Study of Early Events in the Protein Folding of Villin Headpiece using Molecular Dynamics Simulation
Study of Early Events in the Protein Folding of Villin Headpiece using Molecular Dynamics Simulation
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DOI：
10.1080/07391102.2008.10507236
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发表时间：
2008-10
影响因子：
4.4
通讯作者：
U. Sonavane;Sai Kumar Ramadugu;R. Joshi
中科院分区：
文献类型：
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作者：
U. Sonavane;Sai Kumar Ramadugu;R. Joshi
摘要蛋白质折叠是一个在科学和计算上都具有挑战性的问题。蛋白质折叠的早期阶段是有趣的，由于各种事件，如新生的二级结构形成，疏水性崩溃，导致形成非天然或亚稳定构象。与几微秒的总折叠时间相比，这些事件发生在100 ns的非常短的时间跨度内。由于寿命很短，很难在实验上观察到这些事件。分子动力学模拟技术可以有效地探索这些事件的原子水平的详细理解。利用AMBER7软件包对完全溶剂化的绒毛状分子进行了近200ns的全原子分子动力学轨道模拟。最初的疏水性崩溃沿着与二级结构的形成导致部分稳定的非天然构象的形成。二级结构元件的形成和疏水性塌陷在折叠过程中同时发生。
Abstract Protein folding is scientifically and computationally challenging problem. The early phases of protein folding are interesting due to various events like nascent secondary structure formation, hydrophobic collapse leading to formation of non-native or meta-stable conformations. These events occur within a very short time span of 100ns as compared to total folding time of few microseconds. It is highly difficult to observe these events experimentally due to very short lifetime. Molecular dynamics simulation technique can efficiently probe the detailed atomic level understanding about these events. In the present paper, all atom molecular dynamics simulation trajectory of nearly 200ns was carried out for fully solvated villin headpiece with PME treatment using AMBER 7 package. Initial hydrophobic collapse along with secondary structure formation resulted into formation of partially stable non-native conformations. The formation of secondary structural elements and hydrophobic collapse takes place simultaneously in the folding process.