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© Oxford University Press

A Brownian dynamics model for the chromatin fiber

L. Ehrlich 1,3, C. Mükel 1, G. Chirico 2 and J. Langowski 1,4

1Division of Biophysics of Macromolecules, DKFZ Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany
2I.N.F.M.—Dipartimento di Fisica Universia degli Studi di Milano Via Celoria 16, 20133 Milano, Italy

4 To whom correspondence should be addressed

Motivation: We describe a Brownian dynamics model for the folding of the chromatin fiber based on the model of Woodcock et al. (Proc Natl Acad Sci USA, 90, 9021–9025, 1993). The model takes into account the elastic properties of the DNA as well as the electrostatic interaction and nucleosomal excluded-volume interaction. The solvent is described as a viscous medium, the electrostatic interactions by a screened Coulomb potential.

Results: The hydrodynamic properties and their dependence on the solvent's ionic strength are accurately reproduced by the model for nucleosome di- and tetramers. Ionic strength dependent changes in mobility can be attributed to partial screening of the electrostatic repulsion between different segments of linker DNA. Formation of fiber-like structures occurs on time scales of several hundred microseconds for a linear configuration of 25 nucleosomes. The model was implemented by creating user-defined data types. Use of this so-called object-oriented paradigm allowed for a high degree of component reuse in simulation, analysis and visualization contexts.

Availability: The described software is available on request from the authors. Additional information can be found on the WWW at http://www.dkfz-heidelberg.de/Macromol/ehrlich/chromatin.html.

Received on September 17, 1996; revised on January 1, 1997; accepted on January 10, 1997

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Computer Simulation of the 30-Nanometer Chromatin Fiber
Biophys. J., June 1, 2002; 82(6): 2847 - 2859.
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