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

Result code in 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>
Alternative codes found
RIV/68081707:_____/15:00446327 RIV/00216224:14740/15:00080801
Result on the web
<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>

Result language
angličtina
Original language name
Can We Execute Stable Microsecond-Scale Atomistic Simulations of Protein-RNA Complexes?
Original language description
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
Czech name
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Czech description
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Type
J<sub>x</sub> - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)
CEP classification
CF - Physical chemistry and theoretical chemistry
OECD FORD branch
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Project
Result was created during the realization of more than one project. More information in the Projects tab.
Continuities
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Publication year
2015
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

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