rRNA C-Loops: Mechanical Properties of a Recurrent Structural Motif
| Authors | |
|---|---|
| Year of publication | 2017 |
| Type | Article in Periodical |
| Magazine / Source | Journal of Chemical Theory and Computation |
| MU Faculty or unit | |
| Citation | |
| Web | http://pubs.acs.org/doi/abs/10.1021/acs.jctc.7b00061 |
| Doi | http://dx.doi.org/10.1021/acs.jctc.7b00061 |
| Field | Physical chemistry and theoretical chemistry |
| Keywords | MOLECULAR-DYNAMICS SIMULATIONS; RESIDUAL DIPOLAR COUPLINGS; A-SITE FINGER; NUCLEIC-ACIDS; TOPOLOGICAL CONSTRAINTS; ISOSTERICITY MATRICES; SECONDARY STRUCTURE; FREE-ENERGY; BASE-PAIRS; TECTO-RNA |
| Description | 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. |
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