How Does a Protein Search for the Specific Site on Dna: The Role of Disorder.
From: Department of Physics, University of Minnesota, 116 Church Street SE, Minneapolis, Minnesota 55455, USA.
Physical review. E, Statistical, nonlinear, and soft matter physics
- Publish Date: Aug 2006
- ISSN: 1539-3755
- Volume: 74
- Issue: 2 Pt 1
- Pages: 021903
- Medium: Print
- Language: English
- Citation (JAMA): Hu Tao, Shklovskii B I, et al. How Does a Protein Search for the Specific Site on Dna: The Role of Disorder.. Aug 2006;74:021903
Abstract
Proteins can locate their specific targets on DNA up to two orders of magnitude faster than the Smoluchowski three-dimensional diffusion rate. This happens due to nonspecific adsorption of proteins to DNA and subsequent one-dimensional sliding along DNA. We call such a one-dimensional route towards the target an “antenna.” We studied the role of the dispersion of nonspecific binding energies within the antenna due to a quasirandom sequence of natural DNA. A random energy profile for sliding proteins slows the searching rate for the target. We show that this slowdown is different for macroscopic and mesoscopic antennas.
Mesh Headings (Keywords): Adsorption, Binding Sites, Computer Simulation, DNA, DNA-Binding Proteins, Models, Chemical, Models, Molecular, Protein Binding
Check for Full Text / PubMed Unique Identifier (PMID): 17025468
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