Facilitated diffusion of DNA-binding proteins.
The diffusion-controlled limit of reaction times for site-specific DNA-binding proteins is derived from first principles. We follow the generally accepted concept that a protein propagates via two competitive modes, a three-dimensional diffusion in space and a one-dimensional sliding along the DNA. However, our theoretical treatment of the problem is new. The accuracy of our analytical model is verified by numerical simulations. The results confirm that the unspecific binding of protein to DNA, combined with sliding, is capable to reduce the reaction times significantly.
Klenin
Konstantin V
KV
Division of Biophysics of Macromolecules, German Cancer Research Center, D-69120 Heidelberg, Germany.
Merlitz
Holger
H
Langowski
Jörg
J
Wu
Chen-Xu
CX
D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism; D004058:Diffusion; D008956:Models, Chemical; D013379:Substrate Specificity
D004268:DNA-Binding Proteins; D004247:DNA