Facilitated diffusion of DNA-binding proteins: efficient simulation with the method of excess collisions.
In this paper, a new method to efficiently simulate diffusion controlled second order chemical reactions is derived and applied to site-specific DNA-binding proteins. The protein enters a spherical cell and propagates via two competing modes, a free diffusion and a DNA-sliding mode, to search for its specific binding site in the center of the cell. There is no need for a straightforward simulation of this process. Instead, an alternative and exact approach is shown to be essentially faster than explicit random walk simulations. The speed-up of this novel simulation technique is rapidly growing with system size.
Merlitz
Holger
H
Softmatter Laboratory, Department of Physics, Xiamen University, Xiamen 361005, People's Republic of China. merlitz@gmx.de
Klenin
Konstantin V
KV
Wu
Chen-Xu
CX
Langowski
Jörg
J
D001665:Binding Sites; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism; D004058:Diffusion; D008954:Models, Biological; D009690:Nucleic Acid Conformation; D011487:Protein Conformation
D004268:DNA-Binding Proteins; D004247:DNA