Structural Behavior of the Peptaibol Harzianin HK VI in a DMPC Bilayer: Insights from MD Simulations.
Structural Behavior of the Peptaibol Harzianin HK VI in a DMPC Bilayer: Insights from MD Simulations.
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DOI：
10.1016/j.bpj.2017.05.019
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发表时间：
2017-06
影响因子：
3.4
通讯作者：
Marina Putzu;S. Kara;S. Afonin;S. Grage;Andrea Bordessa;G. Chaume;T. Brigaud;A. Ulrich;T. Kubař
中科院分区：
文献类型：
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作者：
Marina Putzu;S. Kara;S. Afonin;S. Grage;Andrea Bordessa;G. Chaume;T. Brigaud;A. Ulrich;T. Kubař
在低肽脂比条件下，对哈茨木素 HK VI (HZ) 与二肉豆蔻酰磷脂酰胆碱双层相互作用进行了微秒分子动力学模拟。发现并表征了双层中 HZ 分子的两个方向。在垂直于双层表面的方向上，HZ 引起双层的局部变薄。当平行于其表面插入双层时，HZ 几乎完全位于双层的疏水区域内。固态核磁共振和圆二色性实验的结合发现后者的方向占主导地位。扩展采样模拟提供了定性结果，并显示出相同的方向，即自由能的全局最小值。对HZ的二级结构进行了表征，发现它位于310螺旋家族中。简要讨论了非极性肽计算机模拟的具体挑战。
Microsecond molecular dynamics simulations of harzianin HK VI (HZ) interacting with a dimyristoylphosphatidylcholine bilayer were performed at the condition of low peptide-to-lipid ratio. Two orientations of HZ molecule in the bilayer were found and characterized. In the orientation perpendicular to the bilayer surface, HZ induces a local thinning of the bilayer. When inserted into the bilayer parallel to its surface, HZ is located nearly completely within the hydrophobic region of the bilayer. A combination of solid-state NMR and circular dichroism experiments found the latter orientation to be dominant. An extended sampling simulation provided qualitative results and showed the same orientation to be a global minimum of free energy. The secondary structure of HZ was characterized, and it was found to be located in the 310-helical family. The specific challenges of computer simulation of nonpolar peptides are discussed briefly.