Nonspecifically bound proteins spin while diffusing along DNA

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 t...

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Published inNature structural & molecular biology Vol. 16; no. 12; pp. 1224 - 1229
Main Authors Xie, X Sunney, Bagchi, Biman, Blainey, Paul C, Kou, S C, Mangel, Walter F, Verdine, Gregory L, Luo, Guobin
Format Journal Article
LanguageEnglish
Published United States Nature Publishing Group 01.12.2009
Subjects
Binding sites
Binding sites (Biochemistry)
Deoxyribonucleic acid
Diffusion
DNA
DNA - chemistry
DNA - metabolism
DNA binding proteins
DNA-Binding Proteins - chemistry
DNA-Binding Proteins - metabolism
Models, Chemical
Molecular biology
Molecular structure
Physiological aspects
Protein Binding
Proteins
United States
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Summary: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.
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Present addresses: Department of Bioengineering, Stanford University, Stanford, California, USA (P.C.B.) and Life Technologies, Carlsbad, California, USA (G.L.).
ISSN:1545-9993
1545-9985
DOI:10.1038/nsmb.1716