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  • Title: Coarse-grained force field for the nucleosome from self-consistent multiscaling.
    Author: Voltz K, Trylska J, Tozzini V, Kurkal-Siebert V, Langowski J, Smith J.
    Journal: J Comput Chem; 2008 Jul 15; 29(9):1429-39. PubMed ID: 18270964.
    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.
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