title: Coarse-grained force field for the nucleosome from self-consistent multiscaling.
abstract: A coarse-grained simulation model for the nucleosome is developed, using a methodology modified from previous work on the ribosome. Protein residues and DNA nucleotides are represented as beads, interacting through harmonic (for neighboring) or Morse (for nonbonded) potentials. Force-field parameters were estimated by Boltzmann inversion of the corresponding radial distribution functions obtained from a 5-ns all-atom molecular dynamics (MD) simulation, and were refined to produce agreement with the all-atom MD simulation. This self-consistent multiscale approach yields a coarse-grained model that is capable of reproducing equilibrium structural properties calculated from a 50-ns all-atom MD simulation. This coarse-grained model speeds up nucleosome simulations by a factor of 10(3) and is expected to be useful in examining biologically relevant dynamical nucleosome phenomena on the microsecond timescale and beyond.
authors.affiliation: Biophysics of Macromolecules, German Cancer Research Center, Heidelberg, Germany.
authors.forename: Karine
authors.initials: K
authors.lastname: Voltz
authors.forename: Joanna
authors.initials: J
authors.lastname: Trylska
authors.forename: Valentina
authors.initials: V
authors.lastname: Tozzini
authors.forename: Vandana
authors.initials: V
authors.lastname: Kurkal-Siebert
authors.forename: Jörg
authors.initials: J
authors.lastname: Langowski
authors.forename: Jeremy
authors.initials: J
authors.lastname: Smith
mesh_terms: D003198:Computer Simulation; D004247:DNA / Q000737:chemistry; D008954:Models, Biological; D009707:Nucleosomes / Q000737:chemistry*; D011506:Proteins / Q000737:chemistry; D011789:Quantum Theory
chemical_list: D009707:Nucleosomes; D011506:Proteins; D004247:DNA