Coarse-Grain Simulations of the R-SNARE Fusion Protein in its Membrane Environment Detect Long-Lived Conformational Sub-States
Coarse-Grain Simulations of the R-SNARE Fusion Protein in its Membrane Environment Detect Long-Lived Conformational Sub-States
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DOI：
10.1002/cphc.200900216
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发表时间：
2009-07-13
期刊：
影响因子：
2.9
通讯作者：
Baaden, Marc
中科院分区：
文献类型：
--
作者：
Durrieu, Marie-Pierre;Bond, Peter J.;Baaden, Marc
粗粒分子动力学用于观察插入脂质双层的 R-SNARE 肽的构象和动态方面。这种方法允许进行微秒级的模拟，从而揭示出在 SNARE 蛋白介导的膜融合机制中可能感兴趣的长寿命构象亚状态。我们表明，这些粗粒度模型与 SNARE 系统的大多数实验数据一致，但在一些可能具有功能意义的细节上有所不同，最显着的是 R-SNARE 可溶部分的方向，该部分似乎无法自发地形成 SNARE 复合体。我们还比较了 R-SNARE 的大鼠和酵母序列，发现它们的行为存在一些细微差异。
Coarse-grain molecular dynamics are used to look at conformational and dynamic aspects of an R-SNARE peptide inserted in a lipid bilayer. This approach allows carrying out microsecond-scale simulations which bring to light long-lived conformational sub-states potentially interesting in the context of the membrane fusion mechanism mediated by the SNARE proteins. We show that these coarse-grain models are in agreement with most experimental data on the SNARE system, but differ in some details that may have a functional interest, most notably in the orientation of the soluble part of R-SNARE that does not appear to be spontaneously accessible for SNARE complex formation. We also compare rat and yeast sequences of R-SNARE and find some minor differences in their behavior.