Berlin 2008 – wissenschaftliches Programm
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BP: Fachverband Biologische Physik
BP 2: DNA and Chromatin
BP 2.10: Vortrag
Montag, 25. Februar 2008, 13:00–13:15, PC 203
Protein-DNA interactions: reaching and recognizing the targets — •A. G. Cherstvy1, A. B. Kolomeisky2, and A. A. Kornyshev3 — 1Theorie-II, IFF, FZ Juelich, D-52425 Juelich, Germany — 2Department of Chemistry, Rice University, Houston, Texas 77005, USA — 3Department of Chemistry, Imperial College London, SW7 2AY, London, UK
Searching and recognizing the targets by DNA binding proteins is one of the fundamental biological processes. Some proteins (e.g. the lac repressor) can find their targets 10-100 times faster than predicted by the 3D diffusion rate. However, recent single-molecule experiments showed that the 1D diffusion constants of protein motion along DNA are very small. This controversy pushed us to revisit the problem of target search. We present a theoretical approach which describes some physical-chemical aspects of the target search and DNA-protein recognition. We consider the search process as a sequence of cycles, with each cycle consisting of 3D and 1D track. It is argued that the search time contains three terms: for the motion on 3D, and 1D segments, as well as the correlation term. We show that the acceleration in search time can be reached by a parallel scanning for target by many proteins. Also, we show how the complementarity of charge patterns on a target DNA sequence and on the protein may result in electrostatic recognition of a specific track on DNA by the protein and lead to its subsequent pinning. We estimate the depth and width of the potential well near the recognition region and typical times proteins can spend in the well.