title: Electrostatic origin of salt-induced nucleosome array compaction.
abstract: The physical mechanism of the folding and unfolding of chromatin is fundamentally related to transcription but is incompletely characterized and not fully understood. We experimentally and theoretically studied chromatin compaction by investigating the salt-mediated folding of an array made of 12 positioning nucleosomes with 177 bp repeat length. Sedimentation velocity measurements were performed to monitor the folding provoked by addition of cations Na(+), K(+), Mg(2+), Ca(2+), spermidine(3+), Co(NH(3))(6)(3+), and spermine(4+). We found typical polyelectrolyte behavior, with the critical concentration of cation needed to bring about maximal folding covering a range of almost five orders of magnitude (from 2 μM for spermine(4+) to 100 mM for Na(+)). A coarse-grained model of the nucleosome array based on a continuum dielectric description and including the explicit presence of mobile ions and charged flexible histone tails was used in computer simulations to investigate the cation-mediated compaction. The results of the simulations with explicit ions are in general agreement with the experimental data, whereas simple Debye-Hückel models are intrinsically incapable of describing chromatin array folding by multivalent cations. We conclude that the theoretical description of the salt-induced chromatin folding must incorporate explicit mobile ions that include ion correlation and ion competition effects.
authors.affiliation: School of Biological Sciences, Nanyang Technological University, Singapore.
authors.forename: Nikolay
authors.initials: N
authors.lastname: Korolev
authors.forename: Abdollah
authors.initials: A
authors.lastname: Allahverdi
authors.forename: Ye
authors.initials: Y
authors.lastname: Yang
authors.forename: Yanping
authors.initials: Y
authors.lastname: Fan
authors.forename: Alexander P
authors.initials: AP
authors.lastname: Lyubartsev
authors.forename: Lars
authors.initials: L
authors.lastname: Nordenskiöld
mesh_terms: D000818:Animals; D003198:Computer Simulation; D006860:Hydrogen Bonding / Q000187:drug effects; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation / Q000187:drug effects; D009707:Nucleosomes / Q000737:chemistry* / Q000187:drug effects*; D011487:Protein Conformation / Q000187:drug effects; D017510:Protein Folding / Q000187:drug effects; D012492:Salts / Q000494:pharmacology*; D055672:Static Electricity; D014461:Ultracentrifugation; D014867:Water / Q000737:chemistry; D014982:Xenopus laevis
chemical_list: D009707:Nucleosomes; D012492:Salts; D014867:Water