Analysis of key parameters for molecular dynamics of pMHC molecules
Analysis of key parameters for molecular dynamics of pMHC molecules
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DOI：
10.1080/08927020802256298
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发表时间：
2008-01-01
影响因子：
2.1
通讯作者：
Schreiner, Wolfgang
中科院分区：
文献类型：
--
作者：
Omasits, Ulrich;Knapp, Bernhard;Schreiner, Wolfgang
对人主要组织相容性复合体（MHC） HLAB*2705络合两种不同肽进行了分子动力学（MD）研究。在模拟过程中，一个肽与MHC部分分离，而另一个肽在几种不同的构型之间来回切换。这些不同的构型与构象底态有关，可以分配到不同水平的化学活性，甚至是免疫信号的分子机制。为了确保MD模拟得出可靠的免疫学结论，我们通过仔细评估初始条件、系统简化、溶剂化壳厚度、水模型/力场组合和模拟长度来准备方法学工具。我们还推导了适当选择模型的指导原则。这种质量评估被视为将多肽负载MHC动力学与t细胞激活联系起来的未来研究的强制性先决条件。
Molecular dynamics (MD) studies of human major histocompatibility complex (MHC) HLAB*2705 complexing two different peptides were performed. During simulation one peptide partially detached from the MHC while the other peptide switched back and forth between several different configurations. These different configurations relate to conformational substates and can be assigned to different levels of chemical activity or even the molecular mechanisms of immunological signalling. To ensure reliable immunological conclusions from MD simulations we prepare the methodological tools by carefully evaluating initial conditions, system simplification, solvation shell thickness, water model/force field combination and simulation length. We also derive a guideline for appropriate model selection. This kind of quality assessment is seen a mandatory prerequisite for coming studies linking peptide-loaded MHC dynamics to T-cell activation.