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@article{1335870,
author = {Havrila, Marek and Zgarbová, Marie and Jurečka, Petr and Banáš, Pavel and Krepl, Miroslav and Otyepka, Michal and Šponer, Jiří},
article_location = {WASHINGTON},
article_number = {49},
doi = {http://dx.doi.org/10.1021/acs.jpcb.5b08876},
keywords = {MOLECULAR-DYNAMICS SIMULATIONS; DIMERIZATION INITIATION SITE; QUANTUM-CHEMICAL COMPUTATIONS; NMR SOLUTION STRUCTURE; 30S RIBOSOMAL-SUBUNIT; PARTICLE MESH EWALD; GENOMIC RNA; REPLICA-EXCHANGE; EXTENDED-DUPLEX; NUCLEIC-ACIDS},
language = {eng},
issn = {1520-6106},
journal = {Journal of Physical Chemistry B},
title = {Microsecond-Scale MD Simulations of HIV-1 DIS Kissing-Loop Complexes Predict Bulged-In Conformation of the Bulged Bases and Reveal Interesting Differences between Available Variants of the AMBER RNA Force Fields},
url = {http://pubs.acs.org/doi/pdf/10.1021/acs.jpcb.5b08876},
volume = {119},
year = {2015}
}
TY - JOUR
ID - 1335870
AU - Havrila, Marek - Zgarbová, Marie - Jurečka, Petr - Banáš, Pavel - Krepl, Miroslav - Otyepka, Michal - Šponer, Jiří
PY - 2015
TI - Microsecond-Scale MD Simulations of HIV-1 DIS Kissing-Loop Complexes Predict Bulged-In Conformation of the Bulged Bases and Reveal Interesting Differences between Available Variants of the AMBER RNA Force Fields
JF - Journal of Physical Chemistry B
VL - 119
IS - 49
SP - 15176-15190
EP - 15176-15190
PB - AMER CHEMICAL SOC
SN - 15206106
KW - MOLECULAR-DYNAMICS SIMULATIONS
KW - DIMERIZATION INITIATION SITE
KW - QUANTUM-CHEMICAL COMPUTATIONS
KW - NMR SOLUTION STRUCTURE
KW - 30S RIBOSOMAL-SUBUNIT
KW - PARTICLE MESH EWALD
KW - GENOMIC RNA
KW - REPLICA-EXCHANGE
KW - EXTENDED-DUPLEX
KW - NUCLEIC-ACIDS
UR - http://pubs.acs.org/doi/pdf/10.1021/acs.jpcb.5b08876
L2 - http://pubs.acs.org/doi/pdf/10.1021/acs.jpcb.5b08876
N2 - We report an extensive set of explicit solvent molecular dynamics (MD) simulations (similar to 25 mu s of accumulated simulation time) of the RNA kissing-loop complex of the HIV-1 virus initiation dimerization site. Despite many structural investigations by X-ray, NMR, and MD techniques, the position of the bulged purines of the kissing complex has not been unambiguously resolved. The X-ray structures consistently show bulged-out positions of the unpaired bases, while several NMR studies show bulged-in conformations. The NMR studies are, however, mutually inconsistent regarding the exact orientations of the bases. The earlier simulation studies predicted the bulged-out conformation; however, this finding could have been biased by the short simulation time scales. Our microsecond-long simulations reveal that all unpaired bases of the kissing-loop complex stay preferably in the interior of the kissing-loop complex. The MD results are discussed in the context of the available experimental data and we suggest that both conformations are biochemically relevant. We also show that MD provides a quite satisfactory description of this RNA system, contrasting recent reports of unsatisfactory performance of the RNA force fields for smaller systems such as tetranucleotides and tetraloops. We explain this by the fact that the kissing complex is primarily stabilized by an extensive network of Watson Crick interactions which are rather well described by the force fields. We tested several different sets of water/ion parameters but they all lead to consistent results. However, we demonstrate that a recently suggested modification of van der Wools interactions of the Cornell et al. force field deteriorates the description of the kissing complex by the loss of key stacking interactions stabilizing the interhelical junction and excessive hydrogen-bonding interactions.
ER -
HAVRILA, Marek, Marie ZGARBOVÁ, Petr JUREČKA, Pavel BANÁŠ, Miroslav KREPL, Michal OTYEPKA a Jiří ŠPONER. Microsecond-Scale MD Simulations of HIV-1 DIS Kissing-Loop Complexes Predict Bulged-In Conformation of the Bulged Bases and Reveal Interesting Differences between Available Variants of the AMBER RNA Force Fields. Online. \textit{Journal of Physical Chemistry B}. WASHINGTON: AMER CHEMICAL SOC, 2015, roč.~119, č.~49, s.~15176-15190. ISSN~1520-6106. Dostupné z: https://dx.doi.org/10.1021/acs.jpcb.5b08876. [citováno 2024-04-23]
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