Toward Reproducing Sequence Trends in Phosphorus Chemical
Shifts for Nucleic Acids by MD/DFT Calculations

J 2013

Toward Reproducing Sequence Trends in Phosphorus Chemical Shifts for Nucleic Acids by MD/DFT Calculations

PŘECECHTĚLOVÁ, Jana; Markéta MUNZAROVÁ; Juha VAARA; Jan NOVOTNÝ; Martin DRAČÍNSKÝ et al.

Základní údaje

Originální název

Toward Reproducing Sequence Trends in Phosphorus Chemical Shifts for Nucleic Acids by MD/DFT Calculations

Autoři

PŘECECHTĚLOVÁ, Jana; Markéta MUNZAROVÁ; Juha VAARA; Jan NOVOTNÝ; Martin DRAČÍNSKÝ a Vladimír SKLENÁŘ

Vydání

Journal of Chemical Theory and Computation, WASHINGTON, AMER CHEMICAL SOC, 2013, 1549-9618

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

Odkazy

URL

Impakt faktor

Impact factor: 5.310

Označené pro přenos do RIV

Ano

Kód RIV

RIV/00216224:14740/13:00067940

Organizační jednotka

Středoevropský technologický institut

DOI

https://doi.org/10.1021/ct300488y

UT WoS

000316168700035

Klíčová slova anglicky

phosphorus chemical shift nucleic acids MD DFT

Štítky

rivok

Změněno: 8. 4. 2014 13:26, Olga Křížová

Anotace

V originále

This work addresses the question of the ability of the MD/DFT approach to reproduce sequence trend in 31P chemical shifts (delta_P) in the backbone of nucleic acids. delta_P for [d(CGCGAATTCGCG)]2 have been computed using DFT calculations on model compounds with geometries cut out of snapshots of classical molecular dynamics (MD) simulations. The values of 31P chemical shifts for two distinct B-DNA subfamilies BI and BII, delta_P/BI and delta_P/BII, have been determined as averages over the BI and BII subparts of the MD trajectory. This has been done for various samplings of MD trajectory and for two sizes of both the model and the solvent embedding. For all of the combinations of trajectory sampling, model size, and embedding size, sequence dependence of delta_P/BI in the order of 0.4–0.5 ppm has been obtained. Weighted averages for individual 31P nuclei in the studied DNA double-helix have been calculated from delta_P/BI and delta_P/BII using BI and BII percentages from free MD simulations as well as from approaches employing NMR structural restraints. A good qualitative agreement is found between experimental sequence trends in delta_P and theoretical delta_P employing short (24 ns) MD run and BI, BII percentages determined by Hartmann et al. or via MD with the inclusion of NMR structural restraints. Theoretical delta_P exhibit a systematic offset of ca. 11 ppm and overestimation of trends by a factor of ca. 1.7. When scaled accordingly, theoretical delta_P/BI and delta_P/BII can be used to determine the expected percentage of BII to match the experimental value of delta_P. The systematic offsets of the theoretical delta_P obtained by MD/DFT approach result primarily from the unrealistic bond lengths employed by classical MD. The findings made in this work provide structure-delta_P relationships for possible use as NMR restraints and suggest that NMR calculations on MD snapshots can be in the future employed for the validation of newly developed force fields.

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

MSM0021622413, záměr

Název: Proteiny v metabolismu a při interakci organismů s prostředím

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Proteiny v metabolismu a při interakci organismů s prostředím

Citovat

PŘECECHTĚLOVÁ, Jana; Markéta MUNZAROVÁ; Juha VAARA; Jan NOVOTNÝ; Martin DRAČÍNSKÝ a Vladimír SKLENÁŘ. Toward Reproducing Sequence Trends in Phosphorus Chemical Shifts for Nucleic Acids by MD/DFT Calculations. Journal of Chemical Theory and Computation. WASHINGTON: AMER CHEMICAL SOC, 2013, roč. 9, č. 3, s. 1641-1656. ISSN 1549-9618. Dostupné z: https://doi.org/10.1021/ct300488y.

@article{1092277,
   author = {Přecechtělová, Jana and Munzarová, Markéta and Vaara, Juha and Novotný, Jan and Dračínský, Martin and Sklenář, Vladimír},
   article_location = {WASHINGTON},
   article_number = {3},
   doi = {https://doi.org/10.1021/ct300488y},
   keywords = {phosphorus chemical shift nucleic acids MD DFT},
   language = {eng},
   issn = {1549-9618},
   journal = {Journal of Chemical Theory and Computation},
   title = {Toward Reproducing Sequence Trends in Phosphorus Chemical Shifts for Nucleic Acids by MD/DFT Calculations},
   url = {http://pubs.acs.org/doi/abs/10.1021/ct300488y?prevSearch=%255BContrib%253A%2BMunzarova%255D&searchHistoryKey=},
   volume = {9},
   year = {2013}
}

TY  - JOUR
ID  - 1092277
AU  - Přecechtělová, Jana - Munzarová, Markéta - Vaara, Juha - Novotný, Jan - Dračínský, Martin - Sklenář, Vladimír
PY  - 2013
TI  - Toward Reproducing Sequence Trends in Phosphorus Chemical Shifts for Nucleic Acids by MD/DFT Calculations
JF  - Journal of Chemical Theory and Computation
VL  - 9
IS  - 3
SP  - 1641-1656
EP  - 1641-1656
PB  - AMER CHEMICAL SOC
SN  - 15499618
KW  - phosphorus chemical shift nucleic acids MD DFT
UR  - http://pubs.acs.org/doi/abs/10.1021/ct300488y?prevSearch=%255BContrib%253A%2BMunzarova%255D&searchHistoryKey=
L2  - http://pubs.acs.org/doi/abs/10.1021/ct300488y?prevSearch=%255BContrib%253A%2BMunzarova%255D&searchHistoryKey=
N2  - This work addresses the question of the ability of the MD/DFT approach to reproduce sequence trend in 31P chemical shifts (delta_P) in the backbone of nucleic acids. delta_P for [d(CGCGAATTCGCG)]2 have been computed using DFT calculations on model compounds with geometries cut out of snapshots of classical molecular dynamics (MD) simulations. The values of 31P chemical shifts for two distinct B-DNA subfamilies BI and BII, delta_P/BI and delta_P/BII, have been determined as averages over the BI and BII subparts of the MD trajectory. This has been done for various samplings of MD trajectory and for two sizes of both the model and the solvent embedding. For all of the combinations of trajectory sampling, model size, and embedding size, sequence dependence of delta_P/BI in the order of 0.4–0.5 ppm has been obtained. Weighted averages for individual 31P nuclei in the studied DNA double-helix have been calculated from delta_P/BI and delta_P/BII using BI and BII percentages from free MD simulations as well as from approaches employing NMR structural restraints. A good qualitative agreement is found between experimental sequence trends in delta_P and theoretical delta_P employing short (24 ns) MD run and BI, BII percentages determined by Hartmann et al. or via MD with the inclusion of NMR structural restraints. Theoretical delta_P exhibit a systematic offset of ca. 11 ppm and overestimation of trends by a factor of ca. 1.7. When scaled accordingly, theoretical delta_P/BI and delta_P/BII can be used to determine the expected percentage of BII to match the experimental value of delta_P. The systematic offsets of the theoretical delta_P obtained by MD/DFT approach result primarily from the unrealistic bond lengths employed by classical MD. The findings made in this work provide structure-delta_P relationships for possible use as NMR restraints and suggest that NMR calculations on MD snapshots can be in the future employed for the validation of newly developed force fields.
ER  -

PŘECECHTĚLOVÁ, Jana; Markéta MUNZAROVÁ; Juha VAARA; Jan NOVOTNÝ; Martin DRAČÍNSKÝ a Vladimír SKLENÁŘ. Toward Reproducing Sequence Trends in Phosphorus Chemical Shifts for Nucleic Acids by MD/DFT Calculations. \textit{Journal of Chemical Theory and Computation}. WASHINGTON: AMER CHEMICAL SOC, 2013, roč.~9, č.~3, s.~1641-1656. ISSN~1549-9618. Dostupné z: https://doi.org/10.1021/ct300488y.

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