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.

Základní údaje

Originální název

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

Autoři

ZGARBOVA, Marie (203 Česká republika), Petr JUREČKA (203 Česká republika), Pavel BANÁŠ (203 Česká republika), Michal OTYEPKA (203 Česká republika), Judit ŠPONEROVÁ (348 Maďarsko, domácí), Neocles B. LEONTIS (840 Spojené státy), Craig L. ZIRBEL (840 Spojené státy) a Jiří ŠPONER (203 Česká republika, garant, domácí)

Vydání

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

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: 2.946

Kód RIV

RIV/00216224:14740/11:00050559

Organizační jednotka

Středoevropský technologický institut

DOI

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

UT WoS

000295700600019

Klíčová slova anglicky

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

Štítky

ok, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 27. 3. 2012 23:44, Olga Křížová

Anotace

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.

Návaznosti

ED1.1.00/02.0068, projekt VaV

Název: CEITEC - central european institute of technology

GD203/09/H046, projekt VaV

Název: Biochemie na rozcestí mezi in silico a in vitro

Investor: Grantová agentura ČR, Biochemie na rozcestí mezi in silico a in vitro

LC06030, projekt VaV

Název: Biomolekulární centrum

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

Citovat

ZGARBOVA, Marie, Petr JUREČKA, Pavel BANÁŠ, Michal OTYEPKA, Judit ŠPONEROVÁ, Neocles B. LEONTIS, Craig L. ZIRBEL a 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, roč. 115, č. 41, s. 11277-11292. ISSN 1089-5639. Dostupné z: 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 a 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, roč.~115, č.~41, s.~11277-11292. ISSN~1089-5639. Dostupné z: https://dx.doi.org/10.1021/jp204820b.

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