rRNA C-Loops: Mechanical Properties of a Recurrent Structural Motif

Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61388963%3A_____%2F17%3A00477547" target="_blank" >RIV/61388963:_____/17:00477547 - isvavai.cz</a>
Alternative codes found
RIV/68081707:_____/17:00477547 RIV/00216224:14740/17:00098093 RIV/60461373:22310/17:43914588
Result on the web
<a href="http://dx.doi.org/10.1021/acs.jctc.7b00061" target="_blank" >http://dx.doi.org/10.1021/acs.jctc.7b00061</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1021/acs.jctc.7b00061" target="_blank" >10.1021/acs.jctc.7b00061</a>

Result language
angličtina
Original language name
rRNA C-Loops: Mechanical Properties of a Recurrent Structural Motif
Original language 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.
Czech name
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Czech description
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Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
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OECD FORD branch
10610 - Biophysics

Project
Result was created during the realization of more than one project. More information in the Projects tab.
Continuities
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Publication year
2017
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

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