The effects of intersegmental transfers on target location by proteins

Physical Biology

Volumn 6, Issue 1, 2009, Pages

  Sheinman, Michael ^a   Kafri, Yariv ^a  

^a TECHNION ISRAEL INSTITUTE OF TECHNOLOGY   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; DNA BINDING PROTEIN;

ARTICLE; CONTROLLED STUDY; DIFFUSION; MATHEMATICAL MODEL; PRIORITY JOURNAL; PROTEIN TARGETING; PROTEIN TRANSPORT; ALGORITHM; BINDING SITE; CHEMISTRY; COMPUTER SIMULATION; ENZYME SPECIFICITY; METABOLISM;

ALGORITHMS; BINDING SITES; COMPUTER SIMULATION; DNA; DNA-BINDING PROTEINS; SUBSTRATE SPECIFICITY;

EID: 60849133933     PISSN: 14783967     EISSN: 14783975     Source Type: Journal    
DOI: 10.1088/1478-3975/6/1/016003     Document Type: Article

References (41)

1. Alberts B, Bray D, Lewis J, Raff M, Roberts K and Watson J D 1994 The Molecular Biology of the Cell 4th edn (New York: Garland)
2. Loverdo C, Benichou O, Moreau M and Voituriez R 2007 Enhanced reaction kinetics in biological cells Nature Phys. 4 134
3. Smoluchowski M 1917 Mathematical theory of the kinetics of the coagulation of colloidal solutions Z. Phys. Chem. 92 129
4. Elowitz M B, Surette M G, Wolf P E, Stock J B and Leibler S 1999 Protein mobility in the cytoplasm of Escherichia coli J. Bacteriol. 181 197
5. Lin S Y and Riggs A D 1972 Lac repressor binding to non-operator DNA: detailed studies and a comparison of equilibrium and rate competition methods J. Mol. Biol. 72 671
6. Riggs A D, Suzuki H and Bourgeois S 1970 Lac repressor-operator interaction: I. Equilibrium studies J. Mol. Biol. 48 67
7. Riggs A D, Bourgeois S and Cohn M 1970 The Lac repressor-operator interaction: III. Kinetic studies J. Mol. Biol. 53 401
8. Berg O G, Winter R B and von Hippel P H 1981 Diffusion-driven mechanisms of protein translocation on nucleic acids: I. Models and theory Biochemistry 20 6929
9. Slutsky M and Mirny L A 2004 Kinetics of protein-DNA interaction: facilitated target location in sequence-dependent potential Biophys. J. 87 4021 (Pubitemid 39602906)
10. Hu T, Grosberg A Y and Shklovskii B I 2006 How proteins search for their specific sites on DNA: the role of DNA conformation Biophys. J. 90 2731
11. Hu T and Shklovskii B I 2007 How proteins search for their specific sites on DNA: the role of intersegment transfer Phys. Rev. E 76 051909 (Pubitemid 350096752)
12. Berg O G and Blomberg C 1976 Association kinetics with coupled diffusional flows. Special application to the Lac repressor-operator system Biophys. Chem. 4 367
13. Halford S E and Marko J F 2004 How do site-specific DNA-binding proteins find their targets? Nucl. Acids Res. 32 3040
14. Belotserkovskii B P and Zarling D A 2004 Analysis of a one-dimensional random walk with irreversible losses at each step: applications for protein movement on DNA J. Theor. Biol. 226 195 (Pubitemid 37468398)
15. Zhou H X 2005 A model for the mediation of processivity of DNA-targeting proteins by nonspecific binding: dependence on DNA length and presence of obstacles Biophys. J. 88 1608 (Pubitemid 40976178)
16. Lomholt M A, Ambjrnsson T and Metzler R 2005 Optimal target search on a fast-folding polymer chain with volume exchange Phys. Rev. Lett. 95 260603 (Pubitemid 43061524)
17. Adam G and Delbruck M 1968 Reduction of dimensionality in biological diffusion processes Structural Chemistry and Molecular Biology ed A Rich and N Davidson (San Francisco, CA: Freeman) pp 198-215
18. Hughes B D 1995 Random Walks and random enviroments Random Walks vol 1 (Oxford: Clarendon)
19. Wang Y M, Austin R H and Cox E C 2006 Single molecule measurement of repressor protein 1d diffusion on DNA Phys. Rev. Lett. 97 048302
20. Elf J, Li G-W and Xie P X 2007 Probing transcription factor dynamics at the simple single-molecule level in a living cell Science 316 1191
21. Kao-Huang Y, Revzin A, Butler A P, O'Conner P, Noble D W and von Hippel P H 1977 Nonspecific DNA binding of genome-regulating proteins as a biological control mechanism: measurement of DNA-bound Escherichia coli Lac repressor in vivo Proc. Natl Acad. Sci. 74 4228 (Pubitemid 8228387)
22. von Hippel P H, Revzin A, Gross C A and Wang A C 1975 Protein-Ligand Interactions ed H Sund and G Blauer (Berlin: de Gruyter & Co) pp 279-347
23. Bresloff J L and Crothers D M 1975 DNA-ethidium reaction kinetics: demonstration of direct ligand transfer between DNA binding sites J. Mol. Biol. 172 263
24. Fickert R and Muller-Hill B 1992 How Lac repressor finds Lac operator in vitro J. Mol. Biol. 226 59
25. Ruusala T and Crothers D M 1992 Sliding and intermolecular transfer of the Lac repressor: kinetic perturbation of a reaction intermediate by a distant DNA sequence Proc. Natl Acad. Sci. 89 4903
26. Lieberman B A and Nordeen S K 1997 DNA intersegment transfer, how steroid receptors search for a target site J. Biol. Chem. 272 1061 (Pubitemid 27034599)
27. Embleton M L, Williams S A, Watson M A and Halford S E 1999 Specificity from the synapsis of DNA elements by the SfiI endonuclease J. Mol. Biol. 289 785
28. Bustamante C, Guthold M, Zhu X and Yang G 1999 Facilitated target location on DNA by individual Escherichia coli RNA polymerase molecules observed with the scanning force microscope operating in liquid ASBMB 274 16665
29. Fried M G and Crothers D M 1984 Kinetics and mechanism in the reaction of gene regulatory proteins with DNA J. Mol. Biol. 172 263
30. van den Broek B, Lomholt M A, Kalisch S M J, Metzler R and Wuite G J L 2008 Kinetics of target site localization of a protein on DNA: a stochastic approach Proc. Natl Acad. Sci. 105 15738
31. Condamin S, Benichou O, Tejedor V, Voituriez R and Klafter J 2007 First-passage times in complex scale-invariant media Nature 450 77 (Pubitemid 350070561)
32. Coppey M, Benichou O, Voituriez R and Moreau M 2004 Kinetics of target site localization of a protein on DNA: a stochastic approach Biophys. J. 87 1640
33. Oshanin G, Moreau M and Burlatsky S 1994 Models of chemical reactions with participation of polymers Adv. Colloid Interface Sci. 49 1
34. Lin S Y and Riggs A D 1975 The general affinity of Lac repressor for E. coli DNA: implication for gene regulation in procaryotes and eucaryotes Cell 4 107
35. Richey B, Cayley D S, Mossing M C, Kolka C, Anderson C F, Farrar T C and Record M T 1987 Variability of the intracellular ionic environment of Escherichia coli. differences between in vitro and in vivo effects of ion concentrations on protein-DNA interactions and gene expression J. Biol. Chem 262 7157
36. Lewis M, Chang G, Horton N C, Kercher M A, Pace H C, Schumacherand M A, Brennan R G and Lu P 1996 Crystal structure of the lactose operon repressor and its complexes with DNA and inducer Science 271 1247
37. Swigon D, Coleman B D and Olson W K 2006 Modeling the Lac repressor-operator assembly: the influence of DNA looping on Lac repressor conformation Proc. Natl Acad. Sci. 103 9879 (Pubitemid 43993591)
38. Edelman L M, Cheong R and Kahn J D 2003 Fluorescence resonance energy transfer over 130 basepairs in hyperstable Lac repressor-DNA loops Biophys. J. 84 1131
39. Watts D J 1999 Small Worlds: The Dynamics of Networks Between Order and Randomness (Princeton, NJ: Princeton University Press)
40. Muller-Hill M 1996 The Lac Operon. A Short History of a Genetic Paradigm (Berlin: de Gruyter & Co)
41. Ruben G C and Roos T B 1997 Conformation of Lac repressor tetramer in solution, bound and unbound to operator DNA Microsc. Res. Tech. 36 400