Reactive Conformation of the Active Site in the Hairpin Ribozyme Achieved by Molecular Dynamics Simulations with epsilon/zeta Force Field Reparametrizations

Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61989592%3A15310%2F15%3A33156513" target="_blank" >RIV/61989592:15310/15:33156513 - isvavai.cz</a>
Alternative codes found
RIV/68081707:_____/15:00446310 RIV/00216224:14740/15:00082890
Result on the web
<a href="http://pubs.acs.org/doi/full/10.1021/jp512069n" target="_blank" >http://pubs.acs.org/doi/full/10.1021/jp512069n</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1021/m512069n" target="_blank" >10.1021/m512069n</a>

Result language
angličtina
Original language name
Reactive Conformation of the Active Site in the Hairpin Ribozyme Achieved by Molecular Dynamics Simulations with epsilon/zeta Force Field Reparametrizations
Original language description
X-ray crystallography can provide important insights into the structure of RNA enzymes (ribozymes). However, the details of a ribozymes active site architecture are often altered by the inactivating chemical modifications necessary to inhibit self-cleavage. Molecular dynamics (MD) simulations are able to complement crystallographic data and model the conformation of the ribozymes active site in its native form. However, the performance of MD simulations is driven by the quality of the force field used.Force fields are primarily parametrized and tested for a description of canonical structures and thus may be less accurate for noncanonical RNA elements, including ribozyme catalytic cores. Here, we show that our recent reparametrization of epsilon/zetatorsions significantly improves the description of the hairpin ribozymes scissile phosphate conformational behavior. In addition, we find that an imbalance in the force field description of the nonbonded interactions of the ribose 2'-OH c
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)<br>S - Specificky vyzkum na vysokych skolach

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

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