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@article{1350874,
author = {Dršata, Tomáš and Zgarbová, Marie and Jurečka, Petr and Šponer, Jiří and Lankaš, Filip},
article_location = {Cambridge},
article_number = {4},
doi = {http://dx.doi.org/10.1016/j.bpj.2015.12.039},
keywords = {B-DNA; MODULATION},
language = {eng},
issn = {0006-3495},
journal = {Biophysical Journal},
title = {On the Use of Molecular Dynamics Simulations for Probing Allostery through DNA},
url = {http://www.sciencedirect.com/science/article/pii/S0006349516000485},
volume = {110},
year = {2016}
}
TY - JOUR
ID - 1350874
AU - Dršata, Tomáš - Zgarbová, Marie - Jurečka, Petr - Šponer, Jiří - Lankaš, Filip
PY - 2016
TI - On the Use of Molecular Dynamics Simulations for Probing Allostery through DNA
JF - Biophysical Journal
VL - 110
IS - 4
SP - 874-876
EP - 874-876
PB - Cell Press
SN - 00063495
KW - B-DNA
KW - MODULATION
UR - http://www.sciencedirect.com/science/article/pii/S0006349516000485
L2 - http://www.sciencedirect.com/science/article/pii/S0006349516000485
N2 - A recent study described an allosteric effect in which the binding of a protein to DNA is influenced by another protein bound nearby. The effect shows a periodicity of similar to 10 basepairs and decays with increasing protein-protein distance. As a mechanistic explanation, the authors reported a similar periodic, decaying pattern of the correlation coefficient between major groove widths inferred from a shorter molecular dynamics simulation. Here we show that in a state-of-the-art, microsecond-long simulation of the same DNA sequence, the periodicity of the correlation coefficient is not observed. To study the problem further, we extend an earlier mechanical model of DNA allostery based on constrained minimization of effective quadratic deformation energy of the DNA. We demonstrate that, if the constraints mimicking the bound proteins are properly applied, the periodicity in the binding energy is indeed recovered.
ER -
DRŠATA, Tomáš, Marie ZGARBOVÁ, Petr JUREČKA, Jiří ŠPONER a Filip LANKAŠ. On the Use of Molecular Dynamics Simulations for Probing Allostery through DNA. \textit{Biophysical Journal}. Cambridge: Cell Press, 2016, roč.~110, č.~4, s.~874-876. ISSN~0006-3495. Dostupné z: https://dx.doi.org/10.1016/j.bpj.2015.12.039.
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