RNA kink-turns are highly anisotropic with respect to lateral
displacement of the flanking stems

J 2022

RNA kink-turns are highly anisotropic with respect to lateral displacement of the flanking stems

MATOUSKOVA, Eva, Tomas DRSATA, Lucie PFEIFFEROVA, Jiri SPONER, Kamila RÉBLOVÁ et. al.

Basic information

Original name

RNA kink-turns are highly anisotropic with respect to lateral displacement of the flanking stems

Authors

MATOUSKOVA, Eva, Tomas DRSATA, Lucie PFEIFFEROVA, Jiri SPONER, Kamila RÉBLOVÁ (203 Czech Republic, guarantor, belonging to the institution) and Filip LANKAS

Edition

Biophysical Journal, Bethesda, USA, Biophysical Society, 2022, 0006-3495

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10610 Biophysics

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 3.400

RIV identification code

RIV/00216224:14740/22:00126464

Organization unit

Central European Institute of Technology

DOI

http://dx.doi.org/10.1016/j.bpj.2022.01.025

UT WoS

000765012800004

Keywords in English

Binding Sites; Molecular Dynamics Simulation; Nucleic Acid Conformation; Ribosomes; RNA

Abstract

V originále

Kink-turns are highly bent internal loop motifs commonly found in the ribosome and other RNA complexes. They frequently act as binding sites for proteins and mediate tertiary interactions in larger RNA structures. Kink-turns have been a topic of intense research, but their elastic properties in the folded state are still poorly understood. Here we use extensive all-atom molecular dynamics simulations to parameterize a model of kink-turn in which the two flanking helical stems are represented by effective rigid bodies. Time series of the full set of six interhelical coordinates enable us to extract minimum energy shapes and harmonic stiffness constants for kink-turns from different RNA functional classes. The analysis suggests that kink-turns exhibit isotropic bending stiffness but are highly anisotropic with respect to lateral displacement of the stems. The most flexible lateral displacement mode is perpendicular to the plane of the static bend. These results may help understand the structural adaptation and mechanical signal transmission by kink-turns in complex natural and artificial RNA structures.

Links

LM2018140, research and development project

Name: e-Infrastruktura CZ (Acronym: e-INFRA CZ)

Investor: Ministry of Education, Youth and Sports of the CR

Citovat

MATOUSKOVA, Eva, Tomas DRSATA, Lucie PFEIFFEROVA, Jiri SPONER, Kamila RÉBLOVÁ and Filip LANKAS. RNA kink-turns are highly anisotropic with respect to lateral displacement of the flanking stems. Biophysical Journal. Bethesda, USA: Biophysical Society, 2022, vol. 121, No 5, p. 705-714. ISSN 0006-3495. Available from: https://dx.doi.org/10.1016/j.bpj.2022.01.025.

@article{2212064,
   author = {Matouskova, Eva and Drsata, Tomas and Pfeifferova, Lucie and Sponer, Jiri and Réblová, Kamila and Lankas, Filip},
   article_location = {Bethesda, USA},
   article_number = {5},
   doi = {http://dx.doi.org/10.1016/j.bpj.2022.01.025},
   keywords = {Binding Sites; Molecular Dynamics Simulation; Nucleic Acid Conformation; Ribosomes; RNA},
   language = {eng},
   issn = {0006-3495},
   journal = {Biophysical Journal},
   title = {RNA kink-turns are highly anisotropic with respect to lateral displacement of the flanking stems},
   url = {https://www.sciencedirect.com/science/article/abs/pii/S0006349522000753?via%3Dihub},
   volume = {121},
   year = {2022}
}

TY  - JOUR
ID  - 2212064
AU  - Matouskova, Eva - Drsata, Tomas - Pfeifferova, Lucie - Sponer, Jiri - Réblová, Kamila - Lankas, Filip
PY  - 2022
TI  - RNA kink-turns are highly anisotropic with respect to lateral displacement of the flanking stems
JF  - Biophysical Journal
VL  - 121
IS  - 5
SP  - 705-714
EP  - 705-714
PB  - Biophysical Society
SN  - 00063495
KW  - Binding Sites
KW  - Molecular Dynamics Simulation
KW  - Nucleic Acid Conformation
KW  - Ribosomes
KW  - RNA
UR  - https://www.sciencedirect.com/science/article/abs/pii/S0006349522000753?via%3Dihub
N2  - Kink-turns are highly bent internal loop motifs commonly found in the ribosome and other RNA complexes. They frequently act as binding sites for proteins and mediate tertiary interactions in larger RNA structures. Kink-turns have been a topic of intense research, but their elastic properties in the folded state are still poorly understood. Here we use extensive all-atom molecular dynamics simulations to parameterize a model of kink-turn in which the two flanking helical stems are represented by effective rigid bodies. Time series of the full set of six interhelical coordinates enable us to extract minimum energy shapes and harmonic stiffness constants for kink-turns from different RNA functional classes. The analysis suggests that kink-turns exhibit isotropic bending stiffness but are highly anisotropic with respect to lateral displacement of the stems. The most flexible lateral displacement mode is perpendicular to the plane of the static bend. These results may help understand the structural adaptation and mechanical signal transmission by kink-turns in complex natural and artificial RNA structures.
ER  -

MATOUSKOVA, Eva, Tomas DRSATA, Lucie PFEIFFEROVA, Jiri SPONER, Kamila RÉBLOVÁ and Filip LANKAS. RNA kink-turns are highly anisotropic with respect to lateral displacement of the flanking stems. \textit{Biophysical Journal}. Bethesda, USA: Biophysical Society, 2022, vol.~121, No~5, p.~705-714. ISSN~0006-3495. Available from: https://dx.doi.org/10.1016/j.bpj.2022.01.025.

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