On the Use of Molecular Dynamics Simulations for Probing Allostery through DNA

Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F60461373%3A22310%2F16%3A43902850" target="_blank" >RIV/60461373:22310/16:43902850 - isvavai.cz</a>
Alternative codes found
RIV/68081707:_____/16:00458973 RIV/61388963:_____/16:00458973 RIV/00216224:14740/16:00090498 RIV/61989592:15310/16:33161265
Result on the web
<a href="http://dx.doi.org/10.1016/j.bpj.2015.12.039" target="_blank" >http://dx.doi.org/10.1016/j.bpj.2015.12.039</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1016/j.bpj.2015.12.039" target="_blank" >10.1016/j.bpj.2015.12.039</a>

Result language
angličtina
Original language name
On the Use of Molecular Dynamics Simulations for Probing Allostery through DNA
Original language description
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 ?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. ? 2016 Biophysical Society.
Czech name
—
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
I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year
2016
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

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