Computational Investigation of RNA CUG repeats responsible for Myotonic Dystrophy 1
Disney, Matthew D
Schatz, George C
Journal of Chemical Theory and Computation
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Yildirim, I., Chakraborty, D., Disney, M. D., Wales, D., & Schatz, G. C. (2015). Computational Investigation of RNA CUG repeats responsible for Myotonic Dystrophy 1. Journal of Chemical Theory and Computation, 11 4943-4958. https://doi.org/10.1021/acs.jctc.5b00728
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 1×1 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 1×1 UU internal loops. In this contribution we employ regular and umbrella sampling molecular dynamics (MD) simulations to describe the structural and thermodynamic properties of 1×1 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 1×1 UU RNA internal loops, revealing that 1×1 UU base pairs are dynamic and strongly prefer the anti-anti conformation. Two 2D PMF surfaces were calculated for the 1×1 UU base pairs, revealing several local minima and three syn-anti↔anti-anti transformation pathways. Although at room temperature the syn-anti↔anti-anti transformation is not observed on the MD time scale, one of these pathways dominates the dynamics of the 1×1 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.
Triplet disease, Myotonic Dystrophy 1, RNA CUG, small molecule, DM1, RNA loop dynamics, molecular dynamics simulations, umbrella sampling, energy landscapes, discrete path sampling
Computations were done in Advanced Research Computing (QUEST) at the Northwestern University, and Theory Group Computing Clusters at the University of Cambridge. This work was supported by the National Science Foundation Grant CHE-1147335) (GCS), PS-OC Center of the NIH/NCI Grant 1U54CA143869-01 (GCS), NIH Grant R01GM097455 (MDD), Muscular Dystrophy Association Grant 254929 (MDD), and the EPSRC Grant EP/I001352/1 (DJW), and the ERC Grant RG59508 (DJW). DC acknowledges financial support from the Cambridge Commonwealth European and International Trust.
European Research Council (267369)
External DOI: https://doi.org/10.1021/acs.jctc.5b00728
This record's URL: https://www.repository.cam.ac.uk/handle/1810/250469
Attribution 2.0 UK: England & Wales
Licence URL: http://creativecommons.org/licenses/by/2.0/uk/