High-affinity quasi-specific sites in the genome: How the DNA-binding proteins cope with them

Biophysical Journal

Volumn 101, Issue 5, 2011, Pages 1123-1129

  Chakrabarti, J ^a,b   Chandra, Navin ^a   Raha, Paromita ^a   Roy, Siddhartha ^a  

^a INDIAN INSTITUTE OF CHEMICAL BIOLOGY   (India)

^b S N BOSE NATIONAL CENTRE FOR BASIC SCIENCES   (India)

Author keywords

[No Author keywords available]

Indexed keywords

DNA BINDING PROTEIN; ESCHERICHIA COLI PROTEIN; GALACTOSE REPRESSOR PROTEINS; PHAGE REPRESSOR PROTEINS; REPRESSOR PROTEIN; VIRUS PROTEIN;

ARTICLE; BACTERIAL GENOME; BINDING SITE; BIOLOGICAL MODEL; ESCHERICHIA COLI; GENETICS; KINETICS; METABOLISM; THERMODYNAMICS;

BINDING SITES; DNA-BINDING PROTEINS; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GENOME, BACTERIAL; KINETICS; MODELS, BIOLOGICAL; REPRESSOR PROTEINS; THERMODYNAMICS; VIRAL REGULATORY AND ACCESSORY PROTEINS;

ESCHERICHIA COLI; PROKARYOTA;

EID: 80052472657     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2011.07.041     Document Type: Article

References (21)

1. O.G. Berg, R.B. Winter, and P.H. von Hippel How do genome-regulatory proteins locate their DNA target sites? Trends Biochem. Sci. 7 1982 52 55
2. A. Sarai, and Y. Takeda λ Repressor recognizes the approximately 2-fold symmetric half-operator sequences asymmetrically Proc. Natl. Acad. Sci. USA 86 1989 6513 6517 (Pubitemid 19236310)
3. Y. Takeda, A. Sarai, and V.M. Rivera Analysis of the sequence-specific interactions between Cro repressor and operator DNA by systematic base substitution experiments Proc. Natl. Acad. Sci. USA 86 1989 439 443 (Pubitemid 19037760)
4. G. Badis, and M.F. Berger M.L. Bulyk Diversity and complexity in DNA recognition by transcription factors Science 324 2009 1720 1723
5. M.L. Bulyk, P.L.F. Johnson, and G.M. Church Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors Nucleic Acids Res. 30 2002 1255 1261 (Pubitemid 34679700)
6. J. Linnell, and R. Mott I.A. Udalova Quantitative high-throughput analysis of transcription factor binding specificities Nucleic Acids Res. 32 2004 e44
7. O.G. Berg, and P.H. von Hippel Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters J. Mol. Biol. 193 1987 723 750
8. S.E. Halford, and J.F. Marko How do site-specific DNA-binding proteins find their targets? Nucleic Acids Res. 32 2004 3040 3052 (Pubitemid 39022995)
9. N.P. Stanford, and M.D. Szczelkun S.E. Halford One- and three-dimensional pathways for proteins to reach specific DNA sites EMBO J. 19 2000 6546 6557
10. M. Lewis, and G. Chang P. Lu Crystal structure of the lactose operon repressor and its complexes with DNA and inducer Science 271 1996 1247 1254
11. S. Stayrook, and P. Jaru-Ampornpan M. Lewis Crystal structure of the λ repressor and a model for pairwise cooperative operator binding Nature 452 2008 1022 1025 (Pubitemid 351589614)
12. R. Rohs, and X. Jin R.S. Mann Origins of specificity in protein-DNA recognition Annu. Rev. Biochem. 79 2010 233 269
13. C.G. Kalodimos, and N. Biris R. Kaptein Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes Science 305 2004 386 389 (Pubitemid 38938152)
14. M. Allen, and D.J. Tildesley Computer Simulations of Liquids 1991 Oxford University Press New York
15. J. Chakrabarti, and S. Roy Simulation of the kinetics of a sphere attached to a fluctuating polymer: Implications for target search by DNA-binding proteins Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 69 2004 021904
16. P.M. Chaikin, and T.C. Lubensky Principles of Condensed Matter Physics 1998 Cambridge University Press Cambridge, UK
17. N. Shepherd, P. Dennis, and H. Bremer Cytoplasmic RNA polymerase in Escherichia coli J. Bacteriol. 183 2001 2527 2534 (Pubitemid 32249761)
18. Y. Kao-Huang, and A. Revzin P.H. von Hippel 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. USA 74 1977 4228 4232 (Pubitemid 8228387)
19. I.B. Dodd, and A.J. Perkins J.B. Egan Octamerization of CI repressor is needed for effective repression of P RM and efficient switching from lysogeny Gene Dev. 15 2001 3013 3022 (Pubitemid 33078951)
20. A. Bakk, and R. Metzler In vivo non-specific binding of λ CI and Cro repressors is significant FEBS Lett. 563 2004 66 68 (Pubitemid 38471575)
21. M. Slutsky, and L.A. Mirny Kinetics of protein-DNA interaction: facilitated target location in sequence-dependent potential Biophys. J. 87 2004 4021 4035 (Pubitemid 39602906)