Coarse-grained force field for the nucleosome from self-consistent multiscaling

✍ Scribed by Karine Voltz; Joanna Trylska; Valentina Tozzini; Vandana Kurkal-Siebert; Jörg Langowski; Jeremy Smith

• Book ID: 102876920
• Publisher: John Wiley and Sons
• Year: 2008
• Tongue: English
• Weight: 785 KB
• Volume: 29
• Category: Article
• ISSN: 0192-8651
• DOI: 10.1002/jcc.20902

✦ Synopsis

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. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008