Molecular Insight into Different Denaturing Efficiency of Urea, Guanidinium, and Methanol: A Comparative Simulation Study
Molecular Insight into Different Denaturing Efficiency of Urea, Guanidinium, and Methanol: A Comparative Simulation Study
复制标题
DOI：
10.1021/ct3010968
复制
发表时间：
2013-06-01
影响因子：
5.5
通讯作者：
Zeng, Xiao Cheng
中科院分区：
文献类型：
--
作者：
Koishi, Takahiro;Yasuoka, Kenji;Zeng, Xiao Cheng
我们设计了各种纳米狭缝系统，其相对表面可以是疏水的，亲水的，或者只是一个水蒸气界面，分别用于三种不同的蛋白质变性剂（即尿素，氯化胍（GdmC1）和甲醇）的密闭水的分子动力学模拟。特别关注变性剂分子在相对表面上的优先吸附和在相邻表面上的相关停留时间，以及它们对不同变性剂分子变性效率的影响。我们的模拟结果表明，在三种变性剂中，甲醇在邻近层的占用率最高，而Gdm的停留时间最长，尽管尿素在邻近层的占用和停留时间都小于其他两种变性剂分子。尿素是一种高效的变性剂，具有“全方位”的特性。三种变性剂的不同特性可能表明蛋白质变性的不同分子机制。这种设计的比较模拟使我们能够在分子水平上获得更多的见解，以了解变性效应和相关的疏水效应。
We have designed various nanoslit systems, whose opposing surfaces can be either hydrophobic, hydrophilic, or simply a water-vapor interface, for the molecular dynamics simulation of confined water with three different protein denaturants, i.e., urea, guanidinium chloride (GdmC1), and methanol, respectively. Particular attention is placed on the preferential adsorption of the denaturant molecules onto the opposing surfaces and associated resident time in the vicinal layer next to the surfaces, as well as their implication in the denaturing efficiency of different denaturant molecules. Our simulation results show that among the three denaturants, the occupancy of methanol in the vicinal layer is the highest while the residence time of Gdm is the longest Although the occupancy and the residence time of urea in the vicinal layer is less than those of the other two denaturant molecules, urea entails "all-around" properties for being a highly effective denaturant The distinct characteristics of three denaturants may suggest a different molecular mechanism for the protein denaturation. This comparative simulation by design allows us to gain additional insights, on the molecular level, into the denaturation effect and related hydrophobic effect.