Li Tanping
700 Choppin Hall, Chemistry Department of Louisiana State University , Baton Rouge, Louisiana 70803, United States.
J Phys Chem B. 2014 Nov 13;118(45):12952-9. doi: 10.1021/jp506599d. Epub 2014 Nov 4.
We report a theoretical study on the relaxation dynamics of Staphylococcus nuclease following photon excitation. Molecular dynamics simulations were implemented for both ground state and excited state surface of Trp140. Over the course of 40 ns ground state simulation, a structural transition was observed from one isomeric protein configuration to another. No obvious isomerization process was exhibited in the excited state simulations. Using linear response theory and direct nonequilibrium approach, time-dependent Stokes shift, as well as its time-infinity value, was evaluated for both ground state isomers. Comparison between these methods exhibits severe disagreement. The nonequilibrium simulations show the similar relaxation dynamics as the excited state linear response approach, whereas they severely differ from the ground state linear response evaluation. Further examination reveals that the isomerization process breaks the characteristics of the energy gap histogram from Gaussian statistics. We also made the comparison between the experimental and simulation results. The significant inertial decay, in theory, is absent in the experiment. The ground state linear response evaluation provides a better agreement with the experimental results among all three approaches.
我们报道了一项关于金黄色葡萄球菌核酸酶在光子激发后弛豫动力学的理论研究。对Trp140的基态和激发态表面进行了分子动力学模拟。在40纳秒的基态模拟过程中，观察到了从一种异构蛋白质构型到另一种构型的结构转变。在激发态模拟中未表现出明显的异构化过程。使用线性响应理论和直接非平衡方法，对两种基态异构体的时间相关斯托克斯位移及其时间无穷大值进行了评估。这些方法之间的比较显示出严重的分歧。非平衡模拟显示出与激发态线性响应方法相似的弛豫动力学，而与基态线性响应评估有很大不同。进一步研究表明，异构化过程打破了能隙直方图符合高斯统计的特征。我们还对实验结果和模拟结果进行了比较。理论上，实验中不存在明显的惯性衰减。在所有三种方法中，基态线性响应评估与实验结果的一致性更好。
