酸转移激酶功能转变为磷蛋白相互作用结构域。在此，我们通过分子动力学（MD）和元动力学模拟，全面描述了丝氨酸突变为脯氨酸后该酶的构象转变。我们的结果表明，丝氨酸在维持野生型GK的封闭构象以及GMP识别方面起着关键作用。相反，S→P突变体呈现出稳定的开放构象，失去了配体结合能力，这解释了其从GK酶到GK结构域的功能转变。此外，通过元动力学获得的自由能分布（FEPs）清楚地表明，野生型GK中开放-封闭构象转变与GMP结合过程呈正相关，表明GK酶存在GMP诱导的封闭运动，而在突变体中未观察到这种现象。此外，FEPs显示S→P突变还会导致对GMP的错误识别，这解释了突变体催化活性的消失。
