ИСТИНА

Protein-DNA complexes play crucial role in genome organization, DNA damage and repair. The key elementary unit of chromatin compaction in eukaryotic genome is a nucleosome. While X-ray crystallography studies of nucleosomes have consistently yielded similar atomistic structures, many biophysical and biochemical techniques suggest that nucleosomes exhibit substantial polymorphism with respect to DNA conformation, which is functionally important. As methods of direct determination of large protein-DNA complexes are not readily available, a strong need of computational approaches is arising, at least at the stage of initial model building. We have developed a variety of methods for experimental data integration with molecular modeling techniques. For instance, we proposed a molecular model of FACT induced structural reorganization of nucleosomes based on single-particle Förster Resonance Energy Transfer data [1]. We used hydroxyl DNA footprinting data in conjunction with atomistic structures of nucleosomes enhanced by molecular dynamics simulations to understand DNA conformation in nucleosomes. An integrative modeling approach based on empirical force field potential for DNA in the internal DNA variables space [2] combined with rigid body docking of histone dimers bound to local DNA regions in conjunction with distance restraints taken from spFRET experiments and DNA footprinting was used to create a model of DNA conformation in chromatosome [3]. We also use restraints from DNA footprinting to create models of nucleosomes in complex with RNA polymerase. Various experimental data bring a lot of indirect restraints to molecular models. In conjunction with relatively simple DNA topology this data may be sufficient for creation of initial models which then can be fitted into EM electron density map. This work was supported by the Russian Science Foundation (grant No. 14-24-00031)