Nucleic Acids Research Advance Access originally published online on July 7, 2007
Nucleic Acids Research 2007 35(16):5275-5283; doi:10.1093/nar/gkm471
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Nucleic Acids Research, 2007, Vol. 35, No. 16 5275-5283
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Molecular Biology |
Correlation between binding rate constants and individual information of E. coli Fis binding sites
1National Cancer Institute at Frederick, Center for Cancer Research Nanobiology Program, 2The Protein Chemistry Laboratory, Advanced Technology Program, SAIC - Frederick, NCI - Frederick Bldg. 469, Rm 237 Frederick, MD 21782 and 3Basic Research Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, MD 21702, USA
*To whom correspondence should be addressed. Tel: +1 301 846 5581 (-5532 for messages); Fax: +1 301 846 5598; Email: toms{at}ncifcrf.gov
Received March 8, 2007. Revised May 26, 2007. Accepted May 29, 2007.
Individual protein binding sites on DNA can be measured in bits of information. This information is related to the free energy of binding by the second law of thermodynamics, but binding kinetics appear to be inaccessible from sequence information since the relative contributions of the on- and off-rates to the binding constant, and hence the free energy, are unknown. However, the on-rate could be independent of the sequence since a protein is likely to bind once it is near a site. To test this, we used surface plasmon resonance and electromobility shift assays to determine the kinetics for binding of the Fis protein to a range of naturally occurring binding sites. We observed that the logarithm of the off-rate is indeed proportional to the individual information of the binding sites, as predicted. However, the on-rate is also related to the information, but to a lesser degree. We suggest that the on-rate is mostly determined by DNA bending, which in turn is determined by the sequence information. Finally, we observed a break in the binding curve around zero bits of information. The break is expected from information theory because it represents the coding demarcation between specific and nonspecific binding.
Present address: Ryan K. Shultzaberger, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
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