量子力学计算的粗粒双链RNA模型,The Journal of Physical Chemistry B

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量子力学计算的粗粒双链RNA模型
The Journal of Physical Chemistry B ( IF 2.8 ) Pub Date : 2018-08-08 , DOI: 10.1021/acs.jpcb.8b03566
Sergio Cruz-León _{1,

2} , Alvaro Vázquez-Mayagoitia ₃ , Simone Melchionna ₄ , Nadine Schwierz ₂ , Maria Fyta ₁

Affiliation

利用从量子力学计算获得的参数，开发了用于模拟双链RNA结构特性的粗粒度模型。该模型遵循先前对双链DNA的参数化，该参数化是基于将全原子图片映射到粗粒四珠方案的。RNA和DNA之间的化学和结构差异已被考虑用于模型开发。参数化基于使用密度泛函理论（DFT）对RNA分子的各个单元进行的模拟，而无需实现实验数据。总能量被分解为四个物理意义的术语：氢键相互作用，堆积相互作用，骨架相互作用和静电相互作用。前三个交互在DFT中处理，而最后一个则包含在平均场近似中。我们的双链RNA粗粒模型可预测RNA的稳定螺旋结构。其他特性（例如结构或机械特性）的复制精度很高。RNA粗粒度模型的开发允许扩展计算机仿真访问的空间和时间长度尺度，并能够对与RNA有关的生物物理过程以及新型RNA纳米结构进行建模。

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Coarse-Grained Double-Stranded RNA Model from Quantum-Mechanical Calculations

A coarse-grained model for simulating structural properties of double-stranded RNA is developed with parameters obtained from quantum-mechanical calculations. This model follows previous parametrization for double-stranded DNA, which is based on mapping the all-atom picture to a coarse-grained four-bead scheme. Chemical and structural differences between RNA and DNA have been taken into account for the model development. The parametrization is based on simulations using density functional theory (DFT) on separate units of the RNA molecule without implementing experimental data. The total energy is decomposed into four terms of physical significance: hydrogen bonding interaction, stacking interactions, backbone interactions, and electrostatic interactions. The first three interactions are treated within DFT, whereas the last one is included within a mean field approximation. Our double-stranded RNA coarse-grained model predicts stable helical structures for RNA. Other characteristics, such as structural or mechanical properties are reproduced with a very good accuracy. The development of the coarse-grained model for RNA allows extending the spatial and temporal length scales accessed by computer simulations and being able to model RNA-related biophysical processes, as well as novel RNA nanostructures.

更新日期：2018-08-08

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