Modeling of the structure of protein–DNA complexes using the data from FRET and footprinting experiments

We discuss the question of constructing three-dimensional models of DNA in complex with proteins using computer modeling and indirect methods of studying the conformation of macromolecules. We consider the methods of interpreting the experimental data obtained by indirect methods of studying the thr...

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Bibliographic Details
Published in:Moscow University biological sciences bulletin 2016, Vol.71 (1), p.29-33
Main Authors: Armeev, G. A, T. K. Gorkovets, D. A. Efimova, K. V. Shaitan, A. K. Shaytan
Format: Article
Language:English
Subjects:
algorithms
computer simulation
DNA
energy transfer
histones
molecular models
nucleosomes
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Summary:We discuss the question of constructing three-dimensional models of DNA in complex with proteins using computer modeling and indirect methods of studying the conformation of macromolecules. We consider the methods of interpreting the experimental data obtained by indirect methods of studying the three-dimensional structure of biomolecules. We discuss some aspects of integrating such data into the process of constructing the molecular models of DNA–protein complexes based on the geometric characteristics of DNA. We propose an algorithm for estimating conformations of such complexes based on the information about the local flexibility of DNA and on the experimental data obtained by Forster resonance energy transfer (FRET) and hydroxyl footprinting. Finally, we use this algorithm to predict the hypothetical configuration of DNA in a nucleosome bound with histone H1.
ISSN:0096-3925
1934-791X