Free-energy landscape of the GB1 hairpin in all-atom explicit solvent simulations with different force fields: Similarities and differences.
Free-energy landscape of the GB1 hairpin in all-atom explicit solvent simulations with different force fields: Similarities and differences.
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DOI：
10.1002/prot.22972
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发表时间：
2011-04
影响因子：
2.9
通讯作者：
Mittal, Jeetain
中科院分区：
文献类型：
--
作者：
Best, Robert B.;Mittal, Jeetain
尽管现在可以在分子动力学模拟中折叠胡椒粉和小蛋白质，但我们在这里并非全部转移到不同的蛋白质，我们研究了蛋白质力场和溶剂模型对折叠能量模型的影响。在典型的两态文件夹中，GB1发夹我们使用广泛的副本 - 交换分子动力学模拟来表征自由能表面作为温度的函数。在所有情况下，在0.2和0.8之间的300 K处，这是2.8 kt的稳定性差异，通常与在此温度下的实验数据一致。被人群，以及未折叠状态的总体维度，在大多数力场中，相对于实验性förster共振能量传递（FRET）数据，该状态的整体尺寸太崩溃了。
Although it is now possible to fold peptides and miniproteins in molecular dynamics simulations, it is well appreciated that force fields are not all transferable to different proteins. Here, we investigate the influence of the protein force field and the solvent model on the folding energy landscape of a prototypical two-state folder, the GB1 hairpin. We use extensive replica-exchange molecular dynamics simulations to characterize the free-energy surface as a function of temperature. Most of these force fields appear similar at a global level, giving a fraction folded at 300 K between 0.2 and 0.8 in all cases, which is a difference in stability of 2.8 kT, and are generally consistent with experimental data at this temperature. The most significant differences appear in the unfolded state, where there are different residual secondary structures which are populated, and the overall dimensions of the unfolded states, which in most of the force fields are too collapsed relative to experimental Förster Resonance Energy Transfer (FRET) data.
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影响因子：
5.5
作者：
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通讯作者：
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影响因子：
3.4
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DOI：
10.1073/pnas.0408970102
发表时间：
2005-05-10
影响因子：
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作者：
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通讯作者：
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影响因子：
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作者：
Best, Robert B.;Mittal, Jeetain
通讯作者：
Mittal, Jeetain