Target-Site Search of DNA-Binding Proteins

Dynamic strategies for target-site search by DNA-binding proteins.

Gene regulatory proteins find their target sites on DNA remarkably quickly; the experimental binding rate for lac repressor is orders-of-magnitude higher than predicted by free diffusion alone. It has been proposed that nonspecific binding aids the search by allowing proteins to slide and hop along DNA. We develop a reaction-diffusion theory of protein translocation that accounts for transport ...

Supporting Material Dynamic Strategies for Target-Site Search by DNA-Binding Proteins

Binding site identification in target proteins

Yi Xiong obtained his PhD degree in bioinformatics from Wuhan University, China, in 2011. He worked as a research assistant at the Department of Bioinformatics and Biostatistics in Shanghai Jiao Tong University, China, from 2009 to 2011. He is currently working as a postdoctoral research associate at the Department of Biological Sciences, Purdue University (IN, USA). He has published several sc...

Site-Specific Binding of Proteins to DNA

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Search by proteins for their DNA target site: 2. The effect of DNA conformation on the dynamics of multidomain proteins

Multidomain transcription factors, which are especially abundant in eukaryotic genomes, are advantageous to accelerate the search kinetics for target site because they can follow the intersegment transfer via the monkey-bar mechanism in which the protein forms a bridged intermediate between two distant DNA regions. Monkey-bar dynamics highly depends on the properties of the multidomain protein ...