Replica-exchange molecular dynamics simulation of diffracted X-ray tracking
Replica-exchange molecular dynamics simulation of diffracted X-ray tracking
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DOI：
10.1080/08927020601067581
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发表时间：
2007-01-01
影响因子：
2.1
通讯作者：
Okamoto, Y.
中科院分区：
文献类型：
--
作者：
Kawashima, Y.;Sasaki, Y. C.;Okamoto, Y.
我们利用具有序列 Ac-YGKAAAAKAAAAKAAAAKC-amide 的肽的复制品交换分子动力学模拟来检查共价键合到一端的纳米晶体的影响，以模拟衍射 X 射线跟踪 (DXT) 方法。我们在这项研究中进行了三种不同的模拟。在衍射DXT法中，进行了无约束模拟、一端固定模拟、以及一端固定并通过改变与纳米晶体共价键合的C末端硫原子的质量来考虑纳米晶体的影响的模拟。对三种模拟的平均配置参数进行了比较和讨论。我们利用主成分分析来分析模拟结果。获得的自由能图谱表明，DXT技术的条件不会影响全局最小状态，但可能会影响折叠路径。
We examine the effects of the nanocrystal covalently bonded to one end, utilizing replica-exchange molecular dynamics simulation of a peptide with the sequence Ac-YGKAAAAKAAAAKAAAAKC-amide, to simulate the diffraction X-ray tracking (DXT) method. We performed three different simulations in this study. A simulation with no constraint, a simulation with one end fixed, and a simulation with one end fixed and also considering the effect of the nanocrystal by changing the mass of the sulfur atom in the C-terminus, which covalently bonded with the An nanocrystal in diffraction DXT method, was performed. The average configuration parameters of the three simulations are compared and discussed. We analyzed our simulation results utilizing principal component analysis. The obtained free-energy landscape indicated that the condition of the DXT technique will not affect the global-minimum state, however, it may affect the folding pathway.