Computational Investigation of RNA CUG Repeats Responsible for Myotonic Dystrophy 1

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• 作者：Ilyas Yildirim ; Debayan Chakraborty ; Matthew D. Disney ; David J. Wales ; George C. Schatz
• 刊名：Journal of Chemical Theory and Computation
• 出版年：2015
• 出版时间：October 13, 2015
• 年：2015
• 卷：11
• 期：10
• 页码：4943-4958
• 全文大小：1200K
• ISSN：1549-9626

文摘

Myotonic Dystrophy 1 (DM1) is a genetic disease caused by expansion of CTG repeats in DNA. Once transcribed, these repeats form RNA hairpins with repeating 1脳1 nucleotide UU internal loop motifs, r(CUG)_n, which attract muscleblind-like 1 (MBNL1) protein leading to the disease. In DM1 CUG can be repeated thousands of times, so these structures are intractable to characterization using structural biology. However, inhibition of MBNL1-r(CUG)_n binding requires a detailed analysis of the 1脳1 UU internal loops. In this contribution we employ regular and umbrella sampling molecular dynamics (MD) simulations to describe the structural and thermodynamic properties of 1脳1 UU internal loops. Calculations were run on a reported crystal structure and a designed system, which mimics an infinitely long RNA molecule with continuous CUG repeats. Two-dimensional (2D) potential of mean force (PMF) surfaces were created by umbrella sampling, and the discrete path sampling (DPS) method was utilized to investigate the energy landscape of 1脳1 UU RNA internal loops, revealing that 1脳1 UU base pairs are dynamic and strongly prefer the anti鈥?i>anti conformation. Two 2D PMF surfaces were calculated for the 1脳1 UU base pairs, revealing several local minima and three syn鈥?i>anti 鈫?anti鈥?i>anti transformation pathways. Although at room temperature the syn鈥?i>anti 鈫?anti鈥?i>anti transformation is not observed on the MD time scale, one of these pathways dominates the dynamics of the 1脳1 UU base pairs in temperature jump MD simulations. This mechanism has now been treated successfully using the DPS approach. Our results suggest that local minima predicted by umbrella sampling calculations could be stabilized by small molecules, which is of great interest for future drug design. Furthermore, distorted GC/CG conformations may be important in understanding how MBNL1 binds to RNA CUG repeats. Hence we provide new insight into the dynamic roles of RNA loops and their contributions to presently incurable diseases.