Wrapped-around models for the lac operon complex

Biophysical Journal

Volumn 98, Issue 12, 2010, Pages 2964-2973

  La Penna, Giovanni ^a   Perico, Angelo ^a  

^a CNR   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ENTEROBACTERIACEAE;

EID: 77953580316     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2010.03.024     Document Type: Article

References (28)

1. Jacob, F., and J. Monod. 1961. Genetic regulatory mechanisms in the synthesis of proteins. J. Mol. Biol. 3: 318-356.
2. Lewis, M. 2005. The lac repressor. C. R. Biol. 328: 521-548.
3. Friedman, A. M., T. O. Fischmann, and T. A. Steitz. 1995. Crystal structure of lac repressor core tetramer and its implications for DNA looping. Science. 268: 1721-1727.
4. Lewis, M., G. Chang,..., P. Lu. 1996. Crystal structure of the lactose Operon repressor and its complexes with DNA and inducer. Science. 271: 1247-1254.
5. Abo, T., T. Inada,..., H. Aiba. 2000. SsrA-mediated tagging and proteolysis of LacI and its role in the regulation of lac operon. EMBO J. 19: 3762-3769.
6. Daber, R., S. Stayrook,..., M. Lewis. 2007. Structural analysis of lac repressor bound to allosteric effectors. J. Mol. Biol. 370: 609-619.
7. Bell, C. E., and M. Lewis. 2001. The Lac repressor: a second generation of structural and functional studies. Curr. Opin. Struct. Biol. 11: 19-25.
8. Guo, F., D. N. Gopaul, and G. D. Van Duyne. 1999. Asymmetric DNA bending in the Cre-loxP site-specific recombination synapse. Proc. Natl. Acad. Sci. USA. 96: 7143-7148.
9. Deibert, M., S. Grazulis,..., R. Huber. 2000. Structure of the tetrameric restriction endonuclease NgoMIV in complex with cleaved DNA. Nat. Struct. Biol. 7: 792-799.
10. Halford, S. E., D. M. Gowers, and R. B. Sessions. 2000. Two are better than one. Nat. Struct. Biol. 7: 705-707.
11. Tsodikov, O. V., R. M. Saecker, ..., M. T. Record, Jr. 1999. Wrapping of flanking non-operator DNA in lac repressor-operator complexes: implications for DNA looping. J. Mol. Biol. 294: 639-655.
12. Swigon, D., B. D. Coleman, and W. K. Olson. 2006. Modeling the Lac repressor-operator assembly: the influence of DNA looping on Lac repressor conformation. Proc. Natl. Acad. Sci. USA. 103: 9879-9884.
13. Romanuka, J., G. E. Folkers, ..., R. Boelens. 2009. Specificity and affinity of Lac repressor for the auxiliary operators O2 and O3 are explained by the structures of their protein-DNA complexes. J. Mol. Biol. 390: 478-1189
14. Balaeff, A., L. L. Mahadevan, and K. Schulten. 2004. Structural basis for cooperative DNA binding by CAP and lac repressor. Structure. 12: 123-132.
15. Luger, K., A. W. Mäder,..., T. J. Richmond. 1997. Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature. 389: 251-260.
16. Goyal, S., T. Lillian,..., N. C. Perkins. 2007. Intrinsic curvature of DNA influences LacR-mediated looping. Biophys. J. 93: 4342-4359.
17. Villa, E., A. Balaeff, and K. Schulten. 2005. Structural dynamics of the lac repressor-DNA complex revealed by a multiscale simulation. Proc. Natl. Acad. Sci. USA. 102: 6783-6788.
18. Morgan, M. A., K. Okamoto,..., D. S. English. 2005. Single-molecule spectroscopic determination of lac repressor-DNA loop conformation. Biophys. J. 89: 2588-2596.
19. Perico, A., G. La Penna, and L. Arcesi. 2006. Electrostatic interactions with histone tails may bend linker DNA in chromatin. Biopolymers. 81: 20-28.
20. Arcesi, L., G. La Penna, and A. Perico. 2007. Generalized electrostatic model of the wrapping of DNA around oppositely charged proteins. Biopolymers. 86: 127-135.
21. Manning, G. S. 2003. Is a small number of charge neutralizations sufficient to bend nucleosome core DNA onto its superhelical ramp? J. Am. Chem. Soc. 125: 15087-15092.
22. Manning, G. S. 2001. Counterion condensation on a helical charge lattice. Macromolecules. 34: 4650-4655.
23. Manning, G. S. 1978. The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides. Q. Rev. Biophys. 11: 179-246.
24. Schiessel, H. 2003. The physics of chromatin. J. Phys. Condens. Matter. 15: R699-R774.
25. Cornell, W. D., P. Cieplak,..., P. A. Kollman. 1995. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 117: 5179-5197.
26. van Dijk, M., and A. M. J. J. Bonvin. 2009.3D-DART: a DNA structure modeling server. Nucleic Acids Res.
27. Lankas, F., R. Lavery, and J. H. Maddocks. 2006. Kinking occurs during molecular dynamics simulations of small DNA minicircles. Structure. 14: 1527-1534.
28. Humphrey, W., A. Dalke, and K. Schulten. 1996. VMD: visual molecular dynamics. J. Mol. Graph. 14: 33-38.