Noncanonical Hydrogen Bonding in Nucleic Acids. Benchmark
Evaluation of Key Base-Phosphate Interactions in Folded RNA
Molecules Using Quantum-Chemical Calculations and Molecular
Dynamics Simulations

J 2011

Noncanonical Hydrogen Bonding in Nucleic Acids. Benchmark Evaluation of Key Base-Phosphate Interactions in Folded RNA Molecules Using Quantum-Chemical Calculations and Molecular Dynamics Simulations

ZGARBOVA, Marie, Petr JUREČKA, Pavel BANÁŠ, Michal OTYEPKA, Judit ŠPONEROVÁ et. al.

Basic information

Original name

Noncanonical Hydrogen Bonding in Nucleic Acids. Benchmark Evaluation of Key Base-Phosphate Interactions in Folded RNA Molecules Using Quantum-Chemical Calculations and Molecular Dynamics Simulations

Authors

ZGARBOVA, Marie (203 Czech Republic), Petr JUREČKA (203 Czech Republic), Pavel BANÁŠ (203 Czech Republic), Michal OTYEPKA (203 Czech Republic), Judit ŠPONEROVÁ (348 Hungary, belonging to the institution), Neocles B. LEONTIS (840 United States of America), Craig L. ZIRBEL (840 United States of America) and Jiří ŠPONER (203 Czech Republic, guarantor, belonging to the institution)

Edition

JOURNAL OF PHYSICAL CHEMISTRY A, Washington, American Chemical Society, 2011, 1089-5639

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: 2.946

RIV identification code

RIV/00216224:14740/11:00050559

Organization unit

Central European Institute of Technology

DOI

http://dx.doi.org/10.1021/jp204820b

UT WoS

000295700600019

Keywords in English

DENSITY-FUNCTIONAL THEORY; LARGE RIBOSOMAL-SUBUNIT; GAUSSIAN-BASIS SETS; INTERMOLECULAR INTERACTION ENERGIES; TRANSITION-STATE STABILIZATION; AB-INITIO CALCULATIONS; ACTIVE-SITE; WATSON-CRICK; HAIRPIN RIBOZYME; TERTIARY INTERACTIONS

Abstract

V originále

RNA molecules are stabilized by a wide range of non canonical interactions that are not present in DNA. Among them, the recently classified base phosphate (BPh) interactions belong to the most important ones. Twelve percent of nucleotides in the ribosomal crystal structures are involved in BPh interactions. BPh interactions are highly conserved and provide major constraints on RNA sequence evolution. Here we provide assessment of the energetics of BPh interactions using MP2 computations extrapolated to the complete basis set of atomic orbitals and corrected for higher-order electron correlation effects. The reference computations are compared with DFT-D and DFT-D3 approaches, the SAPT method, and the molecular mechanics force field. The computations, besides providing the basic benchmark for the BPh interactions, allow some refinements of the original classification, including identification of some potential doubly bonded BPh patterns. The reference computations are followed by analysis of some larger RNA fragments that consider the context of the BPh interactions. The computations demonstrate the complexity of interaction patterns utilizing the BPh interactions in real RNA structures. The BPh interactions are often involved in intricate interaction networks. We studied BPh interactions of protonated adenine that can contribute to catalysis of hairpin ribozyme, the key BPh interaction in the S-turn motif of the sarcin ricin loop, which may predetermine the S-turn topology and complex BPh patterns-from the glmS riboswitch. Finally, the structural stability of BPh interactions in explicit solvent molecular dynamics simulations is assessed. The simulations well preserve key BPh interactions and allow dissection of structurally/functionally important water-meditated BPh bridges, which could not be considered in earlier bioinformatics classification of BPh interactions.

Links

ED1.1.00/02.0068, research and development project

Name: CEITEC - central european institute of technology

GD203/09/H046, research and development project

Name: Biochemie na rozcestí mezi in silico a in vitro

Investor: Czech Science Foundation

LC06030, research and development project

Name: Biomolekulární centrum

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

Citovat

ZGARBOVA, Marie, Petr JUREČKA, Pavel BANÁŠ, Michal OTYEPKA, Judit ŠPONEROVÁ, Neocles B. LEONTIS, Craig L. ZIRBEL and Jiří ŠPONER. Noncanonical Hydrogen Bonding in Nucleic Acids. Benchmark Evaluation of Key Base-Phosphate Interactions in Folded RNA Molecules Using Quantum-Chemical Calculations and Molecular Dynamics Simulations. JOURNAL OF PHYSICAL CHEMISTRY A. Washington: American Chemical Society, 2011, vol. 115, No 41, p. 11277-11292. ISSN 1089-5639. Available from: https://dx.doi.org/10.1021/jp204820b.

@article{975017,
   author = {Zgarbova, Marie and Jurečka, Petr and Banáš, Pavel and Otyepka, Michal and Šponerová, Judit and Leontis, Neocles B. and Zirbel, Craig L. and Šponer, Jiří},
   article_location = {Washington},
   article_number = {41},
   doi = {http://dx.doi.org/10.1021/jp204820b},
   keywords = {DENSITY-FUNCTIONAL THEORY; LARGE RIBOSOMAL-SUBUNIT; GAUSSIAN-BASIS SETS; INTERMOLECULAR INTERACTION ENERGIES; TRANSITION-STATE STABILIZATION; AB-INITIO CALCULATIONS; ACTIVE-SITE; WATSON-CRICK; HAIRPIN RIBOZYME; TERTIARY INTERACTIONS},
   language = {eng},
   issn = {1089-5639},
   journal = {JOURNAL OF PHYSICAL CHEMISTRY A},
   title = {Noncanonical Hydrogen Bonding in Nucleic Acids. Benchmark Evaluation of Key Base-Phosphate Interactions in Folded RNA Molecules Using Quantum-Chemical Calculations and Molecular Dynamics Simulations},
   volume = {115},
   year = {2011}
}

TY  - JOUR
ID  - 975017
AU  - Zgarbova, Marie - Jurečka, Petr - Banáš, Pavel - Otyepka, Michal - Šponerová, Judit - Leontis, Neocles B. - Zirbel, Craig L. - Šponer, Jiří
PY  - 2011
TI  - Noncanonical Hydrogen Bonding in Nucleic Acids. Benchmark Evaluation of Key Base-Phosphate Interactions in Folded RNA Molecules Using Quantum-Chemical Calculations and Molecular Dynamics Simulations
JF  - JOURNAL OF PHYSICAL CHEMISTRY A
VL  - 115
IS  - 41
SP  - 11277-11292
EP  - 11277-11292
PB  - American Chemical Society
SN  - 10895639
KW  - DENSITY-FUNCTIONAL THEORY
KW  - LARGE RIBOSOMAL-SUBUNIT
KW  - GAUSSIAN-BASIS SETS
KW  - INTERMOLECULAR INTERACTION ENERGIES
KW  - TRANSITION-STATE STABILIZATION
KW  - AB-INITIO CALCULATIONS
KW  - ACTIVE-SITE
KW  - WATSON-CRICK
KW  - HAIRPIN RIBOZYME
KW  - TERTIARY INTERACTIONS
N2  - RNA molecules are stabilized by a wide range of non canonical interactions that are not present in DNA. Among them, the recently classified base phosphate (BPh) interactions belong to the most important ones. Twelve percent of nucleotides in the ribosomal crystal structures are involved in BPh interactions. BPh interactions are highly conserved and provide major constraints on RNA sequence evolution. Here we provide assessment of the energetics of BPh interactions using MP2 computations extrapolated to the complete basis set of atomic orbitals and corrected for higher-order electron correlation effects. The reference computations are compared with DFT-D and DFT-D3 approaches, the SAPT method, and the molecular mechanics force field. The computations, besides providing the basic benchmark for the BPh interactions, allow some refinements of the original classification, including identification of some potential doubly bonded BPh patterns. The reference computations are followed by analysis of some larger RNA fragments that consider the context of the BPh interactions. The computations demonstrate the complexity of interaction patterns utilizing the BPh interactions in real RNA structures. The BPh interactions are often involved in intricate interaction networks. We studied BPh interactions of protonated adenine that can contribute to catalysis of hairpin ribozyme, the key BPh interaction in the S-turn motif of the sarcin ricin loop, which may predetermine the S-turn topology and complex BPh patterns-from the glmS riboswitch. Finally, the structural stability of BPh interactions in explicit solvent molecular dynamics simulations is assessed. The simulations well preserve key BPh interactions and allow dissection of structurally/functionally important water-meditated BPh bridges, which could not be considered in earlier bioinformatics classification of BPh interactions.
ER  -

ZGARBOVA, Marie, Petr JUREČKA, Pavel BANÁŠ, Michal OTYEPKA, Judit ŠPONEROVÁ, Neocles B. LEONTIS, Craig L. ZIRBEL and Jiří ŠPONER. Noncanonical Hydrogen Bonding in Nucleic Acids. Benchmark Evaluation of Key Base-Phosphate Interactions in Folded RNA Molecules Using Quantum-Chemical Calculations and Molecular Dynamics Simulations. \textit{JOURNAL OF PHYSICAL CHEMISTRY A}. Washington: American Chemical Society, 2011, vol.~115, No~41, p.~11277-11292. ISSN~1089-5639. Available from: https://dx.doi.org/10.1021/jp204820b.

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