A two-dimensional replica-exchange molecular dynamics method for simulating RNA folding using sparse experimental restraints
A two-dimensional replica-exchange molecular dynamics method for simulating RNA folding using sparse experimental restraints
复制标题
DOI：
10.1016/j.ymeth.2019.05.001
复制
发表时间：
2019-06-01
期刊：
影响因子：
4.8
通讯作者：
Chen, Alan A.
中科院分区：
文献类型：
--
作者：
Ebrahimi, Parisa;Kaur, Simi;Chen, Alan A.
我们提出了一个包含二级结构信息的2D副本交换协议，使用分子动力学模拟显着改善3D RNA折叠。我们表明，将碱基配对约束纳入全原子，显式溶剂模拟可以准确再现4种代表性RNA的全球三级折叠，长度从24到68 nt不等。这种方法可以利用来自各种实验输入的碱基配对信息来预测复杂的RNA三级折叠，包括假结、多环结和非规范相互作用。
We present a 2D replica exchange protocol incorporating secondary structure information to dramatically improve 3D RNA folding using molecular dynamics simulations. We show that incorporating base-pairing restraints into all-atom, explicit solvent simulations enables the accurate recapitulation of the global tertiary fold for 4 representative RNAs ranging in length from 24 to 68 nt. This method can potentially utilize base-pairing information from a wide variety of experimental inputs to predict complex RNA tertiary folds including pseudoknots, multi-loop junctions, and non-canonical interactions.