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

Kód výsledku v 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>

Nalezeny alternativní kódy

RIV/68081707:_____/17:00477547 RIV/00216224:14740/17:00098093 RIV/60461373:22310/17:43914588

Výsledek na webu

<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>

Jazyk výsledku

angličtina

Název v původním jazyce

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

Popis výsledku v původním jazyce

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.

Název v anglickém jazyce

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

Popis výsledku anglicky

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.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10610 - Biophysics

Projekt

Výsledek vznikl pri realizaci vícero projektů. Více informací v záložce Projekty.

Návaznosti

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Rok uplatnění

2017

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

Journal of Chemical Theory and Computation

ISSN

1549-9618

e-ISSN

—

Svazek periodika

13

Číslo periodika v rámci svazku

7

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

13

Strana od-do

3359-3371

Kód UT WoS článku

000405535600025

EID výsledku v databázi Scopus

2-s2.0-85023192414