新隐式溶剂模型下的B型RNA模拟  

Simulation of B-form RNA Duplex with A Novel Implicit Solvent Model

作　　者：刘裕峰 龚海鹏[1] 

机构地区：[1]清华大学生命学院,北京10084

出　　处：《生命科学仪器》2014年第5期30-33,共4页Life Science Instruments

基　　金：高等学校博士学科点专项科研基金新教师基金(20100002120001)

摘　　要：分子动力学模拟是研究包括RNA在内的生物大分子结构和功能的重要方法,但常规的显式溶剂模拟耗时较长,影响了其进一步应用。隐式溶剂模型通过用连续模型代替溶剂分子,能大大加速模拟速度,因此提高模拟效率。然而,现有的隐式溶剂模型都不能很好地描述核酸分子,尤其是RNA。在之前的研究中(已接收),我们提出了一个新的隐式溶剂模型,并分别测试了A型RNA双螺旋、28S r RNA和t RNA等多个系统,验证了该模型可以更好地计算隐式溶剂下的静电相互作用。由于上述系统均以稳定的结构作为起始,因此没有采集到大的构象变化。在本文中,我们将采用B型RNA双螺旋(B-RNA)作为测试系统来验证该模型是否能正确地采集到大尺度的构象转变过程。初步结果表明,在我们的模型下,B-RNA不仅能够正确地采集A型RNA双链构象,而且其搜索速度也比相应的显式模型快。Molecular dynamic simulation is an indispensible method for structural and functional study of biomolecules, including RNA. However, the commonly used explicit solvent models are computationally expensive, which hinders their further application. On the other hand, implicit solvent model, which implicitly describes the solvent molecules using theoretical continuum model, can accelerate the simulation and improve the effi ciency substantially. Nevertheless, current implicit models could not simulate the nucleic acids well, especially for RNA molecules. In our previous research（Accepted, in press）, we proposed a novel implicit solvent model, and illustrated its better estimation of electrostatics interactions compared with other counterpart models, based on the simulation results on three systems including A-form RNA duplex, 28 S r RNA and t RNA. The solute or target molecules in those systems start either from the canonical conformation or crystal structures, therefore did not sample large conformational changes during the process. In this work, we adopted the relatively unstable B-type RNA duplex as the testing system, to see whether our model can correctly sample the B- to A-form duplex transition. The preliminary results indicate that our model can not only successfully reproduce the conformational transition, but also observe the transition within shorter timescale than the explicit solvent model.

关 键 词：分子动力学模拟 B型RNA 隐式溶剂模型 

分 类 号：Q522[生物学—生物化学]