Nonspecifically bound proteins spin while diffusing along DNA

Blainey, Paul C and Luo, Guobin and Kou, SC and Mangel, Walter F and Verdine, Gregory L and Bagchi, Biman and Xie, X Sunney (2009) Nonspecifically bound proteins spin while diffusing along DNA. In: Nature Structural & Molecular Biology, 16 (12). 1224-U34.

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Abstract

It is known that DNA-binding proteins can slide along the DNA helix while searching for specific binding sites, but their path of motion remains obscure. Do these proteins undergo simple one-dimensional (1D) translational diffusion, or do they rotate to maintain a specific orientation with respect to the DNA helix? We measured 1D diffusion constants as a function of protein size while maintaining the DNA-protein interface. Using bootstrap analysis of single-molecule diffusion data, we compared the results to theoretical predictions for pure translational motion and rotation-coupled sliding along the DNA. The data indicate that DNA-binding proteins undergo rotation-coupled sliding along the DNA helix and can be described by a model of diffusion along the DNA helix on a rugged free-energy landscape. A similar analysis including the 1D diffusion constants of eight proteins of varying size shows that rotation-coupled sliding is a general phenomenon. The average free-energy barrier for sliding along the DNA was 1.1 +/- 0.2 k(B)T. Such small barriers facilitate rapid search for binding sites.

Item Type:	Journal Article
Publication:	Nature Structural & Molecular Biology
Publisher:	Nature Publishing Group
Additional Information:	copyright of this article belongs to Nature Publishing Group.
Department/Centre:	Division of Chemical Sciences > Solid State & Structural Chemistry Unit
Date Deposited:	09 Jan 2010 08:14
Last Modified:	19 Sep 2010 05:53
URI:	http://eprints.iisc.ac.in/id/eprint/25302

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