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On the Use of Molecular Dynamics Simulations for Probing Allostery through DNA
T. Dršata, M. Zgarbová, P. Jurečka, J. Šponer, F. Lankaš,
Language English Country United States
Document type Journal Article, Research Support, Non-U.S. Gov't
NLK
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from 1960-01-01 to 1 year ago
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from 1960 to 12 months ago
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from 1960-09-01
- MeSH
- Allosteric Regulation MeSH
- DNA chemistry MeSH
- Nucleic Acid Conformation * MeSH
- Molecular Dynamics Simulation * MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
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.
Central European Institute of Technology Campus Bohunice Brno Czech Republic
Institute of Biophysics Academy of Sciences of the Czech Republic Brno Czech Republic
References provided by Crossref.org
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- $a 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.
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