Multiscale method for modeling binding phenomena involving large objects: application to kinesin motor domains motion along microtubules.
Multiscale method for modeling binding phenomena involving large objects: application to kinesin motor domains motion along microtubules.
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DOI：
10.1038/srep23249
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发表时间：
2016-03-18
影响因子：
4.6
通讯作者：
Alexov E
中科院分区：
文献类型：
--
作者：
Li L;Alper J;Alexov E
许多生物现象都涉及蛋白质与大物体的结合。由于引导结合的静电力作用在大的距离上，因此截断系统的大小以便于计算建模经常产生不准确的结果。我们的多尺度方法实现了一个计算聚焦方法，允许计算的大型系统，而不截断的静电势，并实现建模大分子相互作用所需的高分辨率，同时保持合理的计算时间。我们测试了我们的方法对各种驱动蛋白运动域的运动性。我们发现，静电有助于引导驱动蛋白，因为他们走：N-驱动蛋白对正端，和C-驱动蛋白对微管的负端。我们的方法能够在类似的大型系统中进行计算，包括蛋白质与DNA，病毒和膜的结合。
Many biological phenomena involve the binding of proteins to a large object. Because the electrostatic forces that guide binding act over large distances, truncating the size of the system to facilitate computational modeling frequently yields inaccurate results. Our multiscale approach implements a computational focusing method that permits computation of large systems without truncating the electrostatic potential and achieves the high resolution required for modeling macromolecular interactions, all while keeping the computational time reasonable. We tested our approach on the motility of various kinesin motor domains. We found that electrostatics help guide kinesins as they walk: N-kinesins towards the plus-end, and C-kinesins towards the minus-end of microtubules. Our methodology enables computation in similar, large systems including protein binding to DNA, viruses, and membranes.