Talk Grosberg 07

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Statistical Mechanics and Evolutionary Optimization of Searching by Transcription Factor Proteins (8. Nov. 2007)

Prof. Dr. Alexander Grosberg School of Physics and Astronomy, University of Minnesota, and Max Planck Institute for Polymer Research, Mainz

Transcription factor proteins locate their specific targets on DNA faster than it would be possible by 3D diffusion. It is believed that the search is realized by the jump-slide combination of 1D diffusional sliding along DNA and 3D diffusional jumps between different pieces of DNA - similar to conductivity of nanowires immersed in a poorly conducting matrix. Using a simple model we show that the protein binding time could be minimized in biological evolution under selective pressure by adjusting the spectrum of protein conformational states, similar to impedance matching condition. The optimal binding time is within an order of magnitude of the the lower bound imposed by thermodynamics. Numerical estimates suggest that bacteria do operate in this optimized regime.