Journal
JOURNAL OF COMPUTATIONAL CHEMISTRY
Volume 29, Issue 9, Pages 1429-1439Publisher
WILEY
DOI: 10.1002/jcc.20902
Keywords
chromatin; molecular dynamics; mesoscopic models; radial distribution function; fluctuations
Categories
Funding
- FIC NIH HHS [R03 TW07318] Funding Source: Medline
Ask authors/readers for more resources
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. (C) 2008 Wiley Periodicals, Inc.
Authors
I am an author on this paper
Click your name to claim this paper and add it to your profile.
Reviews
Recommended
No Data Available