The influence of simulation conditions in molecular dynamics investigations of model β-sheet peptides
The influence of simulation conditions in molecular dynamics investigations of model β-sheet peptides
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DOI：
10.1007/s00214-004-0565-4
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发表时间：
2004-07-01
影响因子：
1.7
通讯作者：
Colombo, G
中科院分区：
文献类型：
--
作者：
Monticelli, L;Colombo, G
模拟方法的影响，截止为基础的和粒子网格埃瓦尔德（PME）的准确性，实验得出的核Overhauser效应（NOE）的数据再现，已经研究了使用500 ns长的分子动力学模拟模型β-折叠肽在明确的溶剂。在不同条件下的结构和构象特征进行了评估的灵活性，二级结构的内容，氢键模式和百分比的天然接触作为时间的函数。结果发现，不同的模拟方法强烈影响肽的动力学，证实了以前的观察结果的基础上，理想的肽模型模拟的时间要短得多。此外，我们的模拟结果再次证明，它是必要的，以达到非常长的时间尺度，以获得足够的统计数据，以准确地再现实验NOE的限制，即使在PME方法的情况下，尽管其倾向于稳定的构象，这是结构上密切相关的，通过实验得出的。关于稳定和折叠机制，连同它们的关系，肽模型的实验研究的可能影响，进行了讨论。
The influence of simulation methods, cutoff based and particle mesh Ewald (PME) on the accuracy by which experimentally derived nuclear Overhauser effect (NOE) data are reproduced, has been investigated using 500-ns-long molecular dynamics simulations on a model beta-sheet peptide in explicit solvent. The structural and conformational features under the different conditions were evaluated in terms of flexibility, secondary structure content, hydrogen-bonding pattern and percent of native contacts as a function of time. It was found that the different simulation methods strongly influence the dynamics of the peptide, confirming previous observations based on ideal peptide models simulated for much shorter times. Moreover, the results of our simulations prove once more that it is necessary to reach extremely long time scales to obtain enough statistics to accurately reproduce experimental NOE restraints even in the case of the PME method, despite its tendency to the stabilization of conformations which are structurally closely related to the ones derived through experiment. Possible implications regarding the stabilization and folding mechanisms, together with their relationship to the experimental study of peptide models, are discussed.