Coarse-grained force field for the nucleosome from self-consistent multiscaling.
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.
Voltz
Karine
K
Biophysics of Macromolecules, German Cancer Research Center, Heidelberg, Germany.
Trylska
Joanna
J
Tozzini
Valentina
V
Kurkal-Siebert
Vandana
V
Langowski
Jörg
J
Smith
Jeremy
J
D003198:Computer Simulation; D004247:DNA / Q000737:chemistry; D008954:Models, Biological; D009707:Nucleosomes / Q000737:chemistry*; D011506:Proteins / Q000737:chemistry; D011789:Quantum Theory
D009707:Nucleosomes; D011506:Proteins; D004247:DNA