rRNA C-Loops: Mechanical Properties of a Recurrent Structural Motif
Language English Country United States Media print-electronic
Document type Journal Article
- MeSH
- Entropy MeSH
- Escherichia coli genetics metabolism MeSH
- Nucleic Acid Conformation MeSH
- RNA, Ribosomal chemistry MeSH
- Molecular Dynamics Simulation MeSH
- Publication type
- Journal Article MeSH
- Names of Substances
- RNA, Ribosomal MeSH
C-loop is an internal loop motif found in the ribosome and used in artificial nanostructures. While its geometry has been partially characterized, its mechanical properties remain elusive. Here we propose a method to evaluate global shape and stiffness of an internal loop. The loop is flanked by short A-RNA helices modeled as rigid bodies. Their relative rotation and displacement are fully described by six interhelical coordinates. The deformation energy of the loop is assumed to be a general quadratic function of the interhelical coordinates. The model parameters for isolated C-loops are inferred from unrestrained all-atom molecular dynamics simulations. C-loops exhibit high twist as reported earlier, but also a bend and a lateral displacement of the flanking helices. Their bending stiffness and lateral displacement stiffness are nearly isotropic and similar to the control A-RNA duplexes. Nevertheless, we found systematic variations with the C-loop position in the ribosome and the organism of origin. The results characterize global properties of C-loops in the full six-dimensional interhelical space and enable one to choose an optimally stiff C-loop for use in a nanostructure. Our approach can be readily applied to other internal loops and extended to more complex structural motifs.
References provided by Crossref.org
RNA kink-turns are highly anisotropic with respect to lateral displacement of the flanking stems
The temperature dependence of the helical twist of DNA
RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview
