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.

Základní údaje

Originální název

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

Autoři

RÉBLOVÁ, Kamila ; Zora STŘELCOVÁ; Petr KULHÁNEK; Ivana BEŠŠEOVÁ; David H. MATHEWS; Keith VAN NOSTRAND; Ilyas YILDIRIM; Douglas H. TURNER a Jiří ŠPONER

Vydání

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

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10600 1.6 Biological sciences

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Impakt faktor

Impact factor: 5.138

Označené pro přenos do RIV

Ano

Kód RIV

RIV/00216224:14310/10:00043541

Organizační jednotka

Přírodovědecká fakulta

UT WoS

000275189400029

Klíčová slova anglicky

molecular dynamics; free energy; RNA

Příznaky

Recenzováno

Změněno: 23. 3. 2010 15:52, RNDr. Petr Kulhánek, Ph.D.

Anotace

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.

Návaznosti

LC06030, projekt VaV

Název: Biomolekulární centrum

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Biomolekulární centrum

MSM0021622413, záměr

Název: Proteiny v metabolismu a při interakci organismů s prostředím

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Proteiny v metabolismu a při interakci organismů s prostředím

205872, interní kód MU

Název: Program developing interdisciplinary research POtential for the STudies of BIOMolecular INteractions (Akronym: POSTBIOMIN)

Investor: Evropská unie, Program developing interdisciplinary research POtential for the STudies of BIOMolecular INteractions, Kapacity

Citovat

RÉBLOVÁ, Kamila; Zora STŘELCOVÁ; Petr KULHÁNEK; Ivana BEŠŠEOVÁ; David H. MATHEWS; Keith VAN NOSTRAND; Ilyas YILDIRIM; Douglas H. TURNER a 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, roč. 2010, č. 6, s. 910-929, 19 s. 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 a 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, roč.~2010, č.~6, s.~910-929, 19 s. ISSN~1549-9618.

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