Dresden 2006 – wissenschaftliches Programm

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AKB: Biologische Physik

AKB 30: Poster Session I

AKB 30.19: Poster

Montag, 27. März 2006, 15:30–18:00, P1

Two protein species binding cooperatively and specifically to DNA: physical and functional constraints — •Nico Geisel¹ and Ulrich Gerland² — ¹Arnold Sommerfeld Center for Theoretical Physics (ASC), Georg-August-Universität Göttingen, LMU München — ²Arnold Sommerfeld Center for Theoretical Physics (ASC), Center for Nanoscience (CeNS), LMU München

Cooperative binding of proteins to specific sites on the genomic DNA is indispensable for many genetic mechanisms, in particular in the context of transcription regulation. The equilibrium and non-equilibrium properties of this binding process can be strongly affected by the presence of the genomic background, i.e. the overwhelming majority of the non-functional sites on the DNA. For a single protein species binding independently to the DNA, this background effect has been characterized in Ref.[1]. Here, we extend this analysis to the case of two protein species which bind DNA cooperatively. We consider an explicit theoretical model based on biochemical experiments. We study its equilibrium behavior analytically and its dynamics through kinetic Monte Carlo simulations. We determine the parameter range where physical constraints do not limit the biological functionality.
U. Gerland, J.D. Moroz, and T. Hwa (2002) Proc. Natl. Acad. Sci. USA 99, 12015