Coarse-grained force field for the nucleosome from self-consistent multiscaling
نویسندگان
چکیده
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.
منابع مشابه
Coarse-grained force field for simulating polymer-tethered silsesquioxane self-assembly in solution.
A coarse-grained model has been developed for simulating the self-assembly of nonyl-tethered polyhedral oligomeric silsesquioxane (POSS) nanoparticles in solution. A mapping scheme for groups of atoms in the atomistic molecule onto beads in the coarse-grained model was established. The coarse-grained force field consists of solvent-mediated effective interaction potentials that were derived via...
متن کاملCoarse-grained lattice Monte Carlo simulations with continuous interaction potentials.
A coarse-grained lattice Metropolis Monte Carlo (CG-MMC) method is presented for simulating fluid systems described by standard molecular force fields. First, a thermodynamically consistent coarse-grained interaction potential is obtained numerically and automatically from a continuous force field such as Lennard-Jones. The coarse-grained potential then is used to drive CG-MMC simulations of va...
متن کاملBiological and synthetic membranes: What can be learned from a coarse-grained description?
We discuss the role coarse-grained models play in the investigation of the structure and thermodynamics of bilayer membranes, and we place them in the context of alternative approaches. Because they reduce the degrees of freedom and employ simple and soft effective potentials, coarse-grained models can provide rather direct insight into collective phenomena in membranes on large time and length...
متن کاملnd - m at . s of t ] 1 2 Se p 20 06 Biological and synthetic membranes : What can be learned from a coarse - grained description ?
We discuss the role coarse-grained models play in the investigation of the structure and thermodynamics of bilayer membranes, and we place them in the context of alternative approaches. Because they reduce the degrees of freedom and employ simple and soft effective potentials, coarse-grained models can provide rather direct insight into collective phenomena in membranes on large time and length...
متن کاملnd - m at . s of t ] 1 3 Se p 20 06 Biological and synthetic membranes : What can be learned from a coarse - grained description ?
We discuss the role coarse-grained models play in the investigation of the structure and thermodynamics of bilayer membranes, and we place them in the context of alternative approaches. Because they reduce the degrees of freedom and employ simple and soft effective potentials, coarse-grained models can provide rather direct insight into collective phenomena in membranes on large time and length...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید
ثبت ناماگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید
ورودعنوان ژورنال:
- Journal of computational chemistry
دوره 29 9 شماره
صفحات -
تاریخ انتشار 2008