An RNA Molecular Switch: Intrinsic Flexibility of 23S rRNA
Helices 40 and 68 5 '-UAA/5 '-GAN Internal Loops Studied by
Molecular Dynamics Methods

J 2010

An RNA Molecular Switch: Intrinsic Flexibility of 23S rRNA Helices 40 and 68 5 '-UAA/5 '-GAN Internal Loops Studied by Molecular Dynamics Methods

RÉBLOVÁ, Kamila, Zora STŘELCOVÁ, Petr KULHÁNEK, Ivana BEŠŠEOVÁ, David H. MATHEWS et. al.

Basic information

Original name

An RNA Molecular Switch: Intrinsic Flexibility of 23S rRNA Helices 40 and 68 5 '-UAA/5 '-GAN Internal Loops Studied by Molecular Dynamics Methods

Authors

RÉBLOVÁ, Kamila (203 Czech Republic, guarantor), Zora STŘELCOVÁ (203 Czech Republic), Petr KULHÁNEK (203 Czech Republic), Ivana BEŠŠEOVÁ (703 Slovakia), David H. MATHEWS (840 United States of America), Keith VAN NOSTRAND (840 United States of America), Ilyas YILDIRIM (840 United States of America), Douglas H. TURNER (840 United States of America) and Jiří ŠPONER (203 Czech Republic)

Edition

Journal of Chemical Theory and Computation, 2010, 1549-9618

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10600 1.6 Biological sciences

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

Impact factor

Impact factor: 5.138

RIV identification code

RIV/00216224:14310/10:00043541

Organization unit

Faculty of Science

UT WoS

000275189400029

Keywords in English

molecular dynamics; free energy; RNA

Abstract

V originále

Functional RNA molecules such as ribosomal RNAs (rRNAs) frequently contain highly conserved internal loops with a 5'-UAA/5'-GAN (UAA/GAN) consensus sequence. The UAA/GAN internal loops adopt a distinctive structure inconsistent with secondary structure predictions. The solution structure of an isolated UAA/GAA internal loop shows substantially rearranged base pairing with three consecutive non-Watson-Crick base pairs. Its A/U base pair adopts an incomplete cis Watson-Crick/Sugar edge (dWS) A/U conformation instead of the expected Watson-Crick arrangement. We performed 3.1 mu s of explicit solvent molecular dynamics (MD) simulations of the X-ray and NMR UAA/GAN structures, supplemented by molecular mechanics, Poisson-Boltzmann, and surface area free energy calculations; locally enhanced sampling (LES) runs; targeted MD (TMD); and nudged elastic band (NEB) analysis. As results, the simulations confirm that the UAA/GAN internal loop is a molecular switch RNA module that adopts its functional geometry upon specific tertiary contexts.

Links

LC06030, research and development project

Name: Biomolekulární centrum

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

MSM0021622413, plan (intention)

Name: Proteiny v metabolismu a při interakci organismů s prostředím

Investor: Ministry of Education, Youth and Sports of the CR, Proteins in metabolism and interaction of organisms with the environment

205872, interní kód MU

Name: Program developing interdisciplinary research POtential for the STudies of BIOMolecular INteractions (Acronym: POSTBIOMIN)

Investor: European Union, Program developing interdisciplinary research POtential for the STudies of BIOMolecular INteractions, Capacities

Citovat

RÉBLOVÁ, Kamila, Zora STŘELCOVÁ, Petr KULHÁNEK, Ivana BEŠŠEOVÁ, David H. MATHEWS, Keith VAN NOSTRAND, Ilyas YILDIRIM, Douglas H. TURNER and Jiří ŠPONER. An RNA Molecular Switch: Intrinsic Flexibility of 23S rRNA Helices 40 and 68 5 '-UAA/5 '-GAN Internal Loops Studied by Molecular Dynamics Methods. Journal of Chemical Theory and Computation. 2010, vol. 2010, No 6, p. 910-929, 19 pp. ISSN 1549-9618.

@article{876971,
   author = {Réblová, Kamila and Střelcová, Zora and Kulhánek, Petr and Beššeová, Ivana and Mathews, David H. and Van Nostrand, Keith and Yildirim, Ilyas and Turner, Douglas H. and Šponer, Jiří},
   article_number = {6},
   keywords = {molecular dynamics; free energy; RNA},
   language = {eng},
   issn = {1549-9618},
   journal = {Journal of Chemical Theory and Computation},
   title = {An RNA Molecular Switch: Intrinsic Flexibility of 23S rRNA Helices 40 and 68 5 '-UAA/5 '-GAN Internal Loops Studied by Molecular Dynamics Methods},
   volume = {2010},
   year = {2010}
}

TY  - JOUR
ID  - 876971
AU  - Réblová, Kamila - Střelcová, Zora - Kulhánek, Petr - Beššeová, Ivana - Mathews, David H. - Van Nostrand, Keith - Yildirim, Ilyas - Turner, Douglas H. - Šponer, Jiří
PY  - 2010
TI  - An RNA Molecular Switch: Intrinsic Flexibility of 23S rRNA Helices 40 and 68 5 '-UAA/5 '-GAN Internal Loops Studied by Molecular Dynamics Methods
JF  - Journal of Chemical Theory and Computation
VL  - 2010
IS  - 6
SP  - 910-929
EP  - 910-929
SN  - 15499618
KW  - molecular dynamics
KW  - free energy
KW  - RNA
N2  - Functional RNA molecules such as ribosomal RNAs (rRNAs) frequently contain highly conserved internal loops with a 5'-UAA/5'-GAN (UAA/GAN) consensus sequence. The UAA/GAN internal loops adopt a distinctive structure inconsistent with secondary structure predictions. The solution structure of an isolated UAA/GAA internal loop shows substantially rearranged base pairing with three consecutive non-Watson-Crick base pairs. Its A/U base pair adopts an incomplete cis Watson-Crick/Sugar edge (dWS) A/U conformation instead of the expected Watson-Crick arrangement. We performed 3.1 mu s of explicit solvent molecular dynamics (MD) simulations of the X-ray and NMR UAA/GAN structures, supplemented by molecular mechanics, Poisson-Boltzmann, and surface area free energy calculations; locally enhanced sampling (LES) runs; targeted MD (TMD); and nudged elastic band (NEB) analysis. As results, the simulations confirm that the UAA/GAN internal loop is a molecular switch RNA module that adopts its functional geometry upon specific tertiary contexts.
ER  -

RÉBLOVÁ, Kamila, Zora STŘELCOVÁ, Petr KULHÁNEK, Ivana BEŠŠEOVÁ, David H. MATHEWS, Keith VAN NOSTRAND, Ilyas YILDIRIM, Douglas H. TURNER and Jiří ŠPONER. An RNA Molecular Switch: Intrinsic Flexibility of 23S rRNA Helices 40 and 68 5 '-UAA/5 '-GAN Internal Loops Studied by Molecular Dynamics Methods. \textit{Journal of Chemical Theory and Computation}. 2010, vol.~2010, No~6, p.~910-929, 19 pp. ISSN~1549-9618.

Detailed Information on Publication Record