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.

Basic information

Original name

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

Authors

RÉBLOVÁ, Kamila (203 Czech Republic), Judit ŠPONEROVÁ (348 Hungary, belonging to the institution), Naděžda ŠPAČKOVÁ (203 Czech Republic), Ivana BEŠŠEOVÁ (703 Slovakia) and Jiří ŠPONER (203 Czech Republic, guarantor, belonging to the institution)

Edition

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

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10403 Physical chemistry

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

Impact factor

Impact factor: 3.696

RIV identification code

RIV/00216224:14740/11:00056001

Organization unit

Central European Institute of Technology

DOI

http://dx.doi.org/10.1021/jp2065584

UT WoS

000297195400013

Keywords in English

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

Abstract

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.

Links

ED1.1.00/02.0068, research and development project

Name: CEITEC - central european institute of technology

LC06030, research and development project

Name: Biomolekulární centrum

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

Citovat

RÉBLOVÁ, Kamila, Judit ŠPONEROVÁ, Naděžda ŠPAČKOVÁ, Ivana BEŠŠEOVÁ and 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, vol. 115, No 47, p. 13897-13910. ISSN 1520-6106. Available from: https://dx.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 = {http://dx.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 and 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, vol.~115, No~47, p.~13897-13910. ISSN~1520-6106. Available from: https://dx.doi.org/10.1021/jp2065584.

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