Biophysical Society Thematic Meeting| Les Houches 2019

Multiscale Modeling of Chromatin: Bridging Experiment with Theory

Poster Abstracts

1-POS Board 1 NUCLEOSOME MODELING AT ATOMISTIC DETAIL HELPS TO INTERPRET BIOPHYSICAL EXPERIMENTS Grigoriy A Armeev 1 ; Anna R Panchenko 2 ; Alexey K Shaytan 1 ; 1 Lomonosov Moscow State University, Faculty of Biology, Moscow, Moscow, Russian Federation 2 National Institutes of Health, National Center for Biotechnology Information, Bethesda, Maryland, United States Nucleosomes are the key structural elements of chromatin in all higher organisms. While X-ray crystallography studies of nucleosomes have consistently yielded similar atomistic structures, many biophysical and biochemical techniques suggest that nucleosomes and nucleosome complexes exhibit substantial conformational polymorphism, which is functionally important. Interpretation of such experimental data with sufficient details is often a tedious task. In this presentation we will show how atomistic modeling techniques, including MD simulations, may be exploited to interpret various experimental datasets.We performed full-atom molecular dynamics of nucleosomes and DNA fluorescent labels to sample the conformations used for single particle FörsterResonance Energy Transfer (spFRET) measurements. Such models allow us to correct for the structure of dyes and deduce the positions of labels’ attachment points. We also implemented a set of methods for integrative modeling of nucleosome structures based on spFRET constraints. Using these approaches we have constructed (i) an atomistic model of histone chaperone FACT induced structural reorganization of nucleosomes and (ii) histone H1 induced conformational changes in the linker DNA region. Besides the distances, derived from spFRET, histone - DNA contacts are crucial for nucleosome formation and function. We used hydroxyl DNA footprinting data in conjunction with atomistic structures of nucleosomes enhanced by molecular dynamics simulations to develop a computational method for precise determination of DNA positioning in nucleosomes with single base pair resolution. This method is implemented in software package called HYDROID.This work was supported by Russian Science Foundation grant #18-74-10006 and by the Intramural research program of the national library of medicine, NIH.

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