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Nonspecifically bound proteins spin while diffusing along DNA

Nature Structural & Molecular Biology volume 16, pages 1224–1229 (2009)Cite this article

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 kBT. Such small barriers facilitate rapid search for binding sites.

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Figure 1: Models and definitions.
Figure 2: Schematic of the flow-stretching and fluorescence imaging apparatus (reproduced from ref. 3) and diffusion of hOgg1.
Figure 3: Test of the diffusion models by protein size dependence with consistent (hOgg1) DNA-binding interface.
Figure 4: Global analysis of a diverse set of DNA-binding proteins according to the linear and helical models.

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References

  1. Berg, O.G., Winter, R.B. & Von Hippel, P.H. Diffusion-driven mechanisms of protein translocation on nucleic acids. 1. Models and theory. Biochemistry 20, 6929–6948 (1981).

    Article  CAS  Google Scholar 

  2. Gowers, D.M. & Halford, S.E. Protein motion from non-specific to specific DNA by three-dimensional routes aided by supercoiling. EMBO J. 22, 1410–1418 (2003).

    Article  CAS  Google Scholar 

  3. Blainey, P.C., van Oijen, A.M., Banerjee, A., Verdine, G.L. & Xie, X.S. A base-excision DNA-repair protein finds intrahelical lesion bases by fast sliding in contact with DNA. Proc. Natl. Acad. Sci. USA 103, 5752–5757 (2006).

    Article  CAS  Google Scholar 

  4. Von Hippel, P.H. & Berg, O.G. Facilitated target location in biological systems. J. Biol. Chem. 264, 675–678 (1989).

    CAS  PubMed  Google Scholar 

  5. Schurr, J.M. The one-dimensional diffusion coefficient of proteins absorbed on DNA. Hydrodynamic considerations. Biophys. Chem. 9, 413–414 (1979).

    Article  CAS  Google Scholar 

  6. Sakata-Sogawa, K. & Shimamoto, N. RNA polymerase can track a DNA groove during promoter search. Proc. Natl. Acad. Sci. USA 101, 14731–14735 (2004).

    Article  CAS  Google Scholar 

  7. Gnatt, A.L., Cramer, P., Fu, J., Bushnell, D.A. & Kornberg, R.D. Structural basis of transcription: an RNA polymerase II elongation complex at 3.3 A resolution. Science 292, 1876–1882 (2001).

    Article  CAS  Google Scholar 

  8. Kalodimos, C.G. et al. Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes. Science 305, 386–389 (2004).

    Article  CAS  Google Scholar 

  9. Von Hippel, P.H. BIOCHEMISTRY: Completing the View of Transcriptional Regulation. Science 305, 350–352 (2004).

    Article  CAS  Google Scholar 

  10. Bagchi, B., Blainey, P.C. & Xie, X.S. Diffusion constant of a non-specifically bound protein undergoing curvilinear motion along DNA. J. Phys. Chem. B 112, 6282–6284 (2008).

    Article  CAS  Google Scholar 

  11. Zwanzig, R. Diffusion in a rough potential. Proc. Natl. Acad. Sci. USA 85, 2029–2030 (1988).

    Article  CAS  Google Scholar 

  12. van Oijen, A.M. et al. Single-molecule kinetics of λ exonuclease reveal base dependence and dynamic disorder. Science 301, 1235–1238 (2003).

    Article  CAS  Google Scholar 

  13. Schroeder, C.M., Blainey, P.C., Kim, S.J. & Xie, X.S. Hydrodynamic flow-stretching assay for single-molecule studies of nucleic acid–protein interactions. In: Ha, Taekjip and Selvin, Paul R., editors Single-Molecule Techniques: A Laboratory Manual. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, 461–492 (2008).

    Google Scholar 

  14. Bruner, S.D., Norman, D.P.G. & Verdine, G.L. Structural basis for recognition and repair of the endogenous mutagen 8-oxoguanine in DNA. Nature 403, 859–866 (2000).

    Article  CAS  Google Scholar 

  15. Banerjee, A., Yang, W., Karplus, M. & Verdine, G.L. Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA. Nature 434, 612–618 (2005).

    Article  CAS  Google Scholar 

  16. Banerjee, A., Santos, W.L. & Verdine, G.L. Structure of a DNA glycosylase searching for lesions. Science 311, 1153–1157 (2006).

    Article  CAS  Google Scholar 

  17. Efron, B. & Tibshirani, R.J. An introduction to the bootstrap. Monographs on Statistics and Applied Probability 57. New York: Chapman & Hall, 1993.

  18. Elf, J., Li, G.W. & Xie, X.S. Probing transcription factor dynamics at the single-molecule level in a living cell. Science 316, 1191–1194 (2007).

    Article  CAS  Google Scholar 

  19. Slutsky, M. & Mirny, L.A. Kinetics of protein-DNA interaction: facilitated target location in sequence-dependent potential. Biophys. J. 87, 4021–4035 (2004).

    Article  CAS  Google Scholar 

  20. Tafvizi, A. et al. Tumor suppressor p53 slides on DNA with low friction and high stability. Biophys. J. 95, L01–L03 (2008).

    Article  CAS  Google Scholar 

  21. Liu, S., Abbondanzieri, E.A., Rausch, J.W., Grice, S.F.J. & Zhuang, X. Slide into action: dynamic shuttling of HIV reverse transcriptase on nucleic acid substrates. Science 322, 1092–1097 (2008).

    Article  CAS  Google Scholar 

  22. Lin, Y. et al. Using the bias from flow to elucidate single DNA repair protein sliding and interactions with DNA. Biophys. J. 96, 1911–1917 (2009).

    Article  CAS  Google Scholar 

  23. Kochaniak, A.B. et al. Proliferating cell nuclear antigen uses two distinct modes to move along DNA. J. Biol. Chem. 284, 17700–17710 (2009).

    Article  CAS  Google Scholar 

  24. Ramanathan, S.P. et al. Type III restriction enzymes communicate in 1D without looping between their target sites. Proc. Natl. Acad. Sci. USA 106, 1748–1753 (2009).

    Article  CAS  Google Scholar 

  25. Gupta, S. et al. DNA binding provides a molecular strap activating the adenovirus proteinase. Mol. Cell. Proteomics 3, 950–959 (2004).

    Article  CAS  Google Scholar 

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Acknowledgements

We would like to thank Y. Qi (Harvard Univ.) for providing labeled E. coli MutM, W.J. McGrath and V. Graziano (Brookhaven Natl. Lab.) for a gift of labeled AVP-pVIc, and E.S. Vanamee and A. Aggarwal (Mount Sinai School of Medicine) for a gift of labeled BamHI. We also thank G.W. Li and J. Elf for contributing LacI-Venus diffusion data. B.B. was supported partly by a grant from DST (India) and by a JC Bose Fellowship. Work at Harvard was funded by the NIH Director's Pioneer Award and by NSF.

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Author notes

  1. S C Kou

    Present address: Department of Statistics, Harvard University, Science Center, Cambridge, Massachusetts, USA. Present addresses: Department of Bioengineering, Stanford University, Stanford, California, USA (P.C.B.) and Life Technologies, Carlsbad, California, USA (G.L.).,

Authors and Affiliations

  1. Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA

    Paul C Blainey, Guobin Luo, Gregory L Verdine & X Sunney Xie

  2. Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, India

    Biman Bagchi

  3. Biology Department, Brookhaven National Laboratory, Upton, New York, USA

    Walter F Mangel

  4. Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA

    Gregory L Verdine

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  1. Paul C Blainey
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Corresponding authors

Correspondence to Biman Bagchi or X Sunney Xie.

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Blainey, P., Luo, G., Kou, S. et al. Nonspecifically bound proteins spin while diffusing along DNA. Nat Struct Mol Biol 16, 1224–1229 (2009). https://doi.org/10.1038/nsmb.1716

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