Energies and 2 '-Hydroxyl Group Orientations of RNA Backbone
Conformations. Benchmark CCSD(T)/CBS Database, Electronic
Analysis, and Assessment of DFT Methods and MD Simulations

J 2014

Energies and 2 '-Hydroxyl Group Orientations of RNA Backbone Conformations. Benchmark CCSD(T)/CBS Database, Electronic Analysis, and Assessment of DFT Methods and MD Simulations

MLÁDEK, Arnošt, Pavel BANÁŠ, Petr JUREČKA, Michal OTYEPKA, Marie ZGARBOVÁ et. al.

Basic information

Original name

Energies and 2 '-Hydroxyl Group Orientations of RNA Backbone Conformations. Benchmark CCSD(T)/CBS Database, Electronic Analysis, and Assessment of DFT Methods and MD Simulations

Authors

MLÁDEK, Arnošt (203 Czech Republic), Pavel BANÁŠ (203 Czech Republic), Petr JUREČKA (203 Czech Republic), Michal OTYEPKA (203 Czech Republic), Marie ZGARBOVÁ (203 Czech Republic) and Jiří ŠPONER (203 Czech Republic, guarantor, belonging to the institution)

Edition

Journal of Chemical Theory and Computation, Washington DC, American Chemical Society, 2014, 1549-9618

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

References:

URL

Impact factor

Impact factor: 5.498

RIV identification code

RIV/00216224:14740/14:00075659

Organization unit

Central European Institute of Technology

DOI

http://dx.doi.org/10.1021/ct400837p

UT WoS

000330142400044

Keywords in English

DENSITY-FUNCTIONAL THEORY; SUGAR-PHOSPHATE BACKBONE; QUANTUM-CHEMICAL CALCULATIONS; WATSON-CRICK/SUGAR-EDGE; GAUSSIAN-BASIS SETS; ACID BASE-PAIRS; GENERALIZED GRADIENT APPROXIMATION; CORRELATED MOLECULAR CALCULATIONS; NONEMPIRICAL AB-INITIO

Abstract

V originále

Sugar-phosphate backbone is an electronically complex molecular segment imparting RNA molecules high flexibility and architectonic heterogeneity necessary for their biological functions. The structural variability of RNA molecules is amplified by the presence of the 2'-hydroxyl group, capable of forming multitude of intra- and intermolecular interactions. Bioinformatics studies based on X-ray structure database revealed that RNA backbone samples at least 46 substates known as rotameric families. The present study provides a comprehensive analysis of RNA backbone conformational preferences and 2'-hydroxyl group orientations. First, we create a benchmark database of estimated CCSD(T)/CBS relative energies of all rotameric families and test performance of dispersion-corrected DFT-D3 methods and molecular mechanics in vacuum and in continuum solvent. The performance of the DFT-D3 methods is in general quite satisfactory. The B-LYP-D3 method provides the best trade-off between accuracy and computational demands. B3-LYP-D3 slightly outperforms the new PW6B95-D3 and MPW1B95-D3 and is the second most accurate density functional of the study. The best agreement with CCSD(T)/CBS is provided by DSD-B-LYP-D3 double-hybrid functional, although its large-scale applications may be limited by high computational costs. Molecular mechanics does not reproduce the fine energy differences between the RNA backbone substates. We also demonstrate that the differences in the magnitude of the hyperconjugation effect do not correlate with the energy ranking of the backbone conformations. Further, we investigated the 2'-hydroxyl group orientation preferences. For all families, we conducted a QM and MM hydroxyl group rigid scan in gas phase and solvent. We then carried out set of explicit solvent MD simulations of folded RNAs and analyze 2'-hydroxyl group orientations of different backbone families in MD. The solvent energy profiles determined primarily by the sugar pucker match well with the distribution data derived from the simulations. The QM and MM energy profiles predict the same 2'-hydroxyl group orientation preferences. Finally, we demonstrate that the high energy of unfavorable and rarely sampled 2'-hydroxyl group orientations can be attributed to clashes between occupied orbitals.

Links

ED1.1.00/02.0068, research and development project

Name: CEITEC - central european institute of technology

Citovat

MLÁDEK, Arnošt, Pavel BANÁŠ, Petr JUREČKA, Michal OTYEPKA, Marie ZGARBOVÁ and Jiří ŠPONER. Energies and 2 '-Hydroxyl Group Orientations of RNA Backbone Conformations. Benchmark CCSD(T)/CBS Database, Electronic Analysis, and Assessment of DFT Methods and MD Simulations. Journal of Chemical Theory and Computation. Washington DC: American Chemical Society, 2014, vol. 10, No 1, p. 463-480. ISSN 1549-9618. Available from: https://dx.doi.org/10.1021/ct400837p.

@article{1185382,
   author = {Mládek, Arnošt and Banáš, Pavel and Jurečka, Petr and Otyepka, Michal and Zgarbová, Marie and Šponer, Jiří},
   article_location = {Washington DC},
   article_number = {1},
   doi = {http://dx.doi.org/10.1021/ct400837p},
   keywords = {DENSITY-FUNCTIONAL THEORY; SUGAR-PHOSPHATE BACKBONE; QUANTUM-CHEMICAL CALCULATIONS; WATSON-CRICK/SUGAR-EDGE; GAUSSIAN-BASIS SETS; ACID BASE-PAIRS; GENERALIZED GRADIENT APPROXIMATION; CORRELATED MOLECULAR CALCULATIONS; NONEMPIRICAL AB-INITIO},
   language = {eng},
   issn = {1549-9618},
   journal = {Journal of Chemical Theory and Computation},
   title = {Energies and 2 '-Hydroxyl Group Orientations of RNA Backbone Conformations. Benchmark CCSD(T)/CBS Database, Electronic Analysis, and Assessment of DFT Methods and MD Simulations},
   url = {http://pubs.acs.org/doi/pdfplus/10.1021/ct400837p},
   volume = {10},
   year = {2014}
}

TY  - JOUR
ID  - 1185382
AU  - Mládek, Arnošt - Banáš, Pavel - Jurečka, Petr - Otyepka, Michal - Zgarbová, Marie - Šponer, Jiří
PY  - 2014
TI  - Energies and 2 '-Hydroxyl Group Orientations of RNA Backbone Conformations. Benchmark CCSD(T)/CBS Database, Electronic Analysis, and Assessment of DFT Methods and MD Simulations
JF  - Journal of Chemical Theory and Computation
VL  - 10
IS  - 1
SP  - 463-480
EP  - 463-480
PB  - American Chemical Society
SN  - 15499618
KW  - DENSITY-FUNCTIONAL THEORY
KW  - SUGAR-PHOSPHATE BACKBONE
KW  - QUANTUM-CHEMICAL CALCULATIONS
KW  - WATSON-CRICK/SUGAR-EDGE
KW  - GAUSSIAN-BASIS SETS
KW  - ACID BASE-PAIRS
KW  - GENERALIZED GRADIENT APPROXIMATION
KW  - CORRELATED MOLECULAR CALCULATIONS
KW  - NONEMPIRICAL AB-INITIO
UR  - http://pubs.acs.org/doi/pdfplus/10.1021/ct400837p
L2  - http://pubs.acs.org/doi/pdfplus/10.1021/ct400837p
N2  - Sugar-phosphate backbone is an electronically complex molecular segment imparting RNA molecules high flexibility and architectonic heterogeneity necessary for their biological functions. The structural variability of RNA molecules is amplified by the presence of the 2'-hydroxyl group, capable of forming multitude of intra- and intermolecular interactions. Bioinformatics studies based on X-ray structure database revealed that RNA backbone samples at least 46 substates known as rotameric families. The present study provides a comprehensive analysis of RNA backbone conformational preferences and 2'-hydroxyl group orientations. First, we create a benchmark database of estimated CCSD(T)/CBS relative energies of all rotameric families and test performance of dispersion-corrected DFT-D3 methods and molecular mechanics in vacuum and in continuum solvent. The performance of the DFT-D3 methods is in general quite satisfactory. The B-LYP-D3 method provides the best trade-off between accuracy and computational demands. B3-LYP-D3 slightly outperforms the new PW6B95-D3 and MPW1B95-D3 and is the second most accurate density functional of the study. The best agreement with CCSD(T)/CBS is provided by DSD-B-LYP-D3 double-hybrid functional, although its large-scale applications may be limited by high computational costs. Molecular mechanics does not reproduce the fine energy differences between the RNA backbone substates. We also demonstrate that the differences in the magnitude of the hyperconjugation effect do not correlate with the energy ranking of the backbone conformations. Further, we investigated the 2'-hydroxyl group orientation preferences. For all families, we conducted a QM and MM hydroxyl group rigid scan in gas phase and solvent. We then carried out set of explicit solvent MD simulations of folded RNAs and analyze 2'-hydroxyl group orientations of different backbone families in MD. The solvent energy profiles determined primarily by the sugar pucker match well with the distribution data derived from the simulations. The QM and MM energy profiles predict the same 2'-hydroxyl group orientation preferences. Finally, we demonstrate that the high energy of unfavorable and rarely sampled 2'-hydroxyl group orientations can be attributed to clashes between occupied orbitals.
ER  -

MLÁDEK, Arnošt, Pavel BANÁŠ, Petr JUREČKA, Michal OTYEPKA, Marie ZGARBOVÁ and Jiří ŠPONER. Energies and 2 '-Hydroxyl Group Orientations of RNA Backbone Conformations. Benchmark CCSD(T)/CBS Database, Electronic Analysis, and Assessment of DFT Methods and MD Simulations. \textit{Journal of Chemical Theory and Computation}. Washington DC: American Chemical Society, 2014, vol.~10, No~1, p.~463-480. ISSN~1549-9618. Available from: https://dx.doi.org/10.1021/ct400837p.

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