A Dynamic Structural Model of Expanded RNA CAG Repeats: A Refined X-ray Structure and Computational Investigations Using Molecular Dynamics and Umbrella Sampling Simulations
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- 作者：Ilyas Yildirim ; HaJeung Park ; Matthew D. Disney ; George C. Schatz
- 刊名：The Journal of the American Chemical Society
- 出版年：2013
- 出版时间：March 6, 2013
- 年：2013
- 卷：135
- 期：9
- 页码：3528-3538
- 全文大小：713K
- 年卷期：v.135,no.9(March 6, 2013)
- ISSN：1520-5126
文摘
One class of functionally important RNA is repeating transcripts that cause disease through various mechanisms. For example, expanded CAG repeats can cause Huntington鈥檚 and other disease through translation of toxic proteins. Herein, a crystal structure of r[5鈥?u class="uu">UUGGGC(CAG)3GUCC]2, a model of CAG expanded transcripts, refined to 1.65 脜 resolution is disclosed that shows both anti鈥揳nti and syn鈥揳nti orientations for 1 脳 1 nucleotide AA internal loops. Molecular dynamics (MD) simulations using AMBER force field in explicit solvent were run for over 500 ns on the model systems r(5鈥睪CGCAGCGC)2 (MS1) and r(5鈥睠CGCAGCGG)2 (MS2). In these MD simulations, both anti鈥揳nti and syn鈥揳nti AA base pairs appear to be stable. While anti鈥揳nti AA base pairs were dynamic and sampled multiple anti鈥揳nti conformations, no syn鈥揳nti 鈫?anti鈥揳nti transformations were observed. Umbrella sampling simulations were run on MS2, and a 2D free energy surface was created to extract transformation pathways. In addition, an explicit solvent MD simulation over 800 ns was run on r[5鈥睪GGC(CAG)3GUCC]2, which closely represents the refined crystal structure. One of the terminal AA base pairs (syn鈥揳nti conformation), transformed to anti鈥揳nti conformation. The pathway followed in this transformation was the one predicted by umbrella sampling simulations. Further analysis showed a binding pocket near AA base pairs in syn鈥揳nti conformations. Computational results combined with the refined crystal structure show that global minimum conformation of 1 脳 1 nucleotide AA internal loops in r(CAG) repeats is anti鈥揳nti but can adopt syn鈥揳nti depending on the environment. These results are important to understand RNA dynamic-function relationships and to develop small molecules that target RNA dynamic ensembles.