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• W2626341800 abstract "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." @default.
• W2626341800 created "2017-06-23" @default.
• W2626341800 creator A5004287173 @default.
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• W2626341800 creator A5026399646 @default.
• W2626341800 creator A5036301362 @default.
• W2626341800 date "2017-06-29" @default.
• W2626341800 modified "2023-10-16" @default.
• W2626341800 title "rRNA C-Loops: Mechanical Properties of a Recurrent Structural Motif" @default.
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• W2626341800 doi "https://doi.org/10.1021/acs.jctc.7b00061" @default.
• W2626341800 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/28617589" @default.
• W2626341800 hasPublicationYear "2017" @default.
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