Free Energy Landscape of GAGA and UUCG RNA Tetraloops

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F68081707%3A_____%2F16%3A00471952" target="_blank" >RIV/68081707:_____/16:00471952 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/61989592:15310/16:33161233

Výsledek na webu

<a href="http://dx.doi.org/10.1021/acs.jpclett.6b01905" target="_blank" >http://dx.doi.org/10.1021/acs.jpclett.6b01905</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1021/acs.jpclett.6b01905" target="_blank" >10.1021/acs.jpclett.6b01905</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Free Energy Landscape of GAGA and UUCG RNA Tetraloops

Popis výsledku v původním jazyce

We report the folding thermodynamics of ccUUCGgg and ccGAGAgg RNA tetraloops using atomistic molecular dynamics simulations. We obtain a previously unreported estimation of the folding free energy using parallel tempering in combination with well-tempered metadynamics. A key ingredient is the use of a recently developed metric distance, eRMSD, as a biased collective variable. We find that the native fold of both tetraloops is not the global free energy minimum using the Amber chi(OL3) force field. The estimated folding free energies are 30.2 +/- 0.5 kJ/mol for UUCG and 7.5 +/- 0.6 kJ/mol for GAGA, in striking disagreement with experimental data. We evaluate the viability of all possible one-dimensional backbone force field corrections. We find that disfavoring the gauche(+) region of alpha and zeta angles consistently improves the existing force field. The level of accuracy achieved with these corrections, however, cannot be considered sufficient by judging on the basis of available thermodynamic data and solution experiments.

Název v anglickém jazyce

Free Energy Landscape of GAGA and UUCG RNA Tetraloops

Popis výsledku anglicky

We report the folding thermodynamics of ccUUCGgg and ccGAGAgg RNA tetraloops using atomistic molecular dynamics simulations. We obtain a previously unreported estimation of the folding free energy using parallel tempering in combination with well-tempered metadynamics. A key ingredient is the use of a recently developed metric distance, eRMSD, as a biased collective variable. We find that the native fold of both tetraloops is not the global free energy minimum using the Amber chi(OL3) force field. The estimated folding free energies are 30.2 +/- 0.5 kJ/mol for UUCG and 7.5 +/- 0.6 kJ/mol for GAGA, in striking disagreement with experimental data. We evaluate the viability of all possible one-dimensional backbone force field corrections. We find that disfavoring the gauche(+) region of alpha and zeta angles consistently improves the existing force field. The level of accuracy achieved with these corrections, however, cannot be considered sufficient by judging on the basis of available thermodynamic data and solution experiments.

Druh

J_x - Nezařazeno - Článek v odborném periodiku (Jimp, Jsc a Jost)

CEP obor

BO - Biofyzika

OECD FORD obor

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Projekt

Výsledek vznikl pri realizaci vícero projektů. Více informací v záložce Projekty.

Návaznosti

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Rok uplatnění

2016

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

Journal of Physical Chemistry Letters

ISSN

1948-7185

e-ISSN

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Svazek periodika

7

Číslo periodika v rámci svazku

20

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

7

Strana od-do

4032-4038

Kód UT WoS článku

000386106600001

EID výsledku v databázi Scopus

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