Computational Investigation of RNA CUG Repeats Responsible for Myotonic Dystrophy 1

Ilyas Yildirim, Debayan Chakraborty, Matthew D. Disney, David J. Wales, George C Schatz

Research output: Contribution to journalArticle

11 Citations (Scopus)

Abstract

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 虠 anti-anti transformation pathways. Although at room temperature the syn-anti 虠 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.

Original languageEnglish
Pages (from-to)4943-4958
Number of pages16
JournalJournal of Chemical Theory and Computation
Volume11
Issue number10
DOIs
Publication statusPublished - Aug 28 2015

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RNA
sampling
Sampling
Molecular dynamics
molecular dynamics
Conformations
Molecules
nucleotides
Computer simulation
Nucleotides
biology
Structural properties
molecules
drugs
DNA
Thermodynamic properties
deoxyribonucleic acid
simulation
thermodynamic properties
Crystal structure

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Computer Science Applications

Cite this

Computational Investigation of RNA CUG Repeats Responsible for Myotonic Dystrophy 1. / Yildirim, Ilyas; Chakraborty, Debayan; Disney, Matthew D.; Wales, David J.; Schatz, George C.

In: Journal of Chemical Theory and Computation, Vol. 11, No. 10, 28.08.2015, p. 4943-4958.

Research output: Contribution to journalArticle

Yildirim, Ilyas ; Chakraborty, Debayan ; Disney, Matthew D. ; Wales, David J. ; Schatz, George C. / Computational Investigation of RNA CUG Repeats Responsible for Myotonic Dystrophy 1. In: Journal of Chemical Theory and Computation. 2015 ; Vol. 11, No. 10. pp. 4943-4958.
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abstract = "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 虠 anti-anti transformation pathways. Although at room temperature the syn-anti 虠 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.",
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