聚合物通过蛋白质通道转运的模拟。
Simulation of polymer translocation through protein channels.
作者信息
Muthukumar M, Kong C Y
机构信息
Department of Polymer Science and Engineering, University of Massachusetts, Amherst, MA 01003, USA.
出版信息
Proc Natl Acad Sci U S A. 2006 Apr 4;103(14):5273-8. doi: 10.1073/pnas.0510725103. Epub 2006 Mar 27.
Abstract
A modeling algorithm is presented to compute simultaneously polymer conformations and ionic current, as single polymer molecules undergo translocation through protein channels. The method is based on a combination of Langevin dynamics for coarse-grained models of polymers and the Poisson-Nernst-Planck formalism for ionic current. For the illustrative example of ssDNA passing through the alpha-hemolysin pore, vivid details of conformational fluctuations of the polymer inside the vestibule and beta-barrel compartments of the protein pore, and their consequent effects on the translocation time and extent of blocked ionic current are presented. In addition to yielding insights into several experimentally reported puzzles, our simulations offer experimental strategies to sequence polymers more efficiently.
摘要
提出了一种建模算法，用于在单个聚合物分子通过蛋白质通道进行易位时，同时计算聚合物构象和离子电流。该方法基于聚合物粗粒度模型的朗之万动力学与离子电流的泊松-能斯特-普朗克形式主义的结合。对于单链DNA穿过α-溶血素孔的示例，展示了蛋白质孔前庭和β桶隔室内聚合物构象波动的生动细节，以及它们对易位时间和离子电流阻断程度的影响。除了深入了解一些实验报道的难题外，我们的模拟还提供了更高效地对聚合物进行测序的实验策略。
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