Simulating Biomolecular Machines: ATP Powered DNA Translocation in Helicases

描述（由申请人提供）：解旋酶蛋白诱导双链DNA （dsDNA）的双熔融。链切割是许多DNA相关细胞过程的关键步骤，包括转录、复制和修复。大多数解旋酶沿着单链DNA （ssDNA）转运，并诱导dsDNA/ssDNA连接处的DNA碱基对融化。转录等过程是通过将RNA碱基与现在分离的DNA碱基配对，在双链解绕之后完成的。沿DNA的易位和DNA碱基对的解绕都是由ATP水解驱动的。虽然人们对解旋酶沿DNA易位的机制给予了极大的关注，但对ATP水解、碱基对切割和沿DNA易位之间的耦合却缺乏充分的了解。解旋酶沿DNA运动的反应性和多尺度性质使其成为一个难以计算的问题。通过两种仿真方法的耦合和修改，可以在这个方向上取得重大进展。利用改进的多态经验价键（MS-EVB）方法可以明确地处理ATP水解反应。MS-EVB是一种用于处理水环境中质子转移的反应力场。然而，基本的方法是通用的，可以适应于处理许多化学反应。ATP水解产生的能量被解旋酶蛋白转化为有两个目的的机械能。第一种是诱导碱基对融化，第二种是沿着DNA主链移动。这种多尺度行为与过程的长时间尺度相结合，对标准原子或粗粒度分子动力学（MD）提出了挑战。多尺度粗粒化（MS-CG）技术是利用潜在的原子力系统地粗粒化一个系统。这允许在单个MD模拟中无缝集成多个长度尺度。结合MS-EVB和MS-CG技术将允许首次直接模拟解旋酶蛋白的水解驱动运动。

DESCRIPTION (provided by applicant): Helicase proteins induce duplex melting of double stranded DNA (dsDNA). Strand cleavage is a pivotal step in numerous DNA related cellular processes including transcription, replication and repair. Most helicases translocate along single stranded DNA (ssDNA) and induce melting of DNA base pairs at the dsDNA/ssDNA junction. Processes such as transcription are done subsequent to the unwinding of the duplex by pairing RNA bases to the now separated DNA base. Both translocation along DNA and unwinding of DNA base pairs are powered by ATP hydrolysis. While significant attention has been given to the mechanism of helicase translocation along DNA, a full understanding of the coupling between ATP hydrolysis, base pair cleavage and translocation along DNA is missing. The reactive and multi-scale nature of helicase motion along DNA makes it a difficult problem to approach computationally. Significant strides in this direction can be made with the coupling and modification of two simulation methods. The ATP hydrolysis reaction can be treated explicitly with the use of a modified multi-state empirical valence bond (MS-EVB) method. MS-EVB is a reactive force field developed to treat proton transfer in aqueous environments. The underlying method, however, is general and can be adapted to treat numerous chemical reactions. The energy from ATP hydrolysis is converted into mechanical work for two purposes by the helicase protein. The first is to induce base pair melting and the second is to move along the DNA backbone. This multi-scale behavior combined with the long time scale of the processes present a challenge for standard atomistic or coarse-grained (CG) molecular dynamics (MD). Multi-scale coarse graining (MS-CG) techniques exist to systematically coarse-grain a system using the underlying atomistic forces. This allows for seamless integration of multiple length scales in a single MD simulation. Combining MS-EVB and MS-CG techniques will allow for the first direct simulation of hydrolysis driven motion of helicase proteins. PUBLIC HEALTH RELEVANCE: Helicases are unique motor proteins involved in DNA replication, transcription and repair. Understanding the mechanism by which helicases translocate along the DNA backbone is pivotal to aiding in the design of targeted anti-cancer and anti-genetic disorder drugs. We propose novel computational methods to study the ATP hydrolysis energy transduction process of two helicase proteins.