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| Content Provider | World Health Organization (WHO)-Global Index Medicus |
|---|---|
| Author | Meyer, Sam Everaers, Ralf |
| Description | Country affiliation: France Author Affiliation: Meyer S ( Université de Lyon, Laboratoire de Physique and Centre Blaise Pascal, Ecole normale supérieure de Lyon, UMR CNRS 5672, Lyon, France. Université de Lyon, INSA-Lyon, INRIA, LIRIS, CNRS UMR 5205, Lyon, France. Université de Lyon, Microbiologie Adaptation et Pathogénie, INSA-Lyon, CNRS UMR 5240, Lyon,France.) |
| Abstract | The histone-DNA interaction in the nucleosome is a fundamental mechanism of genomic compaction and regulation, which remains largely unknown despite increasing structural knowledge of the complex. In this paper, we propose a framework for the extraction of a nanoscale histone-DNA force-field from a collection of high-resolution structures, which may be adapted to a larger class of protein-DNA complexes. We applied the procedure to a large crystallographic database extended by snapshots from molecular dynamics simulations. The comparison of the structural models first shows that, at histone-DNA contact sites, the DNA base-pairs are shifted outwards locally, consistent with locally repulsive forces exerted by the histones. The second step shows that the various force profiles of the structures under analysis derive locally from a unique, sequence-independent, quadratic repulsive force-field, while the sequence preferences are entirely due to internal DNA mechanics. We have thus obtained the first knowledge-derived nanoscale interaction potential for histone-DNA in the nucleosome. The conformations obtained by relaxation of nucleosomal DNA with high-affinity sequences in this potential accurately reproduce the experimental values of binding preferences. Finally we address the more generic binding mechanisms relevant to the 80% genomic sequences incorporated in nucleosomes, by computing the conformation of nucleosomal DNA with sequence-averaged properties. This conformation differs from those found in crystals, and the analysis suggests that repulsive histone forces are related to local stretch tension in nucleosomal DNA, mostly between adjacent contact points. This tension could play a role in the stability of the complex. |
| ISSN | 09538984 |
| e-ISSN | 1361648X |
| Journal | Journal of Physics: Condensed Matter |
| Issue Number | 6 |
| Volume Number | 27 |
| Language | English |
| Publisher | IOP Publishing |
| Publisher Date | 2015-02-18 |
| Publisher Place | Great Britain (UK) |
| Access Restriction | Open |
| Subject Keyword | Chemistry Metabolism Histones Molecular Dynamics Simulation Nucleosomes Base Pairing Binding Sites Crystallography, X-ray Genetics Protein Binding Research Support, Non-u.s. Gov't Discipline Condensed Matter Physics |
| Content Type | Text |
| Resource Type | Article |
| Subject | Condensed Matter Physics Materials Science |
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