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Computational approaches to nanobiotechnology: probing the interaction of synthetic molecules with phospholipid bilayers via a coarse grain model

机译:纳米生物技术的计算方法:通过粗粒模型探索合成分子与磷脂双层的相互作用

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This paper illustrates the use of computer simulation in understanding the interaction of nano-scale synthetic molecules with cellular membranes, which are themselves a few nanometres thick. Specifically, the interaction of a membrane-bound synthetic molecule with a model membrane has been studied using so-called coarse-grain (CG) molecular dynamics (MD). The reported CG-MD simulations have been carried out for a pore-promoting hydraphile molecule in a dimyristoylphosphatidylcholine (DMPC) lipid bilayer. Analysis of the CG-MD simulation provides insights into the nature of the interaction of the hydraphile with the lipid molecules and how an initially fully extended trans-membrane hydraphile adjusts its end-to-end distance to match the bilayer thickness. The equilibrium membrane-bound hydraphile conformation observed in the CG-MD simulation agrees well with deductions based on experimental observations. The success of the CG-MD approach in the present example suggests that the methodology could be used as a design tool in related nano-science and engineering applications.
机译:本文说明了计算机模拟在理解纳米级合成分子与细胞膜的相互作用中的作用,而细胞膜本身只有几纳米厚。具体而言,已经使用所谓的粗粒(CG)分子动力学(MD)研究了与膜结合的合成分子与模型膜的相互作用。已对二肉豆蔻酰基磷脂酰胆碱(DMPC)脂质双层中的促孔亲水分子进行了报道的CG-MD模拟。 CG-MD模拟的分析提供了对亲水剂与脂质分子相互作用性质的见解,以及最初完全延伸的跨膜亲水剂如何调节其端对端距离以匹配双层厚度的见解。 CG-MD模拟中观察到的平衡膜结合亲水构象与基于实验观察的推论很好地吻合。 CG-MD方法在本示例中的成功表明该方法可以用作相关纳米科学和工程应用中的设计工具。

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