Publication details

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

Authors

DRŠATA Tomáš ZGARBOVÁ Marie JUREČKA Petr ŠPONER Jiří LANKAŠ Filip

Year of publication 2016
Type Article in Periodical
Magazine / Source Biophysical Journal
MU Faculty or unit

Central European Institute of Technology

Citation
Web http://www.sciencedirect.com/science/article/pii/S0006349516000485
Doi http://dx.doi.org/10.1016/j.bpj.2015.12.039
Field Biophysics
Keywords B-DNA; MODULATION
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 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.
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