A-Minor Tertiary Interactions in RNA Kink-Turns. Molecular
Dynamics and Quantum Chemical Analysis

J 2011

A-Minor Tertiary Interactions in RNA Kink-Turns. Molecular Dynamics and Quantum Chemical Analysis

RÉBLOVÁ, Kamila; Judit ŠPONEROVÁ; Naděžda ŠPAČKOVÁ; Ivana BEŠŠEOVÁ; Jiří ŠPONER et al.

Základní údaje

Originální název

A-Minor Tertiary Interactions in RNA Kink-Turns. Molecular Dynamics and Quantum Chemical Analysis

Autoři

RÉBLOVÁ, Kamila ; Judit ŠPONEROVÁ; Naděžda ŠPAČKOVÁ; Ivana BEŠŠEOVÁ a Jiří ŠPONER

Vydání

JOURNAL OF PHYSICAL CHEMISTRY B, Washington, American Chemical Society, 2011, 1520-6106

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10403 Physical chemistry

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Impakt faktor

Impact factor: 3.696

Označené pro přenos do RIV

Ano

Kód RIV

RIV/00216224:14740/11:00056001

Organizační jednotka

Středoevropský technologický institut

DOI

https://doi.org/10.1021/jp2065584

UT WoS

000297195400013

Klíčová slova anglicky

EDGE BASE-PAIRS; BOX C/D RNA; NUCLEIC-ACIDS; INTERACTION POTENTIALS; ISOSTERICITY MATRICES; STRUCTURAL DYNAMICS; CRYSTAL-STRUCTURE; FORCE-FIELD; BASIS-SETS; SIMULATIONS

Štítky

ok, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 12. 3. 2012 22:50, Olga Křížová

Anotace

V originále

The RNA kink-turn is an important recurrent RNA motif; an internal loop with characteristic consensus sequence forming highly conserved three-dimensional structure. Functional arrangement of RNA kink-turns shows a sharp bend in the phosphodiester backbone. Among other signature interactions, kink-turns form A-minor interaction between their two stems. Most kink-turns possess extended A-minor I (A-I) interaction where adenine of the second A center dot G base pair of the NC-stem interacts with the first canonical pair of the C-stem (i.e., the receptor pair) via trans-sugar-edge/sugar-edge (tSS) and cis-sugar-edge/sugar-edge (cSS) interactions. The remaining kink-turns have less compact A-minor 0 (A-0) interaction with just one tSS contact. We show that kink-turns with A-I in ribosomal X-ray structures keep G=C receptor base pair during evolution while the inverted pair (C=G) is not realized. In contrast, kink-turns with A-0 in the observed structures alternate G=C and C=G base pairs in sequences. We carried out an extended set (similar to 5 mu s) of explicit-solvent molecular dynamics simulations of kink-turns to rationalize this structural/evolutionary pattern. The simulations were done using a net-neutral Na(+) cation atmosphere (with similar to 0.25 M cation concentration) supplemented by simulations with either excess salt KCl atmosphere or inclusion of Mg(2+). The results do not seem to depend on the treatment of ions. The simulations started with X-ray structures of several kink-turns while we tested the response of the simulated system to base substitutions, modest structural perturbations and constraints. Quantum-chemical calculations on all four A-minor triples suggest that there is a different balance of electrostatic and dispersion stabilization in the A-I/G=C and A-I/C=G triples, which may explain different behavior of these otherwise isosteric triples in the context of kink-turns.

Návaznosti

ED1.1.00/02.0068, projekt VaV

Název: CEITEC - central european institute of technology

LC06030, projekt VaV

Název: Biomolekulární centrum

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

Citovat

RÉBLOVÁ, Kamila; Judit ŠPONEROVÁ; Naděžda ŠPAČKOVÁ; Ivana BEŠŠEOVÁ a Jiří ŠPONER. A-Minor Tertiary Interactions in RNA Kink-Turns. Molecular Dynamics and Quantum Chemical Analysis. JOURNAL OF PHYSICAL CHEMISTRY B. Washington: American Chemical Society, 2011, roč. 115, č. 47, s. 13897-13910. ISSN 1520-6106. Dostupné z: https://doi.org/10.1021/jp2065584.

@article{975008,
   author = {Réblová, Kamila and Šponerová, Judit and Špačková, Naděžda and Beššeová, Ivana and Šponer, Jiří},
   article_location = {Washington},
   article_number = {47},
   doi = {https://doi.org/10.1021/jp2065584},
   keywords = {EDGE BASE-PAIRS; BOX C/D RNA; NUCLEIC-ACIDS; INTERACTION POTENTIALS; ISOSTERICITY MATRICES; STRUCTURAL DYNAMICS; CRYSTAL-STRUCTURE; FORCE-FIELD; BASIS-SETS; SIMULATIONS},
   language = {eng},
   issn = {1520-6106},
   journal = {JOURNAL OF PHYSICAL CHEMISTRY B},
   title = {A-Minor Tertiary Interactions in RNA Kink-Turns. Molecular Dynamics and Quantum Chemical Analysis},
   volume = {115},
   year = {2011}
}

TY  - JOUR
ID  - 975008
AU  - Réblová, Kamila - Šponerová, Judit - Špačková, Naděžda - Beššeová, Ivana - Šponer, Jiří
PY  - 2011
TI  - A-Minor Tertiary Interactions in RNA Kink-Turns. Molecular Dynamics and Quantum Chemical Analysis
JF  - JOURNAL OF PHYSICAL CHEMISTRY B
VL  - 115
IS  - 47
SP  - 13897-13910
EP  - 13897-13910
PB  - American Chemical Society
SN  - 15206106
KW  - EDGE BASE-PAIRS
KW  - BOX C/D RNA
KW  - NUCLEIC-ACIDS
KW  - INTERACTION POTENTIALS
KW  - ISOSTERICITY MATRICES
KW  - STRUCTURAL DYNAMICS
KW  - CRYSTAL-STRUCTURE
KW  - FORCE-FIELD
KW  - BASIS-SETS
KW  - SIMULATIONS
N2  - The RNA kink-turn is an important recurrent RNA motif; an internal loop with characteristic consensus sequence forming highly conserved three-dimensional structure. Functional arrangement of RNA kink-turns shows a sharp bend in the phosphodiester backbone. Among other signature interactions, kink-turns form A-minor interaction between their two stems. Most kink-turns possess extended A-minor I (A-I) interaction where adenine of the second A center dot G base pair of the NC-stem interacts with the first canonical pair of the C-stem (i.e., the receptor pair) via trans-sugar-edge/sugar-edge (tSS) and cis-sugar-edge/sugar-edge (cSS) interactions. The remaining kink-turns have less compact A-minor 0 (A-0) interaction with just one tSS contact. We show that kink-turns with A-I in ribosomal X-ray structures keep G=C receptor base pair during evolution while the inverted pair (C=G) is not realized. In contrast, kink-turns with A-0 in the observed structures alternate G=C and C=G base pairs in sequences. We carried out an extended set (similar to 5 mu s) of explicit-solvent molecular dynamics simulations of kink-turns to rationalize this structural/evolutionary pattern. The simulations were done using a net-neutral Na(+) cation atmosphere (with similar to 0.25 M cation concentration) supplemented by simulations with either excess salt KCl atmosphere or inclusion of Mg(2+). The results do not seem to depend on the treatment of ions. The simulations started with X-ray structures of several kink-turns while we tested the response of the simulated system to base substitutions, modest structural perturbations and constraints. Quantum-chemical calculations on all four A-minor triples suggest that there is a different balance of electrostatic and dispersion stabilization in the A-I/G=C and A-I/C=G triples, which may explain different behavior of these otherwise isosteric triples in the context of kink-turns.
ER  -

RÉBLOVÁ, Kamila; Judit ŠPONEROVÁ; Naděžda ŠPAČKOVÁ; Ivana BEŠŠEOVÁ a Jiří ŠPONER. A-Minor Tertiary Interactions in RNA Kink-Turns. Molecular Dynamics and Quantum Chemical Analysis. \textit{JOURNAL OF PHYSICAL CHEMISTRY B}. Washington: American Chemical Society, 2011, roč.~115, č.~47, s.~13897-13910. ISSN~1520-6106. Dostupné z: https://doi.org/10.1021/jp2065584.

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