| MLÝNSKÝ, Vojtěch, Petra KÜHROVÁ, Marie ZGARBOVÁ, Petr JUREČKA, Nils G. WALTER, Michal OTYEPKA, Jiří ŠPONER a Pavel BANÁŠ. Reactive Conformation of the Active Site in the Hairpin Ribozyme Achieved by Molecular Dynamics Simulations with epsilon/zeta Force Field Reparametrizations. Journal of Physical Chemistry B. Washington D.C.: AMER CHEMICAL SOC, 2015, roč. 119, č. 11, s. 4220-4229. ISSN 1520-6106. Dostupné z: https://dx.doi.org/10.1021/jp512069n. |
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@article{1299540,
author = {Mlýnský, Vojtěch and Kührová, Petra and Zgarbová, Marie and Jurečka, Petr and Walter, Nils G. and Otyepka, Michal and Šponer, Jiří and Banáš, Pavel},
article_location = {Washington D.C.},
article_number = {11},
doi = {http://dx.doi.org/10.1021/jp512069n},
keywords = {ACID-BASE CATALYSIS; NUCLEIC-ACIDS; RNA CATALYSIS; STRUCTURAL DYNAMICS; MONOVALENT CATIONS; GLMS RIBOZYME; SELF-CLEAVAGE; IMINO GROUP; MECHANISM; BACKBONE},
language = {eng},
issn = {1520-6106},
journal = {Journal of Physical Chemistry B},
title = {Reactive Conformation of the Active Site in the Hairpin Ribozyme Achieved by Molecular Dynamics Simulations with epsilon/zeta Force Field Reparametrizations},
url = {http://pubs.acs.org/doi/pdf/10.1021/jp512069n},
volume = {119},
year = {2015}
}
TY - JOUR
ID - 1299540
AU - Mlýnský, Vojtěch - Kührová, Petra - Zgarbová, Marie - Jurečka, Petr - Walter, Nils G. - Otyepka, Michal - Šponer, Jiří - Banáš, Pavel
PY - 2015
TI - Reactive Conformation of the Active Site in the Hairpin Ribozyme Achieved by Molecular Dynamics Simulations with epsilon/zeta Force Field Reparametrizations
JF - Journal of Physical Chemistry B
VL - 119
IS - 11
SP - 4220-4229
EP - 4220-4229
PB - AMER CHEMICAL SOC
SN - 15206106
KW - ACID-BASE CATALYSIS
KW - NUCLEIC-ACIDS
KW - RNA CATALYSIS
KW - STRUCTURAL DYNAMICS
KW - MONOVALENT CATIONS
KW - GLMS RIBOZYME
KW - SELF-CLEAVAGE
KW - IMINO GROUP
KW - MECHANISM
KW - BACKBONE
UR - http://pubs.acs.org/doi/pdf/10.1021/jp512069n
L2 - http://pubs.acs.org/doi/pdf/10.1021/jp512069n
N2 - 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/zeta torsions 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 contributes to the conformational behavior observed for the scissile phosphate in the presence of a deprotonated G8(-). On the basis of the new force field, we obtain a reactive conformation for the hairpin ribozyme active site that is consistent with the most recent mechanistic and structural data.
ER -
MLÝNSKÝ, Vojtěch, Petra KÜHROVÁ, Marie ZGARBOVÁ, Petr JUREČKA, Nils G. WALTER, Michal OTYEPKA, Jiří ŠPONER a Pavel BANÁŠ. Reactive Conformation of the Active Site in the Hairpin Ribozyme Achieved by Molecular Dynamics Simulations with epsilon/zeta Force Field Reparametrizations. \textit{Journal of Physical Chemistry B}. Washington D.C.: AMER CHEMICAL SOC, 2015, roč.~119, č.~11, s.~4220-4229. ISSN~1520-6106. Dostupné z: https://dx.doi.org/10.1021/jp512069n.
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