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Physical constraints can encode bacterial promoter regulatory logic

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It is well known that DNA binding proteins in bacteria find their binding sites by a combination of 3D diffusion around and 1D diffusion on the DNA sequence, and the physical parameters for this diffusion process have been recently measured experimentally. We developed a simple physics simulation of this search process based on the previously measured physical parameters. We found three simple and common arrangements of binding sites (which we call “building blocks”) can have a profound impact on the temporal dynamics of protein binding to DNA . We show that combining these building blocks into complex arrangements of binding sites can encode complex regulatory logic and that these complex binding sites arrangements are common and highly conserved in E. coli

This talk is part of the Computational and Systems Biology series.

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