Dresden 2009 – scientific programme
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BP: Fachverband Biologische Physik
BP 18: Regulation and Signaling
BP 18.4: Talk
Thursday, March 26, 2009, 10:45–11:00, HÜL 186
Physical constraints on cooperative transcription factor-DNA interaction — •Nico Geisel1 and Ulrich Gerland2 — 1Departament de Física Fonamental, Universitat de Barcelona — 2Arnold Sommerfeld Center for Theoretical Physics, LMU München
DNA-binding proteins often interact not only with the genomic DNA, but also with each other. In particular for the case of transcription factors (TFs), cooperative binding is fundamental to the nonlinear and combinatorial control of gene expression. Here, we focus on the simplest case of two TFs binding specifically to two neighboring functional sites, in the background of the quasi-random genomic DNA sequence. Within a coarse-grained theoretical model, we characterize both the equilibrium occupancy of the target sites and the non-equilibrium cooperative search kinetics of the TFs. Based on our model and analysis, we identify physical constraints on the optimal choice of protein-protein and protein-DNA interaction parameters in the context of bacterial gene regulation.