Can We Execute Stable Microsecond-Scale Atomistic Simulations of Protein-RNA Complexes?

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61989592%3A15310%2F15%3A33156550" target="_blank" >RIV/61989592:15310/15:33156550 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/68081707:_____/15:00446327 RIV/00216224:14740/15:00080801

Výsledek na webu

<a href="http://pubs.acs.org/doi/full/10.1021/ct5008108" target="_blank" >http://pubs.acs.org/doi/full/10.1021/ct5008108</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1021/ct5008108" target="_blank" >10.1021/ct5008108</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Can We Execute Stable Microsecond-Scale Atomistic Simulations of Protein-RNA Complexes?

Popis výsledku v původním jazyce

We report over 30 mu s of unrestrained molecular dynamics simulations of six protein-RNA complexes in explicit solvent. We utilize the AMBER ff99bsc0 chi(OL3) RNA force field combined with the ff99SB protein force field and its more recent ff12SB versionwith reparametrized side-chain dihedrals. The simulations show variable behavior, ranging from systems that are essentially stable to systems with progressive deviations from the experimental structure, which we could not stabilize anywhere close to thestarting experimental structure. For some systems, microsecond-scale simulations are necessary to achieve stabilization after initial sizable structural perturbations. The results show that simulations of protein-RNA complexes are challenging and everysystem should be treated individually. The simulations are affected by numerous factors, including properties of the starting structures (the initially high force field potential energy, resolution limits, conformational averaging, crysta

Název v anglickém jazyce

Can We Execute Stable Microsecond-Scale Atomistic Simulations of Protein-RNA Complexes?

Popis výsledku anglicky

We report over 30 mu s of unrestrained molecular dynamics simulations of six protein-RNA complexes in explicit solvent. We utilize the AMBER ff99bsc0 chi(OL3) RNA force field combined with the ff99SB protein force field and its more recent ff12SB versionwith reparametrized side-chain dihedrals. The simulations show variable behavior, ranging from systems that are essentially stable to systems with progressive deviations from the experimental structure, which we could not stabilize anywhere close to thestarting experimental structure. For some systems, microsecond-scale simulations are necessary to achieve stabilization after initial sizable structural perturbations. The results show that simulations of protein-RNA complexes are challenging and everysystem should be treated individually. The simulations are affected by numerous factors, including properties of the starting structures (the initially high force field potential energy, resolution limits, conformational averaging, crysta

Druh

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

CEP obor

CF - Fyzikální chemie a teoretická chemie

OECD FORD obor

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Projekt

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

Návaznosti

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Rok uplatnění

2015

Kód důvěrnosti údajů

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

Název periodika

Journal of Chemical Theory and Computation

ISSN

1549-9618

e-ISSN

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Svazek periodika

11

Číslo periodika v rámci svazku

3

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

24

Strana od-do

1220-1243

Kód UT WoS článku

000350918300039

EID výsledku v databázi Scopus

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